2015 |
Lifetimes of long-lived states in inhomogeneous magnetic fields Article de journal M Singh; S Chinthalapalli; G Bodenhausen Chemical Physics Letters, 623 , p. 113–116, 2015. @article{Singh:2015, title = {Lifetimes of long-lived states in inhomogeneous magnetic fields}, author = {M Singh and S Chinthalapalli and G Bodenhausen}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84923362135&doi=10.1016%2fj.cplett.2015.01.045&partnerID=40&md5=2b36e7ceb319f426f98c824dca83ec3d}, doi = {10.1016/j.cplett.2015.01.045}, year = {2015}, date = {2015-01-01}, journal = {Chemical Physics Letters}, volume = {623}, pages = {113--116}, abstract = {Long-lived states (LLS), also known as singlet states, have been widely studied in the last decade. So far, LLS have only been observed in homogeneous magnetic fields, which preclude applications to many biological samples that are inherently inhomogeneous. We present a method to measure the lifetimes TLLS of long-lived states in inhomogeneous magnetic fields, which combines established sequences for the excitation of LLS with their conversion into long-lived coherences (LLC) that can be detected by windowed acquisition. The method is applied to a pair of diastereotopic scalar-coupled protons of glycine in the dipeptide Alanine-Glycine (Ala-Gly). © 2015 Elsevier B.V. All rights reserved.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Long-lived states (LLS), also known as singlet states, have been widely studied in the last decade. So far, LLS have only been observed in homogeneous magnetic fields, which preclude applications to many biological samples that are inherently inhomogeneous. We present a method to measure the lifetimes TLLS of long-lived states in inhomogeneous magnetic fields, which combines established sequences for the excitation of LLS with their conversion into long-lived coherences (LLC) that can be detected by windowed acquisition. The method is applied to a pair of diastereotopic scalar-coupled protons of glycine in the dipeptide Alanine-Glycine (Ala-Gly). © 2015 Elsevier B.V. All rights reserved. |
Hyperpolarized water to study protein-ligand interactions Article de journal Q Chappuis; J Milani; B Vuichoud; A Bornet; A D Gossert; G Bodenhausen; S Jannin Journal of Physical Chemistry Letters, 6 (9), p. 1674–1678, 2015. @article{Chappuis:2015, title = {Hyperpolarized water to study protein-ligand interactions}, author = {Q Chappuis and J Milani and B Vuichoud and A Bornet and A D Gossert and G Bodenhausen and S Jannin}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84928989028&doi=10.1021%2facs.jpclett.5b00403&partnerID=40&md5=aa3b8524db3af8a41f5759b5d321da12}, doi = {10.1021/acs.jpclett.5b00403}, year = {2015}, date = {2015-01-01}, journal = {Journal of Physical Chemistry Letters}, volume = {6}, number = {9}, pages = {1674--1678}, abstract = {The affinity between a chosen target protein and small molecules is a key aspect of drug discovery. Screening by popular NMR methods such as Water-LOGSY suffers from low sensitivity and from false positives caused by aggregated or denatured proteins. This work demonstrates that the sensitivity of Water-LOGSY can be greatly boosted by injecting hyperpolarized water into solutions of proteins and ligands. Ligand binding can be detected in a few seconds, whereas about 30 min is usually required without hyperpolarization. Hyperpolarized water also enhances proton signals of proteins at concentrations below 20 M so that one can verify in a few seconds whether the proteins remain intact or have been denatured © 2015 American Chemical Society.}, keywords = {}, pubstate = {published}, tppubtype = {article} } The affinity between a chosen target protein and small molecules is a key aspect of drug discovery. Screening by popular NMR methods such as Water-LOGSY suffers from low sensitivity and from false positives caused by aggregated or denatured proteins. This work demonstrates that the sensitivity of Water-LOGSY can be greatly boosted by injecting hyperpolarized water into solutions of proteins and ligands. Ligand binding can be detected in a few seconds, whereas about 30 min is usually required without hyperpolarization. Hyperpolarized water also enhances proton signals of proteins at concentrations below 20 M so that one can verify in a few seconds whether the proteins remain intact or have been denatured © 2015 American Chemical Society. |
Hyperpolarized para-ethanol Article de journal D Mammoli; B Vuichoud; A Bornet; J Milani; J -N Dumez; S Jannin; G Bodenhausen Journal of Physical Chemistry B, 119 (10), p. 4048–4052, 2015. @article{Mammoli:2015a, title = {Hyperpolarized para-ethanol}, author = {D Mammoli and B Vuichoud and A Bornet and J Milani and J -N Dumez and S Jannin and G Bodenhausen}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84924546281&doi=10.1021%2fjp512128c&partnerID=40&md5=f879443679648001881aae42f0387661}, doi = {10.1021/jp512128c}, year = {2015}, date = {2015-01-01}, journal = {Journal of Physical Chemistry B}, volume = {119}, number = {10}, pages = {4048--4052}, abstract = {We show that an imbalance between the populations of singlet (S) and triplet (T) states in pairs of magnetically equivalent spins can be generated by dissolution dynamic nuclear polarization. In partly deuterated ethanol (CD3 13CH2OD), this T/S imbalance can be transferred by cross-relaxation to observable, enhanced signals of protons and coupled 13C. © 2015 American Chemical Society.}, keywords = {}, pubstate = {published}, tppubtype = {article} } We show that an imbalance between the populations of singlet (S) and triplet (T) states in pairs of magnetically equivalent spins can be generated by dissolution dynamic nuclear polarization. In partly deuterated ethanol (CD3 13CH2OD), this T/S imbalance can be transferred by cross-relaxation to observable, enhanced signals of protons and coupled 13C. © 2015 American Chemical Society. |
Hyperpolarized NMR of plant and cancer cell extracts at natural abundance Article de journal J -N Dumez; J Milani; B Vuichoud; A Bornet; J Lalande-Martin; I Tea; M Yon; M Maucourt; C Deborde; A Moing; L Frydman; G Bodenhausen; S Jannin; P Giraudeau Analyst, 140 (17), p. 5860–5863, 2015. @article{Dumez:2015, title = {Hyperpolarized NMR of plant and cancer cell extracts at natural abundance}, author = {J -N Dumez and J Milani and B Vuichoud and A Bornet and J Lalande-Martin and I Tea and M Yon and M Maucourt and C Deborde and A Moing and L Frydman and G Bodenhausen and S Jannin and P Giraudeau}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84938948134&doi=10.1039%2fc5an01203a&partnerID=40&md5=6b13832bdb9e5d06b3f5742f223f0542}, doi = {10.1039/c5an01203a}, year = {2015}, date = {2015-01-01}, journal = {Analyst}, volume = {140}, number = {17}, pages = {5860--5863}, abstract = {Natural abundance 13C NMR spectra of biological extracts are recorded in a single scan provided that the samples are hyperpolarized by dissolution dynamic nuclear polarization combined with cross polarization. Heteronuclear 2D correlation spectra of hyperpolarized breast cancer cell extracts can also be obtained in a single scan. Hyperpolarized NMR of extracts opens many perspectives for metabolomics. © The Royal Society of Chemistry.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Natural abundance 13C NMR spectra of biological extracts are recorded in a single scan provided that the samples are hyperpolarized by dissolution dynamic nuclear polarization combined with cross polarization. Heteronuclear 2D correlation spectra of hyperpolarized breast cancer cell extracts can also be obtained in a single scan. Hyperpolarized NMR of extracts opens many perspectives for metabolomics. © The Royal Society of Chemistry. |
Dynamic nuclear polarization enhancement of protons and vanadium-51 in the presence of pH-Dependent vanadyl radicals Article de journal A J Perez Linde; D Carnevale; P Miéville; A Sienkiewicz; G Bodenhausen Magnetic Resonance in Chemistry, 53 (2), p. 88–92, 2015. @article{PerezLinde:2015a, title = {Dynamic nuclear polarization enhancement of protons and vanadium-51 in the presence of pH-Dependent vanadyl radicals}, author = {A J Perez Linde and D Carnevale and P Mi\'{e}ville and A Sienkiewicz and G Bodenhausen}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85027917053&doi=10.1002%2fmrc.4138&partnerID=40&md5=8ae69863743b5bdbdfcdecb309160045}, doi = {10.1002/mrc.4138}, year = {2015}, date = {2015-01-01}, journal = {Magnetic Resonance in Chemistry}, volume = {53}, number = {2}, pages = {88--92}, abstract = {We report applications of dynamic nuclear polarization to enhance proton and vanadium-51 polarization of vanadyl sulfate samples dopedwith TOTAPOL undermagic angle spinning conditions. The electron paramagnetic resonance response stemming from the paramagnetic 51V species was monitored as a function of pH, which can be adjusted to improve the enhancement of the proton polarization. By means of cross-polarization from the proton bath, 51V spins could be hyperpolarized. Enhancement factors, build-up times, and longitudinal relaxation times T1(1H) and T1(51V) were investigated as a function of pH. © 2014 John Wiley & Sons, Ltd.}, keywords = {}, pubstate = {published}, tppubtype = {article} } We report applications of dynamic nuclear polarization to enhance proton and vanadium-51 polarization of vanadyl sulfate samples dopedwith TOTAPOL undermagic angle spinning conditions. The electron paramagnetic resonance response stemming from the paramagnetic 51V species was monitored as a function of pH, which can be adjusted to improve the enhancement of the proton polarization. By means of cross-polarization from the proton bath, 51V spins could be hyperpolarized. Enhancement factors, build-up times, and longitudinal relaxation times T1(1H) and T1(51V) were investigated as a function of pH. © 2014 John Wiley & Sons, Ltd. |
Deuterium MAS NMR studies of dynamics on multiple timescales: Histidine and oxalic acid Article de journal M Chan-Huot; S Wimperis; C Gervais; G Bodenhausen; L Duma ChemPhysChem, 16 (1), p. 204–215, 2015. @article{Chan-Huot:2015, title = {Deuterium MAS NMR studies of dynamics on multiple timescales: Histidine and oxalic acid}, author = {M Chan-Huot and S Wimperis and C Gervais and G Bodenhausen and L Duma}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84920163764&doi=10.1002%2fcphc.201402506&partnerID=40&md5=51145c085188aa600c0d86175c10a8e9}, doi = {10.1002/cphc.201402506}, year = {2015}, date = {2015-01-01}, journal = {ChemPhysChem}, volume = {16}, number = {1}, pages = {204--215}, abstract = {Deuterium (2H) magic-angle spinning(MAS) nuclear magnetic resonance is applied to monitor the dynamics of the exchanging labile deuterons of polycrystalline l-histidine hydrochloride monohydrate-d7 and α-oxalic acid dihydrate-d6. Direct experimental evidence of fast dynamics is obtained from T1Z and T1Q measurements. Further motional information is extracted from two-dimensional single-quantum (SQ) and double-quantum (DQ) MAS spectra. Differences between the SQ and DQ linewidths clearly indicate the presence of motions on intermediate timescales for the carboxylic moiety and the D2O in α oxalic acid dihydrate, and for the amine group and the D2O in l-histidine hydrochloride monohydrate. Comparison of the relaxation rate constants of Zeeman and quadrupolar order with the relaxation rate constants of the DQ coherences suggests the co-existence of fast and slow motional processes. ©2015 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Deuterium (2H) magic-angle spinning(MAS) nuclear magnetic resonance is applied to monitor the dynamics of the exchanging labile deuterons of polycrystalline l-histidine hydrochloride monohydrate-d7 and α-oxalic acid dihydrate-d6. Direct experimental evidence of fast dynamics is obtained from T1Z and T1Q measurements. Further motional information is extracted from two-dimensional single-quantum (SQ) and double-quantum (DQ) MAS spectra. Differences between the SQ and DQ linewidths clearly indicate the presence of motions on intermediate timescales for the carboxylic moiety and the D2O in α oxalic acid dihydrate, and for the amine group and the D2O in l-histidine hydrochloride monohydrate. Comparison of the relaxation rate constants of Zeeman and quadrupolar order with the relaxation rate constants of the DQ coherences suggests the co-existence of fast and slow motional processes. ©2015 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim. |
Asynchronous symmetry-based sequences for homonuclear dipolar recoupling in solid-state nuclear magnetic resonance Article de journal Kong Ooi Tan; M Rajeswari; PK Madhu; Matthias Ernst The Journal of chemical physics, 142 (6), p. 02B605_1, 2015. @article{tan2015asynchronous, title = {Asynchronous symmetry-based sequences for homonuclear dipolar recoupling in solid-state nuclear magnetic resonance}, author = {Kong Ooi Tan and M Rajeswari and PK Madhu and Matthias Ernst}, year = {2015}, date = {2015-01-01}, journal = {The Journal of chemical physics}, volume = {142}, number = {6}, pages = {02B605_1}, publisher = {AIP Publishing}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
2014 |
Solid-state carbon-13 NMR and computational characterization of the N719 ruthenium sensitizer adsorbed on TiO2 nanoparticles Article de journal N Salvi; J Frey; D Carnevale; M Grätzel; G Bodenhausen Dalton Transactions, 43 (17), p. 6389–6395, 2014. @article{Salvi:2014, title = {Solid-state carbon-13 NMR and computational characterization of the N719 ruthenium sensitizer adsorbed on TiO2 nanoparticles}, author = {N Salvi and J Frey and D Carnevale and M Gr\"{a}tzel and G Bodenhausen}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84897556122&doi=10.1039%2fc3dt52543k&partnerID=40&md5=9a9597617886070892bd54d3ff397f65}, doi = {10.1039/c3dt52543k}, year = {2014}, date = {2014-01-01}, journal = {Dalton Transactions}, volume = {43}, number = {17}, pages = {6389--6395}, abstract = {The ruthenium-containing sensitizing dye N719 grafted on TiO2 nanoparticles was investigated by solid-state NMR. The carbon resonances are assigned by means of 13C cross-polarized dipolar dephasing experiments. DFT calculations of the carbon magnetic shielding tensors accurately describe the changes in chemical shifts observed upon grafting onto a titania surface via one or two carboxylic functions in the plane defined by the two isothiocyanate groups. This journal is © the Partner Organisations 2014.}, keywords = {}, pubstate = {published}, tppubtype = {article} } The ruthenium-containing sensitizing dye N719 grafted on TiO2 nanoparticles was investigated by solid-state NMR. The carbon resonances are assigned by means of 13C cross-polarized dipolar dephasing experiments. DFT calculations of the carbon magnetic shielding tensors accurately describe the changes in chemical shifts observed upon grafting onto a titania surface via one or two carboxylic functions in the plane defined by the two isothiocyanate groups. This journal is © the Partner Organisations 2014. |
Drug screening boosted by hyperpolarized long-lived states in NMR Article de journal R Buratto; A Bornet; J Milani; D Mammoli; B Vuichoud; N Salvi; M Singh; A Laguerre; S Passemard; S Gerber-Lemaire; S Jannin; G Bodenhausen ChemMedChem, 9 (11), p. 2509–2515, 2014. @article{Buratto:2014a, title = {Drug screening boosted by hyperpolarized long-lived states in NMR}, author = {R Buratto and A Bornet and J Milani and D Mammoli and B Vuichoud and N Salvi and M Singh and A Laguerre and S Passemard and S Gerber-Lemaire and S Jannin and G Bodenhausen}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84926492670&doi=10.1002%2fcmdc.201402214&partnerID=40&md5=025b6457b1ab2d91f41415fe64d9e603}, doi = {10.1002/cmdc.201402214}, year = {2014}, date = {2014-01-01}, journal = {ChemMedChem}, volume = {9}, number = {11}, pages = {2509--2515}, abstract = {Transverse and longitudinal relaxation times (T1ρ and T1) have been widely exploited in NMR to probe the binding of ligands and putative drugs to target proteins. We have shown recently that long-lived states (LLS) can be more sensitive to ligand binding. LLS can be excited if the ligand comprises at least two coupled spins. Herein we broaden the scope of ligand screening by LLS to arbitrary ligands by covalent attachment of a functional group, which comprises a pair of coupled protons that are isolated from neighboring magnetic nuclei. The resulting functionalized ligands have longitudinal relaxation times T1(1H) that are sufficiently long to allow the powerful combination of LLS with dissolution dynamic nuclear polarization (D-DNP). Hyperpolarized weak "spy ligands" can be displaced by high-affinity competitors. Hyperpolarized LLS allow one to decrease both protein and ligand concentrations to micromolar levels and to significantly increase sample throughput.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Transverse and longitudinal relaxation times (T1ρ and T1) have been widely exploited in NMR to probe the binding of ligands and putative drugs to target proteins. We have shown recently that long-lived states (LLS) can be more sensitive to ligand binding. LLS can be excited if the ligand comprises at least two coupled spins. Herein we broaden the scope of ligand screening by LLS to arbitrary ligands by covalent attachment of a functional group, which comprises a pair of coupled protons that are isolated from neighboring magnetic nuclei. The resulting functionalized ligands have longitudinal relaxation times T1(1H) that are sufficiently long to allow the powerful combination of LLS with dissolution dynamic nuclear polarization (D-DNP). Hyperpolarized weak "spy ligands" can be displaced by high-affinity competitors. Hyperpolarized LLS allow one to decrease both protein and ligand concentrations to micromolar levels and to significantly increase sample throughput. |
Long-lived states of magnetically equivalent spins populated by dissolution-DNP and revealed by enzymatic reactions Article de journal A Bornet; X Ji; D Mammoli; B Vuichoud; J Milani; G Bodenhausen; S Jannin Chemistry - A European Journal, 20 (51), p. 17113–17118, 2014. @article{Bornet:2014a, title = {Long-lived states of magnetically equivalent spins populated by dissolution-DNP and revealed by enzymatic reactions}, author = {A Bornet and X Ji and D Mammoli and B Vuichoud and J Milani and G Bodenhausen and S Jannin}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84915749187&doi=10.1002%2fchem.201404967&partnerID=40&md5=587787bc80dea66600873bfe285a66c7}, doi = {10.1002/chem.201404967}, year = {2014}, date = {2014-01-01}, journal = {Chemistry - A European Journal}, volume = {20}, number = {51}, pages = {17113--17118}, abstract = {Hyperpolarization by dissolution dynamic nuclear polarization (D-DNP) offers a way of enhancing NMR signals by up to five orders of magnitude in metabolites and other small molecules. Nevertheless, the lifetime of hyperpolarization is inexorably limited, as it decays toward thermal equilibrium with the nuclear spin-lattice relaxation time. This lifetime can be extended by storing the hyperpolarization in the form of long-lived states (LLS) that are immune to most dominant relaxation mechanisms. Levitt and co-workers have shown how LLS can be prepared for a pair of inequivalent spins by D-DNP. Here, we demonstrate that this approach can also be applied to magnetically equivalent pairs of spins such as the two protons of fumarate, which can have very long LLS lifetimes. As in the case of para-hydrogen, these hyperpolarized equivalent LLS (HELLS) are not magnetically active. However, a chemical reaction such as the enzymatic conversion of fumarate into malate can break the magnetic equivalence and reveal intense NMR signals.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Hyperpolarization by dissolution dynamic nuclear polarization (D-DNP) offers a way of enhancing NMR signals by up to five orders of magnitude in metabolites and other small molecules. Nevertheless, the lifetime of hyperpolarization is inexorably limited, as it decays toward thermal equilibrium with the nuclear spin-lattice relaxation time. This lifetime can be extended by storing the hyperpolarization in the form of long-lived states (LLS) that are immune to most dominant relaxation mechanisms. Levitt and co-workers have shown how LLS can be prepared for a pair of inequivalent spins by D-DNP. Here, we demonstrate that this approach can also be applied to magnetically equivalent pairs of spins such as the two protons of fumarate, which can have very long LLS lifetimes. As in the case of para-hydrogen, these hyperpolarized equivalent LLS (HELLS) are not magnetically active. However, a chemical reaction such as the enzymatic conversion of fumarate into malate can break the magnetic equivalence and reveal intense NMR signals. |
Hybrid polarizing solids for pure hyperpolarized liquids through dissolution dynamic nuclear polarization Article de journal D Gajan; A Bornet; B Vuichoud; J Milani; R Melzi; H A Van Kalkeren; L Veyre; C Thieuleux; M P Conley; W R Grüning; M Schwarzwälder; A Lesage; C Copéret; G Bodenhausen; L Emsley; S Jannin; T M Swager Proceedings of the National Academy of Sciences of the United States of America, 111 (41), p. 14693–14697, 2014. @article{Gajan:2014, title = {Hybrid polarizing solids for pure hyperpolarized liquids through dissolution dynamic nuclear polarization}, author = {D Gajan and A Bornet and B Vuichoud and J Milani and R Melzi and H A Van Kalkeren and L Veyre and C Thieuleux and M P Conley and W R Gr\"{u}ning and M Schwarzw\"{a}lder and A Lesage and C Cop\'{e}ret and G Bodenhausen and L Emsley and S Jannin and T M Swager}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84907930152&doi=10.1073%2fpnas.1407730111&partnerID=40&md5=394bf5cfca37014ebe159712bb9af6e1}, doi = {10.1073/pnas.1407730111}, year = {2014}, date = {2014-01-01}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {111}, number = {41}, pages = {14693--14697}, abstract = {Hyperpolarization of substrates for magnetic resonance spectroscopy (MRS) and imaging (MRI) by dissolution dynamic nuclear polarization (D-DNP) usually involves saturating the ESR transitions of polarizing agents (PAs; e.g., persistent radicals embedded in frozen glassy matrices). This approach has shown enormous potential to achieve greatly enhanced nuclear spin polarization, but the presence of PAs and/or glassing agents in the sample after dissolution can raise concerns for in vivo MRI applications, such as perturbing molecular interactions, and may induce the erosion of hyperpolarization in spectroscopy and MRI. We show that D-DNP can be performed efficiently with hybrid polarizing solids (HYPSOs) with 2,2,6,6- Tetramethyl-piperidine-1-oxyl radicals incorporated in a mesostructured silica material and homogeneously distributed along its pore channels. The powder is wettedwith a solution containing molecules of interest (for example, metabolites for MRS or MRI) to fill the pore channels (incipient wetness impregnation), and DNP is performed at low temperatures in a very efficient manner. This approach allows high polarization without the need for glass-forming agents and is applicable to a broad range of substrates, including peptides and metabolites. During dissolution, HYPSO is physically retained by simple filtration in the cryostat of the DNP polarizer, and a pure hyperpolarized solution is collected within a few seconds. The resulting solution contains the pure substrate, is free from any paramagnetic or other pollutants, and is ready for in vivo infusion.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Hyperpolarization of substrates for magnetic resonance spectroscopy (MRS) and imaging (MRI) by dissolution dynamic nuclear polarization (D-DNP) usually involves saturating the ESR transitions of polarizing agents (PAs; e.g., persistent radicals embedded in frozen glassy matrices). This approach has shown enormous potential to achieve greatly enhanced nuclear spin polarization, but the presence of PAs and/or glassing agents in the sample after dissolution can raise concerns for in vivo MRI applications, such as perturbing molecular interactions, and may induce the erosion of hyperpolarization in spectroscopy and MRI. We show that D-DNP can be performed efficiently with hybrid polarizing solids (HYPSOs) with 2,2,6,6- Tetramethyl-piperidine-1-oxyl radicals incorporated in a mesostructured silica material and homogeneously distributed along its pore channels. The powder is wettedwith a solution containing molecules of interest (for example, metabolites for MRS or MRI) to fill the pore channels (incipient wetness impregnation), and DNP is performed at low temperatures in a very efficient manner. This approach allows high polarization without the need for glass-forming agents and is applicable to a broad range of substrates, including peptides and metabolites. During dissolution, HYPSO is physically retained by simple filtration in the cryostat of the DNP polarizer, and a pure hyperpolarized solution is collected within a few seconds. The resulting solution contains the pure substrate, is free from any paramagnetic or other pollutants, and is ready for in vivo infusion. |
Determination of sample temperature in unstable static fields by combining solid-state 79Br and 13C NMR Article de journal R N Purusottam; G Bodenhausen; P Tekely Journal of Magnetic Resonance, 246 , p. 69–71, 2014. @article{Purusottam:2014a, title = {Determination of sample temperature in unstable static fields by combining solid-state 79Br and 13C NMR}, author = {R N Purusottam and G Bodenhausen and P Tekely}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84905197285&doi=10.1016%2fj.jmr.2014.06.021&partnerID=40&md5=f465af14bb1c757fd8d84cb7fc28e588}, doi = {10.1016/j.jmr.2014.06.021}, year = {2014}, date = {2014-01-01}, journal = {Journal of Magnetic Resonance}, volume = {246}, pages = {69--71}, abstract = {Monitoring the isotropic chemical shifts to calibrate the sample temperature presupposes a perfect stability of the static magnetic field. It can be difficult to satisfy this requirement in solid-state NMR measurements. This paper describes a simple way to recover the accurate temperature dependence of the 79Br resonance after subtracting changes of resonance frequency due to variations of the static field, monitored by the 13C resonance. © 2014 Elsevier Inc. All rights reserved.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Monitoring the isotropic chemical shifts to calibrate the sample temperature presupposes a perfect stability of the static magnetic field. It can be difficult to satisfy this requirement in solid-state NMR measurements. This paper describes a simple way to recover the accurate temperature dependence of the 79Br resonance after subtracting changes of resonance frequency due to variations of the static field, monitored by the 13C resonance. © 2014 Elsevier Inc. All rights reserved. |
Cross polarization from 1H to quadrupolar 6Li nuclei for dissolution DNP Article de journal A J Perez Linde; A Bornet; J Milani; B Vuichoud; R Melzi; S Jannin; G Bodenhausen Physical Chemistry Chemical Physics, 16 (45), p. 24813–24817, 2014. @article{PerezLinde:2014, title = {Cross polarization from 1H to quadrupolar 6Li nuclei for dissolution DNP}, author = {A J Perez Linde and A Bornet and J Milani and B Vuichoud and R Melzi and S Jannin and G Bodenhausen}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84908431154&doi=10.1039%2fc4cp03592e&partnerID=40&md5=12d4c6115fd340be2b69b9a01c2c4c40}, doi = {10.1039/c4cp03592e}, year = {2014}, date = {2014-01-01}, journal = {Physical Chemistry Chemical Physics}, volume = {16}, number = {45}, pages = {24813--24817}, abstract = {Cross polarization from protons to quadrupolar 6Li nuclei is combined with dynamic nuclear polarization of protons at 1.2 K and 6.7 T using TEMPOL as a polarizing agent followed by rapid dissolution. Compared to direct 6Li DNP without cross-polarization, a higher nuclear spin polarization P(6Li) can be obtained in a shorter time. A double resonance 1H-6Li probe was designed that is equipped for Longitudinally Detected Electron Spin Resonance. © the Partner Organisations 2014.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Cross polarization from protons to quadrupolar 6Li nuclei is combined with dynamic nuclear polarization of protons at 1.2 K and 6.7 T using TEMPOL as a polarizing agent followed by rapid dissolution. Compared to direct 6Li DNP without cross-polarization, a higher nuclear spin polarization P(6Li) can be obtained in a shorter time. A double resonance 1H-6Li probe was designed that is equipped for Longitudinally Detected Electron Spin Resonance. © the Partner Organisations 2014. |
Multiple scale dynamics in proteins probed at multiple time scales through fluctuations of NMR chemical shifts Article de journal P Calligari; D Abergel Journal of Physical Chemistry B, 118 (14), p. 3823–3831, 2014. @article{Calligari:2014, title = {Multiple scale dynamics in proteins probed at multiple time scales through fluctuations of NMR chemical shifts}, author = {P Calligari and D Abergel}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84898494069&doi=10.1021%2fjp412125d&partnerID=40&md5=a15bc633ce9414ef73e0fd4a197bfc4a}, doi = {10.1021/jp412125d}, year = {2014}, date = {2014-01-01}, journal = {Journal of Physical Chemistry B}, volume = {118}, number = {14}, pages = {3823--3831}, abstract = {Fluctuations of NMR resonance frequency shifts and their relation with protein exchanging conformations are usually analyzed in terms of simple two-site jump processes. However, this description is unable to account for the presence of multiple time scale dynamics. In this work, we present an alternative model for the interpretation of the stochastic processes underlying these fluctuations of resonance frequencies. Time correlation functions of 15N amide chemical shifts computed from molecular dynamics simulations (MD) were analyzed in terms of a transiently fractional diffusion process. The analysis of MD trajectories spanning dramatically different time scales (∼200 ns and 1 ms [ Shaw, D. E.; Science 2010, 330, 341-346 ]) allowed us to show that our model could capture the multiple scale structure of chemical shift fluctuations. Moreover, the predicted exchange contribution Rex to the NMR transverse relaxation rate is in qualitative agreement with experimental results. These observations suggest that the proposed fractional diffusion model may provide significative improvement to the analysis of NMR dispersion experiments. © 2014 American Chemical Society.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Fluctuations of NMR resonance frequency shifts and their relation with protein exchanging conformations are usually analyzed in terms of simple two-site jump processes. However, this description is unable to account for the presence of multiple time scale dynamics. In this work, we present an alternative model for the interpretation of the stochastic processes underlying these fluctuations of resonance frequencies. Time correlation functions of 15N amide chemical shifts computed from molecular dynamics simulations (MD) were analyzed in terms of a transiently fractional diffusion process. The analysis of MD trajectories spanning dramatically different time scales (∼200 ns and 1 ms [ Shaw, D. E.; Science 2010, 330, 341-346 ]) allowed us to show that our model could capture the multiple scale structure of chemical shift fluctuations. Moreover, the predicted exchange contribution Rex to the NMR transverse relaxation rate is in qualitative agreement with experimental results. These observations suggest that the proposed fractional diffusion model may provide significative improvement to the analysis of NMR dispersion experiments. © 2014 American Chemical Society. |
On the reliability of NMR relaxation data analyses: A Markov Chain Monte Carlo approach Article de journal D Abergel; A Volpato; E P Coutant; A Polimeno Journal of Magnetic Resonance, 246 , p. 94–103, 2014. @article{Abergel:2014, title = {On the reliability of NMR relaxation data analyses: A Markov Chain Monte Carlo approach}, author = {D Abergel and A Volpato and E P Coutant and A Polimeno}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84907371539&doi=10.1016%2fj.jmr.2014.07.007&partnerID=40&md5=4e1d83617c8aeeb054edd31419293baf}, doi = {10.1016/j.jmr.2014.07.007}, year = {2014}, date = {2014-01-01}, journal = {Journal of Magnetic Resonance}, volume = {246}, pages = {94--103}, abstract = {The analysis of NMR relaxation data is revisited along the lines of a Bayesian approach. Using a Markov Chain Monte Carlo strategy of data fitting, we investigate conditions under which relaxation data can be effectively interpreted in terms of internal dynamics. The limitations to the extraction of kinetic parameters that characterize internal dynamics are analyzed, and we show that extracting characteristic time scales shorter than a few tens of ps is very unlikely. However, using MCMC methods, reliable estimates of the marginal probability distributions and estimators (average, standard deviations, etc.) can still be obtained for subsets of the model parameters. Thus, unlike more conventional strategies of data analysis, the method avoids a model selection process. In addition, it indicates what information may be extracted from the data, but also what cannot. © 2014 Elsevier Inc. All rights reserved.}, keywords = {}, pubstate = {published}, tppubtype = {article} } The analysis of NMR relaxation data is revisited along the lines of a Bayesian approach. Using a Markov Chain Monte Carlo strategy of data fitting, we investigate conditions under which relaxation data can be effectively interpreted in terms of internal dynamics. The limitations to the extraction of kinetic parameters that characterize internal dynamics are analyzed, and we show that extracting characteristic time scales shorter than a few tens of ps is very unlikely. However, using MCMC methods, reliable estimates of the marginal probability distributions and estimators (average, standard deviations, etc.) can still be obtained for subsets of the model parameters. Thus, unlike more conventional strategies of data analysis, the method avoids a model selection process. In addition, it indicates what information may be extracted from the data, but also what cannot. © 2014 Elsevier Inc. All rights reserved. |
Broad-band DREAM recoupling sequence Article de journal Kong Ooi Tan; Anders B Nielsen; Beat H Meier; Matthias Ernst The journal of physical chemistry letters, 5 (19), p. 3366–3372, 2014. @article{tan2014broad, title = {Broad-band DREAM recoupling sequence}, author = {Kong Ooi Tan and Anders B Nielsen and Beat H Meier and Matthias Ernst}, year = {2014}, date = {2014-01-01}, journal = {The journal of physical chemistry letters}, volume = {5}, number = {19}, pages = {3366\textendash3372}, publisher = {American Chemical Society}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Improved decoupling during symmetry-based C9-TOBSY sequences Article de journal Kong Ooi Tan; Ingo Scholz; Jacco D van Beek; Beat H Meier; Matthias Ernst Journal of Magnetic Resonance, 239 , p. 61–68, 2014. @article{tan2014improved, title = {Improved decoupling during symmetry-based C9-TOBSY sequences}, author = {Kong Ooi Tan and Ingo Scholz and Jacco D van Beek and Beat H Meier and Matthias Ernst}, year = {2014}, date = {2014-01-01}, journal = {Journal of Magnetic Resonance}, volume = {239}, pages = {61\textendash68}, publisher = {Academic Press}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Toward quantitative measurements of enzyme kinetics by dissolution dynamic nuclear polarization Article de journal E Miclet; D Abergel; A Bornet; J Milani; S Jannin; G Bodenhausen Journal of Physical Chemistry Letters, 5 (19), p. 3290–3295, 2014. @article{Miclet:2014, title = {Toward quantitative measurements of enzyme kinetics by dissolution dynamic nuclear polarization}, author = {E Miclet and D Abergel and A Bornet and J Milani and S Jannin and G Bodenhausen}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84907810112&doi=10.1021%2fjz501411d&partnerID=40&md5=030f0f1d07ad207b009f50bcb517449d}, doi = {10.1021/jz501411d}, year = {2014}, date = {2014-01-01}, journal = {Journal of Physical Chemistry Letters}, volume = {5}, number = {19}, pages = {3290--3295}, abstract = {Dissolution dynamic nuclear polarization (D-DNP) experiments enabled us to study the kinetics of the enzymatic phosphorylation reaction of glucose to form glucose-6-phosphate (G6P) by hexokinase (HK), with or without the presence of an excess of G6P, which is known to be an inhibitor of the enzyme. Against all expectations, our observations demonstrate that the phosphorylation of both and glucose anomers occurs with comparable kinetics. The catalytic constant of the reaction was estimated based on a simple kinetic model tailored for hyperpolarized systems. © 2014 American Chemical Society.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Dissolution dynamic nuclear polarization (D-DNP) experiments enabled us to study the kinetics of the enzymatic phosphorylation reaction of glucose to form glucose-6-phosphate (G6P) by hexokinase (HK), with or without the presence of an excess of G6P, which is known to be an inhibitor of the enzyme. Against all expectations, our observations demonstrate that the phosphorylation of both and glucose anomers occurs with comparable kinetics. The catalytic constant of the reaction was estimated based on a simple kinetic model tailored for hyperpolarized systems. © 2014 American Chemical Society. |
Solid-state NMR measurements and DFT calculations of the magnetic shielding tensors of protons of water trapped in barium chlorate monohydrate Article de journal D Carnevale; S E Ashbrook; G Bodenhausen RSC Advances, 4 (99), p. 56248–56258, 2014. @article{Carnevale:2014, title = {Solid-state NMR measurements and DFT calculations of the magnetic shielding tensors of protons of water trapped in barium chlorate monohydrate}, author = {D Carnevale and S E Ashbrook and G Bodenhausen}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84908635302&doi=10.1039%2fc4ra09992c&partnerID=40&md5=9c97c81045e20ae0514bdc0f6645bdb2}, doi = {10.1039/c4ra09992c}, year = {2014}, date = {2014-01-01}, journal = {RSC Advances}, volume = {4}, number = {99}, pages = {56248--56258}, abstract = {The magnetic shielding tensors of protons of water in barium chlorate monohydrate are investigated at room temperature by means of solid-state NMR spectroscopy, both for static powders and under magic-angle spinning conditions, using one- and two-dimensional techniques. First-principles DFT calculations based on a periodic planewave pseudopotential formalism for a static periodic system provide support for our spectral interpretation and corroborate the experimental findings in the fast motion regime. © The Royal Society of Chemistry 2014.}, keywords = {}, pubstate = {published}, tppubtype = {article} } The magnetic shielding tensors of protons of water in barium chlorate monohydrate are investigated at room temperature by means of solid-state NMR spectroscopy, both for static powders and under magic-angle spinning conditions, using one- and two-dimensional techniques. First-principles DFT calculations based on a periodic planewave pseudopotential formalism for a static periodic system provide support for our spectral interpretation and corroborate the experimental findings in the fast motion regime. © The Royal Society of Chemistry 2014. |
R N Purusottam; G Bodenhausen; P Tekely Chemical Physics Letters, 614 , p. 220–225, 2014. @article{Purusottam:2014, title = {Sensitivity improvement during heteronuclear spin decoupling in solid-state nuclear magnetic resonance experiments at high spinning frequencies and moderate radio-frequency amplitudes}, author = {R N Purusottam and G Bodenhausen and P Tekely}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84907626052&doi=10.1016%2fj.cplett.2014.09.044&partnerID=40&md5=6c6535815972fa522c7f4c489f3c7d7d}, doi = {10.1016/j.cplett.2014.09.044}, year = {2014}, date = {2014-01-01}, journal = {Chemical Physics Letters}, volume = {614}, pages = {220--225}, abstract = {Searching for optimal conditions during one- and multi-dimensional solid-state NMR experiments in high static fields may require spinning the sample at frequencies above 40 kHz. This implies challenging requirements for heteronuclear spin decoupling. We have compared the performance of the latest heteronuclear decoupling schemes at high magic-angle spinning frequencies. The results demonstrate that at commonly used rf amplitudes between 80 and 120 kHz, PISSARRO decoupling provides substantial sensitivity improvement. The performance of low-amplitude decoupling at different spinning speeds is also compared and its dependence on the inherent inhomogeneity of the rf field is probed by numerical simulations. © 2014 Published by Elsevier B.V.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Searching for optimal conditions during one- and multi-dimensional solid-state NMR experiments in high static fields may require spinning the sample at frequencies above 40 kHz. This implies challenging requirements for heteronuclear spin decoupling. We have compared the performance of the latest heteronuclear decoupling schemes at high magic-angle spinning frequencies. The results demonstrate that at commonly used rf amplitudes between 80 and 120 kHz, PISSARRO decoupling provides substantial sensitivity improvement. The performance of low-amplitude decoupling at different spinning speeds is also compared and its dependence on the inherent inhomogeneity of the rf field is probed by numerical simulations. © 2014 Published by Elsevier B.V. |
Fast proton exchange in histidine: Measurement of rate constants through indirect detection by NMR spectroscopy Article de journal A A Sehgal; L Duma; G Bodenhausen; P Pelupessy Chemistry - A European Journal, 20 (21), p. 6332–6338, 2014. @article{Sehgal:2014, title = {Fast proton exchange in histidine: Measurement of rate constants through indirect detection by NMR spectroscopy}, author = {A A Sehgal and L Duma and G Bodenhausen and P Pelupessy}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84900832469&doi=10.1002%2fchem.201304992&partnerID=40&md5=1c3f9fec2bdda87d11029e2c307fce5a}, doi = {10.1002/chem.201304992}, year = {2014}, date = {2014-01-01}, journal = {Chemistry - A European Journal}, volume = {20}, number = {21}, pages = {6332--6338}, abstract = {Owing to its imidazole side chain, histidine participates in various processes such as enzyme catalysis, pH regulation, metal binding, and phosphorylation. The determination of exchange rates of labile protons for such a system is important for understanding its functions. However, these rates are too fast to be measured directly in an aqueous solution by using NMR spectroscopy. We have obtained the exchange rates of the NH3 + amino protons and the labile NHε2 and NH δ1 protons of the imidazole ring by indirect detection through nitrogen-15 as a function of temperature (272K<T<293K) and pH (1.3<pH<4.9) of uniformly nitrogen-15- and carbon-13-labeled L-histidine-HCl-H2O. Exchange rates up to 8.5×10 4s-1 could be determined (i.e., lifetimes as short as 12μs). The three chemical shifts δHi of the invisible exchanging protons Hi and the three one-bond scalar coupling constants 1J(N,Hi) could also be determined accurately. Seeking the invisible: The protons attached to the N atoms of histidine in an aqueous solution have hitherto escaped detection owing to the very fast exchange of these protons with the solvent. The exchange rate constants along with the one-bond scalar couplings and chemical shifts of these elusive protons have been determined for a pH range in which the three N nuclei are protonated (see figure). © 2014 The Authors. Published by Wiley-VCH Verlag GmbH & Co. KGaA. This is an open access article under the terms of Creative Commons Attribution NonCommercial-NoDerivs License, which permits use and distribution in any medium, provided the original work is properly cited, the use is non-commercial and no modifications or adaptations are made.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Owing to its imidazole side chain, histidine participates in various processes such as enzyme catalysis, pH regulation, metal binding, and phosphorylation. The determination of exchange rates of labile protons for such a system is important for understanding its functions. However, these rates are too fast to be measured directly in an aqueous solution by using NMR spectroscopy. We have obtained the exchange rates of the NH3 + amino protons and the labile NHε2 and NH δ1 protons of the imidazole ring by indirect detection through nitrogen-15 as a function of temperature (272K<T<293K) and pH (1.3<pH<4.9) of uniformly nitrogen-15- and carbon-13-labeled L-histidine-HCl-H2O. Exchange rates up to 8.5×10 4s-1 could be determined (i.e., lifetimes as short as 12μs). The three chemical shifts δHi of the invisible exchanging protons Hi and the three one-bond scalar coupling constants 1J(N,Hi) could also be determined accurately. Seeking the invisible: The protons attached to the N atoms of histidine in an aqueous solution have hitherto escaped detection owing to the very fast exchange of these protons with the solvent. The exchange rate constants along with the one-bond scalar couplings and chemical shifts of these elusive protons have been determined for a pH range in which the three N nuclei are protonated (see figure). © 2014 The Authors. Published by Wiley-VCH Verlag GmbH & Co. KGaA. This is an open access article under the terms of Creative Commons Attribution NonCommercial-NoDerivs License, which permits use and distribution in any medium, provided the original work is properly cited, the use is non-commercial and no modifications or adaptations are made. |
Hyperpolarization of deuterated metabolites via remote cross-polarization and dissolution dynamic nuclear polarization Article de journal B Vuichoud; J Milani; A Bornet; R Melzi; S Jannin; G Bodenhausen Journal of Physical Chemistry B, 118 (5), p. 1411–1415, 2014. @article{Vuichoud:2014, title = {Hyperpolarization of deuterated metabolites via remote cross-polarization and dissolution dynamic nuclear polarization}, author = {B Vuichoud and J Milani and A Bornet and R Melzi and S Jannin and G Bodenhausen}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84893878018&doi=10.1021%2fjp4118776&partnerID=40&md5=ec7f0219f12f98bc7048c0805beeda63}, doi = {10.1021/jp4118776}, year = {2014}, date = {2014-01-01}, journal = {Journal of Physical Chemistry B}, volume = {118}, number = {5}, pages = {1411--1415}, abstract = {In deuterated molecules such as [1-13C]pyruvate-d3, the nuclear spin polarization of 13C nuclei can be enhanced by combining Hartmann-Hahn cross-polarization (CP) at low temperatures (1.2 K) with dissolution dynamic nuclear polarization (D-DNP). The polarization is transferred from remote solvent protons to the 13C spins of interest. This allows one not only to slightly reduce build-up times but also to increase polarization levels and extend the lifetimes T1(13C) of the enhanced 13C polarization during and after transfer from the polarizer to the NMR or MRI system. This extends time scales over which metabolic processes and chemical reactions can be monitored. © 2014 American Chemical Society.}, keywords = {}, pubstate = {published}, tppubtype = {article} } In deuterated molecules such as [1-13C]pyruvate-d3, the nuclear spin polarization of 13C nuclei can be enhanced by combining Hartmann-Hahn cross-polarization (CP) at low temperatures (1.2 K) with dissolution dynamic nuclear polarization (D-DNP). The polarization is transferred from remote solvent protons to the 13C spins of interest. This allows one not only to slightly reduce build-up times but also to increase polarization levels and extend the lifetimes T1(13C) of the enhanced 13C polarization during and after transfer from the polarizer to the NMR or MRI system. This extends time scales over which metabolic processes and chemical reactions can be monitored. © 2014 American Chemical Society. |
Exploring Weak Ligand-Protein Interactions by Long-Lived NMR States: Improved Contrast in Fragment-Based Drug Screening Article de journal R Buratto; D Mammoli; E Chiarparin; G Williams; G Bodenhausen Angewandte Chemie - International Edition, 53 (42), p. 11376–11380, 2014. @article{Buratto:2014, title = {Exploring Weak Ligand-Protein Interactions by Long-Lived NMR States: Improved Contrast in Fragment-Based Drug Screening}, author = {R Buratto and D Mammoli and E Chiarparin and G Williams and G Bodenhausen}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84907856120&doi=10.1002%2fanie.201404921&partnerID=40&md5=63404051d238a18c9cde44dd7caaee9f}, doi = {10.1002/anie.201404921}, year = {2014}, date = {2014-01-01}, journal = {Angewandte Chemie - International Edition}, volume = {53}, number = {42}, pages = {11376--11380}, abstract = {Ligands that have an affinity for protein targets can be screened very effectively by exploiting favorable properties of long-lived states (LLS) in NMR spectroscopy. In this work, we describe the use of LLS for competitive binding experiments to measure accurate dissociation constants of fragments that bind weakly to the ATP binding site of the N-terminal ATPase domain of heat shock protein 90 (Hsp90), a therapeutic target for cancer treatment. The LLS approach allows one to characterize ligands with an exceptionally wide range of affinities, since it can be used for ligand concentrations [L] that are several orders of magnitude smaller than the dissociation constants KD. This property makes the LLS method particularly attractive for the initial steps of fragment-based drug screening, where small molecular fragments that bind weakly to a target protein must be identified, which is a difficult task for many other biophysical methods. © 2014 The Authors. Published by Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Ligands that have an affinity for protein targets can be screened very effectively by exploiting favorable properties of long-lived states (LLS) in NMR spectroscopy. In this work, we describe the use of LLS for competitive binding experiments to measure accurate dissociation constants of fragments that bind weakly to the ATP binding site of the N-terminal ATPase domain of heat shock protein 90 (Hsp90), a therapeutic target for cancer treatment. The LLS approach allows one to characterize ligands with an exceptionally wide range of affinities, since it can be used for ligand concentrations [L] that are several orders of magnitude smaller than the dissociation constants KD. This property makes the LLS method particularly attractive for the initial steps of fragment-based drug screening, where small molecular fragments that bind weakly to a target protein must be identified, which is a difficult task for many other biophysical methods. © 2014 The Authors. Published by Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim. |
Microwave frequency modulation to enhance Dissolution Dynamic Nuclear Polarization Dedicated to To Martial Rey, as a token of appreciation. Article de journal A Bornet; J Milani; B Vuichoud; A J Perez Linde; G Bodenhausen; S Jannin Chemical Physics Letters, 602 , p. 63–67, 2014. @article{Bornet:2014, title = {Microwave frequency modulation to enhance Dissolution Dynamic Nuclear Polarization Dedicated to To Martial Rey, as a token of appreciation.}, author = {A Bornet and J Milani and B Vuichoud and A J Perez Linde and G Bodenhausen and S Jannin}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84899826641&doi=10.1016%2fj.cplett.2014.04.013&partnerID=40&md5=d71fec60363f7f894325661f0c3454de}, doi = {10.1016/j.cplett.2014.04.013}, year = {2014}, date = {2014-01-01}, journal = {Chemical Physics Letters}, volume = {602}, pages = {63--67}, abstract = {Hyperpolarization by Dissolution Dynamic Nuclear Polarization is usually achieved by monochromatic microwave irradiation of the ESR spectrum of free radicals embedded in glasses at 1.2 K and 3.35 T. Hovav et al. (2014) have recently shown that by using frequency-modulated (rather than monochromatic) microwave irradiation one can improve DNP at 3.35 T in the temperature range 10-50 K. We show in this Letter that this is also true under Dissolution-DNP conditions at 1.2 K and 6.7 T. We demonstrate the many virtues of using frequency-modulated microwave irradiation: higher polarizations, faster build-up rates, lower radical concentrations, less paramagnetic broadening, more efficient cross-polarization, and less critical frequency adjustments. © 2014 The Authors. Published by Elsevier B.V.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Hyperpolarization by Dissolution Dynamic Nuclear Polarization is usually achieved by monochromatic microwave irradiation of the ESR spectrum of free radicals embedded in glasses at 1.2 K and 3.35 T. Hovav et al. (2014) have recently shown that by using frequency-modulated (rather than monochromatic) microwave irradiation one can improve DNP at 3.35 T in the temperature range 10-50 K. We show in this Letter that this is also true under Dissolution-DNP conditions at 1.2 K and 6.7 T. We demonstrate the many virtues of using frequency-modulated microwave irradiation: higher polarizations, faster build-up rates, lower radical concentrations, less paramagnetic broadening, more efficient cross-polarization, and less critical frequency adjustments. © 2014 The Authors. Published by Elsevier B.V. |
Probing 27Al-13C proximities in metal-organic frameworks using dynamic nuclear polarization enhanced NMR spectroscopy Article de journal F Pourpoint; A S L Thankamony; C Volkringer; T Loiseau; J Trébosc; F Aussenac; D Carnevale; G Bodenhausen; H Vezin; O Lafon; J -P Amoureux Chemical Communications, 50 (8), p. 933–935, 2014. @article{Pourpoint:2014, title = {Probing 27Al-13C proximities in metal-organic frameworks using dynamic nuclear polarization enhanced NMR spectroscopy}, author = {F Pourpoint and A S L Thankamony and C Volkringer and T Loiseau and J Tr\'{e}bosc and F Aussenac and D Carnevale and G Bodenhausen and H Vezin and O Lafon and J -P Amoureux}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84890833330&doi=10.1039%2fc3cc47208f&partnerID=40&md5=d58bb0ac7778852b5654031a64d6602b}, doi = {10.1039/c3cc47208f}, year = {2014}, date = {2014-01-01}, journal = {Chemical Communications}, volume = {50}, number = {8}, pages = {933--935}, abstract = {We show how 27Al-13C proximities in the microporous metal-organic framework MIL-100(Al) can be probed using advanced 27Al-13C NMR methods boosted by Dynamic Nuclear Polarization. © 2014 The Royal Society of Chemistry.}, keywords = {}, pubstate = {published}, tppubtype = {article} } We show how 27Al-13C proximities in the microporous metal-organic framework MIL-100(Al) can be probed using advanced 27Al-13C NMR methods boosted by Dynamic Nuclear Polarization. © 2014 The Royal Society of Chemistry. |
2013 |
Nanosecond time scale motions in proteins revealed by high-resolution nmr relaxometry Article de journal C Charlier; S N Khan; T Marquardsen; P Pelupessy; V Reiss; D Sakellariou; G Bodenhausen; F Engelke; F Ferrage Journal of the American Chemical Society, 135 (49), p. 18665–18672, 2013. @article{Charlier:2013, title = {Nanosecond time scale motions in proteins revealed by high-resolution nmr relaxometry}, author = {C Charlier and S N Khan and T Marquardsen and P Pelupessy and V Reiss and D Sakellariou and G Bodenhausen and F Engelke and F Ferrage}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84890530312&doi=10.1021%2fja409820g&partnerID=40&md5=cad2df7fde0c75536a95f1b37bc77f66}, doi = {10.1021/ja409820g}, year = {2013}, date = {2013-01-01}, journal = {Journal of the American Chemical Society}, volume = {135}, number = {49}, pages = {18665--18672}, abstract = {Understanding the molecular determinants underlying protein function requires the characterization of both structure and dynamics at atomic resolution. Nuclear relaxation rates allow a precise characterization of protein dynamics at the Larmor frequencies of spins. This usually limits the sampling of motions to a narrow range of frequencies corresponding to high magnetic fields. At lower fields one cannot achieve sufficient sensitivity and resolution in NMR. Here, we use a fast shuttle device where the polarization builds up and the signals are detected at high field, while longitudinal relaxation takes place at low fields 0.5 < B0 < 14.1 T. The sample is propelled over a distance up to 50 cm by a blowgun-like system in about 50 ms. The analysis of nitrogen-15 relaxation in the protein ubiquitin over such a wide range of magnetic fields offers unprecedented insights into molecular dynamics. Some key regions of the protein feature structural fluctuations on nanosecond time scales, which have so far been overlooked in high-field relaxation studies. Nanosecond motions in proteins may have been underestimated by traditional high-field approaches, and slower supra-τc motions that have no effect on relaxation may have been overestimated. High-resolution relaxometry thus opens the way to a quantitative characterization of nanosecond motions in proteins. © 2013 American Chemical Society.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Understanding the molecular determinants underlying protein function requires the characterization of both structure and dynamics at atomic resolution. Nuclear relaxation rates allow a precise characterization of protein dynamics at the Larmor frequencies of spins. This usually limits the sampling of motions to a narrow range of frequencies corresponding to high magnetic fields. At lower fields one cannot achieve sufficient sensitivity and resolution in NMR. Here, we use a fast shuttle device where the polarization builds up and the signals are detected at high field, while longitudinal relaxation takes place at low fields 0.5 < B0 < 14.1 T. The sample is propelled over a distance up to 50 cm by a blowgun-like system in about 50 ms. The analysis of nitrogen-15 relaxation in the protein ubiquitin over such a wide range of magnetic fields offers unprecedented insights into molecular dynamics. Some key regions of the protein feature structural fluctuations on nanosecond time scales, which have so far been overlooked in high-field relaxation studies. Nanosecond motions in proteins may have been underestimated by traditional high-field approaches, and slower supra-τc motions that have no effect on relaxation may have been overestimated. High-resolution relaxometry thus opens the way to a quantitative characterization of nanosecond motions in proteins. © 2013 American Chemical Society. |
Side chain dynamics of carboxyl and carbonyl groups in the catalytic function of escherichia coli ribonuclease Ħ Article de journal K A Stafford; F Ferrage; J -H Cho; A G Palmer Journal of the American Chemical Society, 135 (48), p. 18024–18027, 2013. @article{Stafford:2013, title = {Side chain dynamics of carboxyl and carbonyl groups in the catalytic function of escherichia coli ribonuclease {H}}, author = {K A Stafford and F Ferrage and J -H Cho and A G Palmer}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84889763704&doi=10.1021%2fja409479y&partnerID=40&md5=1eb8f79b0bb1106d099ad41b74b8c967}, doi = {10.1021/ja409479y}, year = {2013}, date = {2013-01-01}, journal = {Journal of the American Chemical Society}, volume = {135}, number = {48}, pages = {18024--18027}, abstract = {Many proteins use Asx and Glx (x = n, p, or u) side chains as key functional groups in enzymatic catalysis and molecular recognition. In this study, NMR spin relaxation experiments and molecular dynamics simulations are used to measure the dynamics of the side chain amide and carboxyl groups, 13Cγ/δ, in Escherichia coli ribonuclease HI (RNase H). Model-free analysis shows that the catalytic residues in RNase H are preorganized on ps-ns time scales via a network of electrostatic interactions. However, chemical exchange line broadening shows that these residues display significant conformational dynamics on μs-ms time scales upon binding of Mg2+ ions. Two groups of catalytic residues exhibit differential line broadening, implicating distinct reorganizational processes upon binding of metal ions. These results support the "mobile metal ion" hypothesis, which was inferred from structural studies of RNase H. © 2013 American Chemical Society.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Many proteins use Asx and Glx (x = n, p, or u) side chains as key functional groups in enzymatic catalysis and molecular recognition. In this study, NMR spin relaxation experiments and molecular dynamics simulations are used to measure the dynamics of the side chain amide and carboxyl groups, 13Cγ/δ, in Escherichia coli ribonuclease HI (RNase H). Model-free analysis shows that the catalytic residues in RNase H are preorganized on ps-ns time scales via a network of electrostatic interactions. However, chemical exchange line broadening shows that these residues display significant conformational dynamics on μs-ms time scales upon binding of Mg2+ ions. Two groups of catalytic residues exhibit differential line broadening, implicating distinct reorganizational processes upon binding of metal ions. These results support the "mobile metal ion" hypothesis, which was inferred from structural studies of RNase H. © 2013 American Chemical Society. |
Solid-state NMR enhanced by dynamic nuclear polarization as a novel tool for ribosome structural biology Article de journal I Gelis; V Vitzthum; N Dhimole; M A Caporini; A Schedlbauer; D Carnevale; S R Connell; P Fucini; G Bodenhausen Journal of Biomolecular NMR, 56 (2), p. 85–93, 2013. @article{Gelis:2013, title = {Solid-state NMR enhanced by dynamic nuclear polarization as a novel tool for ribosome structural biology}, author = {I Gelis and V Vitzthum and N Dhimole and M A Caporini and A Schedlbauer and D Carnevale and S R Connell and P Fucini and G Bodenhausen}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84879801263&doi=10.1007%2fs10858-013-9721-2&partnerID=40&md5=c4d4ed5ac773e3a49ded1a649ebf4046}, doi = {10.1007/s10858-013-9721-2}, year = {2013}, date = {2013-01-01}, journal = {Journal of Biomolecular NMR}, volume = {56}, number = {2}, pages = {85--93}, abstract = {The impact of Nuclear Magnetic Resonance (NMR) on studies of large macromolecular complexes hinges on improvements in sensitivity and resolution. Dynamic nuclear polarization (DNP) in the solid state can offer improved sensitivity, provided sample preparation is optimized to preserve spectral resolution. For a few nanomoles of intact ribosomes and an 800 kDa ribosomal complex we demonstrate that the combination of DNP and magic-angle spinning NMR (MAS-NMR) allows one to overcome current sensitivity limitations so that homo- and heteronuclear 13C and 15N NMR correlation spectra can be recorded. Ribosome particles, directly pelleted and frozen into an NMR rotor, yield DNP signal enhancements on the order of textasciitilde25-fold and spectra that exhibit narrow linewidths, suitable for obtaining site-specific information. We anticipate that the same approach is applicable to other high molecular weight complexes. © 2013 Springer Science+Business Media Dordrecht.}, keywords = {}, pubstate = {published}, tppubtype = {article} } The impact of Nuclear Magnetic Resonance (NMR) on studies of large macromolecular complexes hinges on improvements in sensitivity and resolution. Dynamic nuclear polarization (DNP) in the solid state can offer improved sensitivity, provided sample preparation is optimized to preserve spectral resolution. For a few nanomoles of intact ribosomes and an 800 kDa ribosomal complex we demonstrate that the combination of DNP and magic-angle spinning NMR (MAS-NMR) allows one to overcome current sensitivity limitations so that homo- and heteronuclear 13C and 15N NMR correlation spectra can be recorded. Ribosome particles, directly pelleted and frozen into an NMR rotor, yield DNP signal enhancements on the order of textasciitilde25-fold and spectra that exhibit narrow linewidths, suitable for obtaining site-specific information. We anticipate that the same approach is applicable to other high molecular weight complexes. © 2013 Springer Science+Business Media Dordrecht. |
Quantitative one- and two-dimensional 13C spectra of microcrystalline proteins with enhanced intensity Article de journal R N Purusottam; G Bodenhausen; P Tekely Journal of Biomolecular NMR, 57 (1), p. 11–19, 2013. @article{Purusottam:2013, title = {Quantitative one- and two-dimensional 13C spectra of microcrystalline proteins with enhanced intensity}, author = {R N Purusottam and G Bodenhausen and P Tekely}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84883560275&doi=10.1007%2fs10858-013-9759-1&partnerID=40&md5=551f7a45fc1aceaeb0b3acd8ea0f0faf}, doi = {10.1007/s10858-013-9759-1}, year = {2013}, date = {2013-01-01}, journal = {Journal of Biomolecular NMR}, volume = {57}, number = {1}, pages = {11--19}, abstract = {We recorded quantitative, uniformly enhanced one- and two-dimensional 13C spectra of labelled microcrystalline proteins. The approach takes advantage of efficient equilibration of magnetization by low-power proton irradiation using Phase Alternated Recoupling Irradiation Schemes and benefits simultaneously from uniform sensitivity enhancement due to efficient spin exchange that can overcome T1(13C) constraints and the presence of heteronuclear Overhauser effects. Graphical Abstract: [Figure not available: see fulltext.] © 2013 Springer Science+Business Media Dordrecht.}, keywords = {}, pubstate = {published}, tppubtype = {article} } We recorded quantitative, uniformly enhanced one- and two-dimensional 13C spectra of labelled microcrystalline proteins. The approach takes advantage of efficient equilibration of magnetization by low-power proton irradiation using Phase Alternated Recoupling Irradiation Schemes and benefits simultaneously from uniform sensitivity enhancement due to efficient spin exchange that can overcome T1(13C) constraints and the presence of heteronuclear Overhauser effects. Graphical Abstract: [Figure not available: see fulltext.] © 2013 Springer Science+Business Media Dordrecht. |
Determination of transverse relaxation rates in systems with scalar-coupled spins: The role of antiphase coherences Article de journal T F Segawa; G Bodenhausen Journal of Magnetic Resonance, 237 , p. 139–146, 2013. @article{Segawa:2013, title = {Determination of transverse relaxation rates in systems with scalar-coupled spins: The role of antiphase coherences}, author = {T F Segawa and G Bodenhausen}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84887115250&doi=10.1016%2fj.jmr.2013.10.002&partnerID=40&md5=b0479661a91c176841a027adf031ceec}, doi = {10.1016/j.jmr.2013.10.002}, year = {2013}, date = {2013-01-01}, journal = {Journal of Magnetic Resonance}, volume = {237}, pages = {139--146}, abstract = {Homogeneous line-widths that arise from transverse relaxation tend to be masked by B0 field inhomogeneity and by multiplets due to homonuclear J-couplings. Besides well-known spin-locking sequences that lead to signals that decay with a rate R1ρ without any modulations, alternative experiments allow one to determine the transverse relaxation rates R2 in systems with scalar-coupled spins. We evaluate three recent strategies by experiment and simulation: (i) moderate-amplitude SITCOM-CPMG sequences (Dittmer and Bodenhausen, 2006 [2]), (ii) multiple-quantum filtered (MQF) sequences (Barr\`{e}re et al., 2011 [4]) and (iii) PROJECT sequences (Aguilar et al., 2012 [5]). Experiments where the J-evolution is suppressed by spin-locking measure the pure relaxation rate R2(Ix) of an in-phase component. Experiments based on J-refocusing yield a mixture of in-phase rates R2(Ix) and antiphase rates R 2(2IySz), where the latter are usually faster than the former. Moderate-amplitude SITCOM-CPMG and PROJECT methods can be applied to systems with many coupled spins, but applications of MQF sequences are limited to two-spin systems since modulations in larger systems can only partly be suppressed. © 2013 Elsevier Inc. All rights reserved.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Homogeneous line-widths that arise from transverse relaxation tend to be masked by B0 field inhomogeneity and by multiplets due to homonuclear J-couplings. Besides well-known spin-locking sequences that lead to signals that decay with a rate R1ρ without any modulations, alternative experiments allow one to determine the transverse relaxation rates R2 in systems with scalar-coupled spins. We evaluate three recent strategies by experiment and simulation: (i) moderate-amplitude SITCOM-CPMG sequences (Dittmer and Bodenhausen, 2006 [2]), (ii) multiple-quantum filtered (MQF) sequences (Barrère et al., 2011 [4]) and (iii) PROJECT sequences (Aguilar et al., 2012 [5]). Experiments where the J-evolution is suppressed by spin-locking measure the pure relaxation rate R2(Ix) of an in-phase component. Experiments based on J-refocusing yield a mixture of in-phase rates R2(Ix) and antiphase rates R 2(2IySz), where the latter are usually faster than the former. Moderate-amplitude SITCOM-CPMG and PROJECT methods can be applied to systems with many coupled spins, but applications of MQF sequences are limited to two-spin systems since modulations in larger systems can only partly be suppressed. © 2013 Elsevier Inc. All rights reserved. |
Analysis of sensitivity enhancement by dynamic nuclear polarization in solid-state NMR: A case study of functionalized mesoporous materials Article de journal T Kobayashi; O Lafon; A S Lilly Thankamony; I I Slowing; K Kandel; D Carnevale; V Vitzthum; H Vezin; J -P Amoureux; G Bodenhausen; M Pruski Physical Chemistry Chemical Physics, 15 (15), p. 5553–5562, 2013. @article{Kobayashi:2013, title = {Analysis of sensitivity enhancement by dynamic nuclear polarization in solid-state NMR: A case study of functionalized mesoporous materials}, author = {T Kobayashi and O Lafon and A S Lilly Thankamony and I I Slowing and K Kandel and D Carnevale and V Vitzthum and H Vezin and J -P Amoureux and G Bodenhausen and M Pruski}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84875424472&doi=10.1039%2fc3cp00039g&partnerID=40&md5=80048542dfa3e1a997ce9d600131d864}, doi = {10.1039/c3cp00039g}, year = {2013}, date = {2013-01-01}, journal = {Physical Chemistry Chemical Physics}, volume = {15}, number = {15}, pages = {5553--5562}, abstract = {We systematically studied the enhancement factor (per scan) and the sensitivity enhancement (per unit time) in 13C and 29Si cross-polarization magic angle spinning (CP-MAS) NMR boosted by dynamic nuclear polarization (DNP) of functionalized mesoporous silica nanoparticles (MSNs). Specifically, we separated contributions due to: (i) microwave irradiation, (ii) quenching by paramagnetic effects, (iii) the presence of frozen solvent, (iv) the temperature, as well as changes in (v) relaxation and (vi) cross-polarization behaviour. No line-broadening effects were observed for MSNs when lowering the temperature from 300 to 100 K. Notwithstanding a significant signal reduction due to quenching by TOTAPOL radicals, DNP-CP-MAS at 100 K provided global sensitivity enhancements of 23 and 45 for 13C and 29Si, respectively, relative to standard CP-MAS measurements at room temperature. The effects of DNP were also ascertained by comparing with state-of-the-art two-dimensional heteronuclear 1H13C and 29Si1H correlation spectra, using, respectively, indirect detection or Carr-Purcell-Meiboom-Gill (CPMG) refocusing to boost signal acquisition. This study highlights opportunities for further improvements through the development of high-field DNP, better polarizing agents, and improved capabilities for low-temperature MAS. © 2013 the Owner Societies.}, keywords = {}, pubstate = {published}, tppubtype = {article} } We systematically studied the enhancement factor (per scan) and the sensitivity enhancement (per unit time) in 13C and 29Si cross-polarization magic angle spinning (CP-MAS) NMR boosted by dynamic nuclear polarization (DNP) of functionalized mesoporous silica nanoparticles (MSNs). Specifically, we separated contributions due to: (i) microwave irradiation, (ii) quenching by paramagnetic effects, (iii) the presence of frozen solvent, (iv) the temperature, as well as changes in (v) relaxation and (vi) cross-polarization behaviour. No line-broadening effects were observed for MSNs when lowering the temperature from 300 to 100 K. Notwithstanding a significant signal reduction due to quenching by TOTAPOL radicals, DNP-CP-MAS at 100 K provided global sensitivity enhancements of 23 and 45 for 13C and 29Si, respectively, relative to standard CP-MAS measurements at room temperature. The effects of DNP were also ascertained by comparing with state-of-the-art two-dimensional heteronuclear 1H13C and 29Si1H correlation spectra, using, respectively, indirect detection or Carr-Purcell-Meiboom-Gill (CPMG) refocusing to boost signal acquisition. This study highlights opportunities for further improvements through the development of high-field DNP, better polarizing agents, and improved capabilities for low-temperature MAS. © 2013 the Owner Societies. |
Broadband excitation in solid-state NMR using interleaved DANTE pulse trains with N pulses per rotor period Article de journal X Lu; J Trébosc; O Lafon; D Carnevale; S Ulzega; G Bodenhausen; J -P Amoureux Journal of Magnetic Resonance, 236 , p. 105–116, 2013. @article{Lu:2013, title = {Broadband excitation in solid-state NMR using interleaved DANTE pulse trains with N pulses per rotor period}, author = {X Lu and J Tr\'{e}bosc and O Lafon and D Carnevale and S Ulzega and G Bodenhausen and J -P Amoureux}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84884933432&doi=10.1016%2fj.jmr.2013.09.003&partnerID=40&md5=7742b9779f337ffb29e4e650336e50de}, doi = {10.1016/j.jmr.2013.09.003}, year = {2013}, date = {2013-01-01}, journal = {Journal of Magnetic Resonance}, volume = {236}, pages = {105--116}, abstract = {We analyze the direct excitation of wide one-dimensional spectra of nuclei with spin I = 1/2 or 1 in rotating solids submitted to pulse trains in the manner of Delays Alternating with Nutations for Tailored Excitation (DANTE), either with one short rotor-synchronized pulse of duration τp in each of K rotor periods (D1K) or with N interleaved equally spaced pulses τp in each rotor period, globally also extending over K rotor periods (DNK). The excitation profile of DNK scheme is a comb of rf-spikelets with NνR = N/TR spacing from the carrier frequency, and a width of each spikelet inversely proportional to the length, KTR, of DNK scheme. Since the individual pulse lengths, τp, are typically of a few hundreds of ns, DNK scheme can readily excite spinning sidebands families covering several MHz, provided the rf carrier frequency is close enough to the resonance frequency of one the spinning sidebands. If the difference of isotropic chemical shifts between distinct chemical sites is less than about 1.35/(KTR), DNK scheme can excite the spinning sidebands families of several sites. For nuclei with I = 1/2, if the homogeneous and inhomogeneous decays of coherences during the DANTE sequence are neglected, the K pulses of a D1K train have a linearly cumulative effect, so that the total nutation angle is θtot = K2πν1τ p, where ν1 is the rf-field amplitude. This allows obtaining nearly ideal 90 pulses for excitation or 180 rotations for inversion and refocusing across wide MAS spectra comprising many spinning sidebands. If one uses interleaved DANTE trains DNK with N > 1, only spinning sidebands separated by intervals of NνR with respect to the carrier frequency are observed as if the effective spinning speed was NνR. The other sidebands have vanishing intensities because of the cancellation of the N contributions with opposite signs. However, the intensities of the remaining sidebands obey the same rules as in spectra obtained with νR. With increasing N, the intensities of the non-vanishing sidebands increase, but the total intensity integrated over all sidebands decreases. Furthermore, the NK pulses in a DNK train do not have a simple cumulative effect and the optimal cumulated flip angle for optimal excitation, θtotopt=NK2πν1τp, exceeds 90. Such DNK pulse trains allow achieving efficient broadband excitation, but they are not recommended for broadband inversion or refocusing as they cannot provide proper 180 rotations. Since DNK pulse trains with N > 1 are shorter than basic D1K sequences, they are useful for broadband excitation in samples with rapid homogeneous or inhomogeneous decay. For nuclei with I = 1 (e.g., for 14N), the response to basic D1K pulse train is moreover affected by inhomogeneous decay due to 2nd-order quadrupole interactions, since these are not of rank 2 and therefore cannot be eliminated by spinning about the magic angle. For large quadrupole interactions, the signal decay produced by second-order quadrupole interaction can be minimized by (i) reducing the length of DNK pulse trains using N > 1, (ii) fast spinning, (iii) large rf-field, and (iv) using high magnetic fields to reduce the 2nd-order quadrupole interaction. © 2013 Elsevier Inc. All rights reserved.}, keywords = {}, pubstate = {published}, tppubtype = {article} } We analyze the direct excitation of wide one-dimensional spectra of nuclei with spin I = 1/2 or 1 in rotating solids submitted to pulse trains in the manner of Delays Alternating with Nutations for Tailored Excitation (DANTE), either with one short rotor-synchronized pulse of duration τp in each of K rotor periods (D1K) or with N interleaved equally spaced pulses τp in each rotor period, globally also extending over K rotor periods (DNK). The excitation profile of DNK scheme is a comb of rf-spikelets with NνR = N/TR spacing from the carrier frequency, and a width of each spikelet inversely proportional to the length, KTR, of DNK scheme. Since the individual pulse lengths, τp, are typically of a few hundreds of ns, DNK scheme can readily excite spinning sidebands families covering several MHz, provided the rf carrier frequency is close enough to the resonance frequency of one the spinning sidebands. If the difference of isotropic chemical shifts between distinct chemical sites is less than about 1.35/(KTR), DNK scheme can excite the spinning sidebands families of several sites. For nuclei with I = 1/2, if the homogeneous and inhomogeneous decays of coherences during the DANTE sequence are neglected, the K pulses of a D1K train have a linearly cumulative effect, so that the total nutation angle is θtot = K2πν1τ p, where ν1 is the rf-field amplitude. This allows obtaining nearly ideal 90 pulses for excitation or 180 rotations for inversion and refocusing across wide MAS spectra comprising many spinning sidebands. If one uses interleaved DANTE trains DNK with N > 1, only spinning sidebands separated by intervals of NνR with respect to the carrier frequency are observed as if the effective spinning speed was NνR. The other sidebands have vanishing intensities because of the cancellation of the N contributions with opposite signs. However, the intensities of the remaining sidebands obey the same rules as in spectra obtained with νR. With increasing N, the intensities of the non-vanishing sidebands increase, but the total intensity integrated over all sidebands decreases. Furthermore, the NK pulses in a DNK train do not have a simple cumulative effect and the optimal cumulated flip angle for optimal excitation, θtotopt=NK2πν1τp, exceeds 90. Such DNK pulse trains allow achieving efficient broadband excitation, but they are not recommended for broadband inversion or refocusing as they cannot provide proper 180 rotations. Since DNK pulse trains with N > 1 are shorter than basic D1K sequences, they are useful for broadband excitation in samples with rapid homogeneous or inhomogeneous decay. For nuclei with I = 1 (e.g., for 14N), the response to basic D1K pulse train is moreover affected by inhomogeneous decay due to 2nd-order quadrupole interactions, since these are not of rank 2 and therefore cannot be eliminated by spinning about the magic angle. For large quadrupole interactions, the signal decay produced by second-order quadrupole interaction can be minimized by (i) reducing the length of DNK pulse trains using N > 1, (ii) fast spinning, (iii) large rf-field, and (iv) using high magnetic fields to reduce the 2nd-order quadrupole interaction. © 2013 Elsevier Inc. All rights reserved. |
Boosting dissolution dynamic nuclear polarization by cross polarization Article de journal A Bornet; R Melzi; A J Perez Linde; P Hautle; B Van Den Brandt; S Jannin; G Bodenhausen Journal of Physical Chemistry Letters, 4 (1), p. 111–114, 2013. @article{Bornet:2013, title = {Boosting dissolution dynamic nuclear polarization by cross polarization}, author = {A Bornet and R Melzi and A J Perez Linde and P Hautle and B Van Den Brandt and S Jannin and G Bodenhausen}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84872182422&doi=10.1021%2fjz301781t&partnerID=40&md5=77c8dc351657a4892f54538f08d5fc94}, doi = {10.1021/jz301781t}, year = {2013}, date = {2013-01-01}, journal = {Journal of Physical Chemistry Letters}, volume = {4}, number = {1}, pages = {111--114}, abstract = {The efficiency of dissolution dynamic nuclear polarization can be boosted by Hartmann-Hahn cross polarization at temperatures near 1.2 K. This enables high throughput of hyperpolarized solutions with substantial gains in buildup times and polarization levels. During dissolution and transport, the 13C nuclear spin polarization P(13C) merely decreases from 45 to 40%. © 2012 American Chemical Society.}, keywords = {}, pubstate = {published}, tppubtype = {article} } The efficiency of dissolution dynamic nuclear polarization can be boosted by Hartmann-Hahn cross polarization at temperatures near 1.2 K. This enables high throughput of hyperpolarized solutions with substantial gains in buildup times and polarization levels. During dissolution and transport, the 13C nuclear spin polarization P(13C) merely decreases from 45 to 40%. © 2012 American Chemical Society. |
How to tickle spins with a fourier transform NMR spectrometer Article de journal T F Segawa; D Carnevale; G Bodenhausen ChemPhysChem, 14 (2), p. 369–373, 2013. @article{Segawa:2013a, title = {How to tickle spins with a fourier transform NMR spectrometer}, author = {T F Segawa and D Carnevale and G Bodenhausen}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84873813149&doi=10.1002%2fcphc.201200858&partnerID=40&md5=c24973268b639940f0dea15866ab5b3d}, doi = {10.1002/cphc.201200858}, year = {2013}, date = {2013-01-01}, journal = {ChemPhysChem}, volume = {14}, number = {2}, pages = {369--373}, abstract = {In the long bygone days of continuous-wave nuclear magnetic resonance (NMR) spectroscopy, a selected transition within a multiplet of a high-resolution spectrum could be irradiated by a highly selective continuous-wave (CW) radio-frequency (rf) field with a very weak amplitude textbackslashomega -2 /(2π)≤J. This causes splittings of connected transitions, allowing one to map the connectivities of all transitions within the energy-level diagram of the spin system. Such "tickling" experiments stimulated the invention of two-dimensional spectroscopy, but seem to have been forgotten for nearly 50 years. We show that tickling can readily be achieved in homonuclear systems with Fourier transform spectrometers by applying short pulses in the intervals between the sampling points. Extensions to heteronuclear systems are even more straightforward since they can be carried out using very weak CW rf fields. Tickling transitions: When a nuclear magnetic resonance is irradiated with a weak radio-frequency amplitude ω 2/(2π)≤J, all connected transitions split. The type of the connectivity can be identified by the line broadening (see picture). © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.}, keywords = {}, pubstate = {published}, tppubtype = {article} } In the long bygone days of continuous-wave nuclear magnetic resonance (NMR) spectroscopy, a selected transition within a multiplet of a high-resolution spectrum could be irradiated by a highly selective continuous-wave (CW) radio-frequency (rf) field with a very weak amplitude textbackslashomega -2 /(2π)≤J. This causes splittings of connected transitions, allowing one to map the connectivities of all transitions within the energy-level diagram of the spin system. Such "tickling" experiments stimulated the invention of two-dimensional spectroscopy, but seem to have been forgotten for nearly 50 years. We show that tickling can readily be achieved in homonuclear systems with Fourier transform spectrometers by applying short pulses in the intervals between the sampling points. Extensions to heteronuclear systems are even more straightforward since they can be carried out using very weak CW rf fields. Tickling transitions: When a nuclear magnetic resonance is irradiated with a weak radio-frequency amplitude ω 2/(2π)≤J, all connected transitions split. The type of the connectivity can be identified by the line broadening (see picture). © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim. |
Mesoporous silica nanoparticles loaded with surfactant: Low temperature magic angle spinning 13C and 29Si NMR enhanced by dynamic nuclear polarization Article de journal O Lafon; A S L Thankamony; T Kobayashi; D Carnevale; V Vitzthum; I I Slowing; K Kandel; H Vezin; J -P Amoureux; G Bodenhausen; M Pruski Journal of Physical Chemistry C, 117 (3), p. 1375–1382, 2013. @article{Lafon:2013, title = {Mesoporous silica nanoparticles loaded with surfactant: Low temperature magic angle spinning 13C and 29Si NMR enhanced by dynamic nuclear polarization}, author = {O Lafon and A S L Thankamony and T Kobayashi and D Carnevale and V Vitzthum and I I Slowing and K Kandel and H Vezin and J -P Amoureux and G Bodenhausen and M Pruski}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84872856525&doi=10.1021%2fjp310109s&partnerID=40&md5=e45ea6bbf2d7b3c234b573fc82dc9431}, doi = {10.1021/jp310109s}, year = {2013}, date = {2013-01-01}, journal = {Journal of Physical Chemistry C}, volume = {117}, number = {3}, pages = {1375--1382}, abstract = {We show that dynamic nuclear polarization (DNP) can be used to enhance NMR signals of 13C and 29Si nuclei located in mesoporous organic/inorganic hybrid materials, at several hundreds of nanometers from stable radicals (TOTAPOL) trapped in the surrounding frozen disordered water. The approach is demonstrated using mesoporous silica nanoparticles (MSN), functionalized with 3-(N-phenylureido)propyl (PUP) groups, filled with the surfactant cetyltrimethylammonium bromide (CTAB). The DNP-enhanced proton magnetization is transported into the mesopores via 1H-1H spin diffusion and transferred to rare spins by cross-polarization, yielding signal enhancements εon/off of around 8. When the CTAB molecules are extracted, so that the radicals can enter the mesopores, the enhancements increase to εon/off ≈ 30 for both nuclei. A quantitative analysis of the signal enhancements in MSN with and without surfactant is based on a one-dimensional proton spin diffusion model. The effect of solvent deuteration is also investigated. © 2012 American Chemical Society.}, keywords = {}, pubstate = {published}, tppubtype = {article} } We show that dynamic nuclear polarization (DNP) can be used to enhance NMR signals of 13C and 29Si nuclei located in mesoporous organic/inorganic hybrid materials, at several hundreds of nanometers from stable radicals (TOTAPOL) trapped in the surrounding frozen disordered water. The approach is demonstrated using mesoporous silica nanoparticles (MSN), functionalized with 3-(N-phenylureido)propyl (PUP) groups, filled with the surfactant cetyltrimethylammonium bromide (CTAB). The DNP-enhanced proton magnetization is transported into the mesopores via 1H-1H spin diffusion and transferred to rare spins by cross-polarization, yielding signal enhancements εon/off of around 8. When the CTAB molecules are extracted, so that the radicals can enter the mesopores, the enhancements increase to εon/off ≈ 30 for both nuclei. A quantitative analysis of the signal enhancements in MSN with and without surfactant is based on a one-dimensional proton spin diffusion model. The effect of solvent deuteration is also investigated. © 2012 American Chemical Society. |
"On-the-fly" kinetics of enzymatic racemization using deuterium NMR in DNA-based chiral oriented media Article de journal M Chan-Huot; P Lesot; P Pelupessy; L Duma; G Bodenhausen; P Duchambon; M D Toney; U V Reddy; N Suryaprakash Analytical Chemistry, 85 (9), p. 4694–4697, 2013. @article{Chan-Huot:2013, title = {"On-the-fly" kinetics of enzymatic racemization using deuterium NMR in DNA-based chiral oriented media}, author = {M Chan-Huot and P Lesot and P Pelupessy and L Duma and G Bodenhausen and P Duchambon and M D Toney and U V Reddy and N Suryaprakash}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84877355478&doi=10.1021%2fac4004002&partnerID=40&md5=039b427031ff3ff169871e716da1a2ae}, doi = {10.1021/ac4004002}, year = {2013}, date = {2013-01-01}, journal = {Analytical Chemistry}, volume = {85}, number = {9}, pages = {4694--4697}, abstract = {We report the in situ and real-time monitoring of the interconversion of l- and d-alanine-d3 by alanine racemase from Bacillus stearothermophilus directly observed by 2H NMR spectroscopy in anisotropic phase. The enantiomers are distinguished by the difference of their 2H quadrupolar splittings in a chiral liquid crystal containing short DNA fragments. The proof-of-principle, the reliability, and the robustness of this new method is demonstrated by the determination of the turnover rates of the enzyme using the Michaelis-Menten model. © 2013 American Chemical Society.}, keywords = {}, pubstate = {published}, tppubtype = {article} } We report the in situ and real-time monitoring of the interconversion of l- and d-alanine-d3 by alanine racemase from Bacillus stearothermophilus directly observed by 2H NMR spectroscopy in anisotropic phase. The enantiomers are distinguished by the difference of their 2H quadrupolar splittings in a chiral liquid crystal containing short DNA fragments. The proof-of-principle, the reliability, and the robustness of this new method is demonstrated by the determination of the turnover rates of the enzyme using the Michaelis-Menten model. © 2013 American Chemical Society. |
Solid-state proton NMR of paramagnetic metal complexes: DANTE spin echoes for selective excitation in inhomogeneously broadened lines Article de journal D Carnevale; A J Perez Linde; G Bauer; G Bodenhausen Chemical Physics Letters, 580 , p. 172–178, 2013. @article{Carnevale:2013, title = {Solid-state proton NMR of paramagnetic metal complexes: DANTE spin echoes for selective excitation in inhomogeneously broadened lines}, author = {D Carnevale and A J Perez Linde and G Bauer and G Bodenhausen}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84880920455&doi=10.1016%2fj.cplett.2013.06.052&partnerID=40&md5=77a4db4c70122ba60944260fd83001cf}, doi = {10.1016/j.cplett.2013.06.052}, year = {2013}, date = {2013-01-01}, journal = {Chemical Physics Letters}, volume = {580}, pages = {172--178}, abstract = {The paramagnetic complex bis(oxazolinylphenyl)amine-Fe(III)Cl2 is investigated by means of solid-state proton NMR at 18.8 T (800 MHz) using magic-angle spinning at 65 kHz. Spin echoes that are excited and refocused by combs of rotor-synchronized pulses in the manner of 'Delays Alternating with Nutation for Tailored Excitation' (DANTE) allow one to characterize different chemical environments that severely overlap in conventional MAS spectra. Such sequences combine two apparently contradictory features: an overall bandwidth exceeding several MHz, and very selective irradiation of a few kHz within inhomogeneously broadened sidebands. The experimental hyperfine interactions correlate well with DFT calculations. © 2013 Elsevier B.V. All rights reserved.}, keywords = {}, pubstate = {published}, tppubtype = {article} } The paramagnetic complex bis(oxazolinylphenyl)amine-Fe(III)Cl2 is investigated by means of solid-state proton NMR at 18.8 T (800 MHz) using magic-angle spinning at 65 kHz. Spin echoes that are excited and refocused by combs of rotor-synchronized pulses in the manner of 'Delays Alternating with Nutation for Tailored Excitation' (DANTE) allow one to characterize different chemical environments that severely overlap in conventional MAS spectra. Such sequences combine two apparently contradictory features: an overall bandwidth exceeding several MHz, and very selective irradiation of a few kHz within inhomogeneously broadened sidebands. The experimental hyperfine interactions correlate well with DFT calculations. © 2013 Elsevier B.V. All rights reserved. |
Towards analytically useful two-dimensional Fourier transform ion cyclotron resonance mass spectrometry Article de journal M A Van Agthoven; M -A Delsuc; G Bodenhausen; C Rolando Analytical and Bioanalytical Chemistry, 405 (1), p. 51–61, 2013. @article{VanAgthoven:2013, title = {Towards analytically useful two-dimensional Fourier transform ion cyclotron resonance mass spectrometry}, author = {M A Van Agthoven and M -A Delsuc and G Bodenhausen and C Rolando}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84872327966&doi=10.1007%2fs00216-012-6422-8&partnerID=40&md5=db22212de938ad4ee249b51794f5211e}, doi = {10.1007/s00216-012-6422-8}, year = {2013}, date = {2013-01-01}, journal = {Analytical and Bioanalytical Chemistry}, volume = {405}, number = {1}, pages = {51--61}, abstract = {Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometry (MS) achieves high resolution and mass accuracy, allowing the identification of the raw chemical formulae of ions in complex samples. Using ion isolation and fragmentation (MS/MS), we can obtain more structural information, but MS/MS is time- and sample-consuming because each ion must be isolated before fragmentation. In 1987, Pf\"{a}ndler et al. proposed an experiment for 2D FT-ICR MS in order to fragment ions without isolating them and to visualize the fragmentations of complex samples in a single 2D mass spectrum, like 2D NMR spectroscopy. Because of limitations of electronics and computers, few studies have been conducted with this technique. The improvement of modern computers and the use of digital electronics for FT-ICR hardware now make it possible to acquire 2D mass spectra over a broad mass range. The original experiments used in-cell collision-induced dissociation, which caused a loss of resolution. Gas-free fragmentation modes such as infrared multiphoton dissociation and electron capture dissociation allow one to measure high-resolution 2D mass spectra. Consequently, there is renewed interest to develop 2D FT-ICR MS into an efficient analytical method. Improvements introduced in 2D NMR spectroscopy can also be transposed to 2D FT-ICR MS. We describe the history of 2D FT-ICR MS, introduce recent improvements, and present analytical applications to map the fragmentation of peptides. Finally, we provide a glossary which defines a few keywords for the 2D FT-ICR MS field. © 2012 Springer-Verlag Berlin Heidelberg.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometry (MS) achieves high resolution and mass accuracy, allowing the identification of the raw chemical formulae of ions in complex samples. Using ion isolation and fragmentation (MS/MS), we can obtain more structural information, but MS/MS is time- and sample-consuming because each ion must be isolated before fragmentation. In 1987, Pfändler et al. proposed an experiment for 2D FT-ICR MS in order to fragment ions without isolating them and to visualize the fragmentations of complex samples in a single 2D mass spectrum, like 2D NMR spectroscopy. Because of limitations of electronics and computers, few studies have been conducted with this technique. The improvement of modern computers and the use of digital electronics for FT-ICR hardware now make it possible to acquire 2D mass spectra over a broad mass range. The original experiments used in-cell collision-induced dissociation, which caused a loss of resolution. Gas-free fragmentation modes such as infrared multiphoton dissociation and electron capture dissociation allow one to measure high-resolution 2D mass spectra. Consequently, there is renewed interest to develop 2D FT-ICR MS into an efficient analytical method. Improvements introduced in 2D NMR spectroscopy can also be transposed to 2D FT-ICR MS. We describe the history of 2D FT-ICR MS, introduce recent improvements, and present analytical applications to map the fragmentation of peptides. Finally, we provide a glossary which defines a few keywords for the 2D FT-ICR MS field. © 2012 Springer-Verlag Berlin Heidelberg. |
Selective inversion of 1H resonances in solid-state nuclear magnetic resonance: Use of double-DANTE pulse sequence Article de journal Venus Singh Mithu; Kong Ooi Tan; PK Madhu Journal of Magnetic Resonance, 237 , p. 11–16, 2013. @article{mithu2013selective, title = {Selective inversion of 1H resonances in solid-state nuclear magnetic resonance: Use of double-DANTE pulse sequence}, author = {Venus Singh Mithu and Kong Ooi Tan and PK Madhu}, year = {2013}, date = {2013-01-01}, journal = {Journal of Magnetic Resonance}, volume = {237}, pages = {11\textendash16}, publisher = {Academic Press}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
2012 |
Spin echo NMR spectra without J modulation Article de journal J A Aguilar; M Nilsson; G Bodenhausen; G A Morris Chemical Communications, 48 (6), p. 811–813, 2012. @article{Aguilar:2012, title = {Spin echo NMR spectra without J modulation}, author = {J A Aguilar and M Nilsson and G Bodenhausen and G A Morris}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84055188671&doi=10.1039%2fc1cc16699a&partnerID=40&md5=d3cb100c8cb2249d05c59ea164157d37}, doi = {10.1039/c1cc16699a}, year = {2012}, date = {2012-01-01}, journal = {Chemical Communications}, volume = {48}, number = {6}, pages = {811--813}, abstract = {The spin echo is the single most important building block in modern NMR spectroscopy, but echo modulation by scalar couplings J can severely complicate its use. We show for the first time that a general but unacknowledged solution to such complications already exists.}, keywords = {}, pubstate = {published}, tppubtype = {article} } The spin echo is the single most important building block in modern NMR spectroscopy, but echo modulation by scalar couplings J can severely complicate its use. We show for the first time that a general but unacknowledged solution to such complications already exists. |
Ultrahigh-resolution magnetic resonance in inhomogeneous magnetic fields: Two-dimensional long-lived-coherence correlation spectroscopy Article de journal S Chinthalapalli; A Bornet; T F Segawa; R Sarkar; S Jannin; G Bodenhausen Physical Review Letters, 109 (4), 2012. @article{Chinthalapalli:2012, title = {Ultrahigh-resolution magnetic resonance in inhomogeneous magnetic fields: Two-dimensional long-lived-coherence correlation spectroscopy}, author = {S Chinthalapalli and A Bornet and T F Segawa and R Sarkar and S Jannin and G Bodenhausen}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84864245185&doi=10.1103%2fPhysRevLett.109.047602&partnerID=40&md5=6c3fccac606ca3da4e112b3ac2d192ca}, doi = {10.1103/PhysRevLett.109.047602}, year = {2012}, date = {2012-01-01}, journal = {Physical Review Letters}, volume = {109}, number = {4}, abstract = {A half-century quest for improving resolution in Nuclear Magnetic Resonance (NMR) and Magnetic Resonance Imaging (MRI) has enabled the study of molecular structures, biological interactions, and fine details of anatomy. This progress largely relied on the advent of sophisticated superconducting magnets that can provide stable and homogeneous fields with temporal and spatial variations below ΔB 0/B 0<0.01ppm. In many cases however, inherent properties of the objects under investigation, pulsating arteries, breathing lungs, tissue-air interfaces, surgical implants, etc., lead to fluctuations and losses of local homogeneity. A new method dubbed "long-lived-coherence correlation spectroscopy" (LLC-COSY) opens the way to overcome both inhomogeneous and homogeneous broadening, which arise from local variations in static fields and fluctuating dipole-dipole interactions, respectively. LLC-COSY makes it possible to obtain ultrahigh resolution two-dimensional spectra, with linewidths on the order of Δν=0.1 to 1 Hz, even in very inhomogeneous fields (ΔB 0/B 0>10ppm or 5000 Hz at 9.7 T), and can improve resolution by a factor up to 9 when the homogeneous linewidths are determined by dipole-dipole interactions. The resulting LLC-COSY spectra display chemical shift differences and scalar couplings in two orthogonal dimensions, like in "J spectroscopy." LLC-COSY does not require any sophisticated gradient switching or frequency-modulated pulses. Applications to in-cell NMR and to magnetic resonance spectroscopy (MRS) of selected volume elements in MRI appear promising, particularly when susceptibility variations tend to preclude high resolution. © 2012 American Physical Society.}, keywords = {}, pubstate = {published}, tppubtype = {article} } A half-century quest for improving resolution in Nuclear Magnetic Resonance (NMR) and Magnetic Resonance Imaging (MRI) has enabled the study of molecular structures, biological interactions, and fine details of anatomy. This progress largely relied on the advent of sophisticated superconducting magnets that can provide stable and homogeneous fields with temporal and spatial variations below ΔB 0/B 0<0.01ppm. In many cases however, inherent properties of the objects under investigation, pulsating arteries, breathing lungs, tissue-air interfaces, surgical implants, etc., lead to fluctuations and losses of local homogeneity. A new method dubbed "long-lived-coherence correlation spectroscopy" (LLC-COSY) opens the way to overcome both inhomogeneous and homogeneous broadening, which arise from local variations in static fields and fluctuating dipole-dipole interactions, respectively. LLC-COSY makes it possible to obtain ultrahigh resolution two-dimensional spectra, with linewidths on the order of Δν=0.1 to 1 Hz, even in very inhomogeneous fields (ΔB 0/B 0>10ppm or 5000 Hz at 9.7 T), and can improve resolution by a factor up to 9 when the homogeneous linewidths are determined by dipole-dipole interactions. The resulting LLC-COSY spectra display chemical shift differences and scalar couplings in two orthogonal dimensions, like in "J spectroscopy." LLC-COSY does not require any sophisticated gradient switching or frequency-modulated pulses. Applications to in-cell NMR and to magnetic resonance spectroscopy (MRS) of selected volume elements in MRI appear promising, particularly when susceptibility variations tend to preclude high resolution. © 2012 American Physical Society. |
Transverse Relaxation of Scalar Coupled Protons in Magnetic Resonance of Non-Deuterated Proteins Article de journal T F Segawa; B Baishya; G Bodenhausen Applied Magnetic Resonance, 42 (3), p. 353–361, 2012. @article{Segawa:2012, title = {Transverse Relaxation of Scalar Coupled Protons in Magnetic Resonance of Non-Deuterated Proteins}, author = {T F Segawa and B Baishya and G Bodenhausen}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84857920485&doi=10.1007%2fs00723-011-0298-1&partnerID=40&md5=1c6c4a0927cb9d3ec38f676be64ad90a}, doi = {10.1007/s00723-011-0298-1}, year = {2012}, date = {2012-01-01}, journal = {Applied Magnetic Resonance}, volume = {42}, number = {3}, pages = {353--361}, abstract = {The transverse relaxation rates R 2 = 1/T 2 of protons can be determined by spin-echo sequences with multiple refocusing pulses using moderate radio-frequency field strengths and properly chosen inter-pulse delays so as to suppress echo modulations due to homonuclear scalar couplings. Combination with 2D heteronuclear correlation spectroscopy (HSQC) allows one to measure R 2 of arbitrary protons attached to nitrogen-15 or carbon-13 nuclei. Decays of six amide protons in the protein Ubiquitin that is nitrogen-15 enriched (but not deuterated) were measured at different temperatures. © 2011 Springer-Verlag.}, keywords = {}, pubstate = {published}, tppubtype = {article} } The transverse relaxation rates R 2 = 1/T 2 of protons can be determined by spin-echo sequences with multiple refocusing pulses using moderate radio-frequency field strengths and properly chosen inter-pulse delays so as to suppress echo modulations due to homonuclear scalar couplings. Combination with 2D heteronuclear correlation spectroscopy (HSQC) allows one to measure R 2 of arbitrary protons attached to nitrogen-15 or carbon-13 nuclei. Decays of six amide protons in the protein Ubiquitin that is nitrogen-15 enriched (but not deuterated) were measured at different temperatures. © 2011 Springer-Verlag. |
Uniform broadband excitation of crystallites in rotating solids using interleaved sequences of delays alternating with nutation Article de journal V Vitzthum; M A Caporini; S Ulzega; J Trébosc; O Lafon; J -P Amoureux; G Bodenhausen Journal of Magnetic Resonance, 223 , p. 228–236, 2012. @article{Vitzthum:2012a, title = {Uniform broadband excitation of crystallites in rotating solids using interleaved sequences of delays alternating with nutation}, author = {V Vitzthum and M A Caporini and S Ulzega and J Tr\'{e}bosc and O Lafon and J -P Amoureux and G Bodenhausen}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84866729754&doi=10.1016%2fj.jmr.2012.05.024&partnerID=40&md5=acffb1f76b2506200af44c834a7f2253}, doi = {10.1016/j.jmr.2012.05.024}, year = {2012}, date = {2012-01-01}, journal = {Journal of Magnetic Resonance}, volume = {223}, pages = {228--236}, abstract = {In solids that are spinning about the magic angle, trains of short pulses in the manner of Delays Alternating with Nutations for Tailored Excitation (DANTE) allow one to improve the efficiency of the excitation of magnetization compared to rectangular pulses. By interleaving N pulse trains with N > 1, one obtains 'DANTE-N' sequences comprising N pulses per rotor period that extend over K rotor periods. Optimized interleaved DANTE schemes with N > 1 are shorter than basic DANTE-1 sequences with N = 1. Therefore, they are less affected by coherent or incoherent decays, thus leading to higher signal intensities than can be obtained with basic DANTE-1 or with rectangular pulses. Furthermore, the shorter length of DANTE-N with N > 1 increases the width of the spikelets in the excitation profile, allowing one to cover the range of isotropic chemical shifts and second-order quadrupolar effects typical for side-chain and backbone amide 14N sites in peptides at B 0 = 18.8 T. In DANTE-N, spinning sidebands only appear at multiples of the spinning frequency ν rot, as if the samples were rotating at Nν rot. We show applications to direct detection of nitrogen-14 nuclei with spin I = 1 subject to large quadrupole interactions, using fast magic angle spinning (typically ν rot ≥ 60 kHz), backed up by simulations that provide insight into the properties of basic and interleaved DANTE sequences. When used for indirect detection, we show by numerical simulations that even basic DANTE-1 sequences can lead to a four-fold boost of efficiency compared to standard rectangular pulses. © 2012 Elsevier Inc. All rights reserved.}, keywords = {}, pubstate = {published}, tppubtype = {article} } In solids that are spinning about the magic angle, trains of short pulses in the manner of Delays Alternating with Nutations for Tailored Excitation (DANTE) allow one to improve the efficiency of the excitation of magnetization compared to rectangular pulses. By interleaving N pulse trains with N > 1, one obtains 'DANTE-N' sequences comprising N pulses per rotor period that extend over K rotor periods. Optimized interleaved DANTE schemes with N > 1 are shorter than basic DANTE-1 sequences with N = 1. Therefore, they are less affected by coherent or incoherent decays, thus leading to higher signal intensities than can be obtained with basic DANTE-1 or with rectangular pulses. Furthermore, the shorter length of DANTE-N with N > 1 increases the width of the spikelets in the excitation profile, allowing one to cover the range of isotropic chemical shifts and second-order quadrupolar effects typical for side-chain and backbone amide 14N sites in peptides at B 0 = 18.8 T. In DANTE-N, spinning sidebands only appear at multiples of the spinning frequency ν rot, as if the samples were rotating at Nν rot. We show applications to direct detection of nitrogen-14 nuclei with spin I = 1 subject to large quadrupole interactions, using fast magic angle spinning (typically ν rot ≥ 60 kHz), backed up by simulations that provide insight into the properties of basic and interleaved DANTE sequences. When used for indirect detection, we show by numerical simulations that even basic DANTE-1 sequences can lead to a four-fold boost of efficiency compared to standard rectangular pulses. © 2012 Elsevier Inc. All rights reserved. |
Large-scale production of microcrystals and precipitates of proteins and their complexes Article de journal M Chan-Huot; L Duma; J -B Charbonnier; J -E Herbert-Pucheta; L Assairi; Y Blouquit; D Abergel; G Bodenhausen Crystal Growth and Design, 12 (12), p. 6199–6207, 2012. @article{Chan-Huot:2012, title = {Large-scale production of microcrystals and precipitates of proteins and their complexes}, author = {M Chan-Huot and L Duma and J -B Charbonnier and J -E Herbert-Pucheta and L Assairi and Y Blouquit and D Abergel and G Bodenhausen}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84870857311&doi=10.1021%2fcg301378j&partnerID=40&md5=fbed3f0f606a05400e3d33bd32f752cc}, doi = {10.1021/cg301378j}, year = {2012}, date = {2012-01-01}, journal = {Crystal Growth and Design}, volume = {12}, number = {12}, pages = {6199--6207}, abstract = {The optimum conditions for the formation of plate-like and urchin-like microcrystals of biomolecules and their transfer to rotors for solid-state NMR spectroscopy depend on a variety of factors, of which minimizing the manipulation of the microcrystals and storing the sample for several months at 277 K (4 °C) play an important role. Three biological systems were investigated: Hen Egg-White (HEW) lysozyme (129 residues), the lengthened C-terminal domain (LCter) of Human centrin 2 (89 residues), and the complex between the C-terminal domain (Cter) of Human centrin 2 (79 residues) and the P17-XPC peptide (17 residues). © 2012 American Chemical Society.}, keywords = {}, pubstate = {published}, tppubtype = {article} } The optimum conditions for the formation of plate-like and urchin-like microcrystals of biomolecules and their transfer to rotors for solid-state NMR spectroscopy depend on a variety of factors, of which minimizing the manipulation of the microcrystals and storing the sample for several months at 277 K (4 °C) play an important role. Three biological systems were investigated: Hen Egg-White (HEW) lysozyme (129 residues), the lengthened C-terminal domain (LCter) of Human centrin 2 (89 residues), and the complex between the C-terminal domain (Cter) of Human centrin 2 (79 residues) and the P17-XPC peptide (17 residues). © 2012 American Chemical Society. |
Toward the characterization of fractional stochastic processes underlying methyl dynamics in proteins Article de journal P Calligari; D Abergel Journal of Physical Chemistry B, 116 (43), p. 12955–12965, 2012. @article{Calligari:2012a, title = {Toward the characterization of fractional stochastic processes underlying methyl dynamics in proteins}, author = {P Calligari and D Abergel}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84868247033&doi=10.1021%2fjp307050v&partnerID=40&md5=2a86b70ce840d0141b8fa146c163a076}, doi = {10.1021/jp307050v}, year = {2012}, date = {2012-01-01}, journal = {Journal of Physical Chemistry B}, volume = {116}, number = {43}, pages = {12955--12965}, abstract = {In this article, we investigate the multiple-scale structure of methyl side chain dynamics in proteins. We show that the orientational correlation functions of CH3 methyl groups are well described by a fractional Brownian dynamics model. Typical angular correlation functions involved in NMR relaxation were computed from MD simulations performed on two different proteins. These correlation functions were shown to be very well fitted by a fractional Ornstein-Uhlenbeck process in the presence of effective local potentials at the C-H and C-C methyl bonds. In addition, our analysis highlights the presence of the asymptotic power law decay of the waiting time probability density of the stochastic process involved, thereby illustrating the connection between approaches based on fractional diffusion equations and the continuous time random walk. © 2012 American Chemical Society.}, keywords = {}, pubstate = {published}, tppubtype = {article} } In this article, we investigate the multiple-scale structure of methyl side chain dynamics in proteins. We show that the orientational correlation functions of CH3 methyl groups are well described by a fractional Brownian dynamics model. Typical angular correlation functions involved in NMR relaxation were computed from MD simulations performed on two different proteins. These correlation functions were shown to be very well fitted by a fractional Ornstein-Uhlenbeck process in the presence of effective local potentials at the C-H and C-C methyl bonds. In addition, our analysis highlights the presence of the asymptotic power law decay of the waiting time probability density of the stochastic process involved, thereby illustrating the connection between approaches based on fractional diffusion equations and the continuous time random walk. © 2012 American Chemical Society. |
Time scales of slow motions in ubiquitin explored by heteronuclear double resonance Article de journal N Salvi; S Ulzega; F Ferrage; G Bodenhausen Journal of the American Chemical Society, 134 (5), p. 2481–2484, 2012. @article{Salvi:2012, title = {Time scales of slow motions in ubiquitin explored by heteronuclear double resonance}, author = {N Salvi and S Ulzega and F Ferrage and G Bodenhausen}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84856707634&doi=10.1021%2fja210238g&partnerID=40&md5=9c95497eae6bea06e795f4fa66f2bff7}, doi = {10.1021/ja210238g}, year = {2012}, date = {2012-01-01}, journal = {Journal of the American Chemical Society}, volume = {134}, number = {5}, pages = {2481--2484}, abstract = {Understanding how proteins function at the atomic level relies in part on a detailed characterization of their dynamics. Ubiquitin, a small single-domain protein, displays rich dynamic properties over a wide range of time scales. In particular, several regions of ubiquitin show the signature of chemical exchange, including the hydrophobic patch and the β4-α2 loop, which are both involved in many interactions. Here, we use multiple-quantum relaxation techniques to identify the extent of chemical exchange in ubiquitin. We employ our recently developed heteronuclear double resonance method to determine the time scales of motions that give rise to chemical exchange. Dispersion profiles are obtained for the backbone NH N pairs of several residues in the hydrophobic patch and the β4-α2 loop, as well as the C-terminus of helix α1. We show that a single time scale (ca. 50 μs) can be used to fit the data for most residues. Potential mechanisms for the propagation of motions and the possible extent of correlation of these motions are discussed. © 2011 American Chemical Society.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Understanding how proteins function at the atomic level relies in part on a detailed characterization of their dynamics. Ubiquitin, a small single-domain protein, displays rich dynamic properties over a wide range of time scales. In particular, several regions of ubiquitin show the signature of chemical exchange, including the hydrophobic patch and the β4-α2 loop, which are both involved in many interactions. Here, we use multiple-quantum relaxation techniques to identify the extent of chemical exchange in ubiquitin. We employ our recently developed heteronuclear double resonance method to determine the time scales of motions that give rise to chemical exchange. Dispersion profiles are obtained for the backbone NH N pairs of several residues in the hydrophobic patch and the β4-α2 loop, as well as the C-terminus of helix α1. We show that a single time scale (ca. 50 μs) can be used to fit the data for most residues. Potential mechanisms for the propagation of motions and the possible extent of correlation of these motions are discussed. © 2011 American Chemical Society. |
Protein dynamics by 15n nuclear magnetic relaxation Livre F Ferrage 2012. @book{Ferrage:2012, title = {Protein dynamics by 15n nuclear magnetic relaxation}, author = {F Ferrage}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84855888985&doi=10.1007%2f978-1-61779-480-3_9&partnerID=40&md5=f6d991298a85e4a71fdf2e33d0dec123}, doi = {10.1007/978-1-61779-480-3_9}, year = {2012}, date = {2012-01-01}, volume = {831}, series = {Methods in Molecular Biology}, abstract = {Nitrogen-15 relaxation is the most ubiquitous source of information about protein (backbone) dynamics used by NMR spectroscopists. It provides the general characteristics of hydrodynamics as well as internal motions on subnanosecond, micro- and millisecond timescales of a biomolecule. Here, we present a full protocol to perform and analyze a series of experiments to measure the 15N longitudinal relaxation rate, the 15N transverse relaxation rate under an echo train or a single echo, the 15N- 1H dipolar cross-relaxation rate, as well as the longitudinal and transverse cross-relaxation rates due to the cross-correlation of the nitrogen-15 chemical shift anisotropy and the dipolar coupling with the adjacent proton. These rates can be employed to carry out model-free analyses and can be used to quantify accurately the contribution of chemical exchange to transverse relaxation. © 2012 Springer Science+Business Media, LLC.}, keywords = {}, pubstate = {published}, tppubtype = {book} } Nitrogen-15 relaxation is the most ubiquitous source of information about protein (backbone) dynamics used by NMR spectroscopists. It provides the general characteristics of hydrodynamics as well as internal motions on subnanosecond, micro- and millisecond timescales of a biomolecule. Here, we present a full protocol to perform and analyze a series of experiments to measure the 15N longitudinal relaxation rate, the 15N transverse relaxation rate under an echo train or a single echo, the 15N- 1H dipolar cross-relaxation rate, as well as the longitudinal and transverse cross-relaxation rates due to the cross-correlation of the nitrogen-15 chemical shift anisotropy and the dipolar coupling with the adjacent proton. These rates can be employed to carry out model-free analyses and can be used to quantify accurately the contribution of chemical exchange to transverse relaxation. © 2012 Springer Science+Business Media, LLC. |
Structure and dynamics of the second CARD of human RIG-I provide mechanistic insights into regulation of RIG-I activation Article de journal F Ferrage; K Dutta; E Nistal-Villán; J R Patel; M T Sánchez-Aparicio; P De Ioannes; A Buku; G G Aseguinolaza; A García-Sastre; A K Aggarwal Structure, 20 (12), p. 2048–2061, 2012. @article{Ferrage:2012a, title = {Structure and dynamics of the second CARD of human RIG-I provide mechanistic insights into regulation of RIG-I activation}, author = {F Ferrage and K Dutta and E Nistal-Vill\'{a}n and J R Patel and M T S\'{a}nchez-Aparicio and P De Ioannes and A Buku and G G Aseguinolaza and A Garc\'{i}a-Sastre and A K Aggarwal}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84870502910&doi=10.1016%2fj.str.2012.09.003&partnerID=40&md5=29b0738971b7246179125527be1f9b5f}, doi = {10.1016/j.str.2012.09.003}, year = {2012}, date = {2012-01-01}, journal = {Structure}, volume = {20}, number = {12}, pages = {2048--2061}, abstract = {RIG-I is a cytosolic sensor of viral RNA, comprised of two N-terminal CARDs followed by helicase and C-terminal regulatory domains (helicase-CTD). Viral RNA binds to the helicase-CTD and "exposes" the CARDs for downstream signaling. The role of the second CARD (CARD2) is essential as RIG-I activation requires dephosphorylation of Thr170 followed by ubiquitination at Lys172. Here, we present the solution structure and dynamics of human RIG-I CARD2. Surprisingly, we find that Thr170 is mostly buried. Parallel studies on the phosphomimetic T170E mutant suggest that the loss of function upon Thr170 phosphorylation is likely associated with changes in the CARD1-CARD2 interface that may prevent Lys172 ubiquitination and/or binding to free K63-linked polyubiquitin. We also demonstrate a strong interaction between CARD2 and the helicase-CTD, and show that mutations at the interface result in constitutive activation of RIG-I. Collectively, our data suggests a close interplay between phosphorylation, ubiquitination, and activation of human RIG-I, all mediated by CARD2. © 2012 Elsevier Ltd.}, keywords = {}, pubstate = {published}, tppubtype = {article} } RIG-I is a cytosolic sensor of viral RNA, comprised of two N-terminal CARDs followed by helicase and C-terminal regulatory domains (helicase-CTD). Viral RNA binds to the helicase-CTD and "exposes" the CARDs for downstream signaling. The role of the second CARD (CARD2) is essential as RIG-I activation requires dephosphorylation of Thr170 followed by ubiquitination at Lys172. Here, we present the solution structure and dynamics of human RIG-I CARD2. Surprisingly, we find that Thr170 is mostly buried. Parallel studies on the phosphomimetic T170E mutant suggest that the loss of function upon Thr170 phosphorylation is likely associated with changes in the CARD1-CARD2 interface that may prevent Lys172 ubiquitination and/or binding to free K63-linked polyubiquitin. We also demonstrate a strong interaction between CARD2 and the helicase-CTD, and show that mutations at the interface result in constitutive activation of RIG-I. Collectively, our data suggests a close interplay between phosphorylation, ubiquitination, and activation of human RIG-I, all mediated by CARD2. © 2012 Elsevier Ltd. |
Efficient determination of diffusion coefficients by monitoring transport during recovery delays in NMR Article de journal R Augustyniak; F Ferrage; C Damblon; G Bodenhausen; P Pelupessy Chemical Communications, 48 (43), p. 5307–5309, 2012. @article{Augustyniak:2012, title = {Efficient determination of diffusion coefficients by monitoring transport during recovery delays in NMR}, author = {R Augustyniak and F Ferrage and C Damblon and G Bodenhausen and P Pelupessy}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84860787097&doi=10.1039%2fc2cc30578j&partnerID=40&md5=382700df0a8a8bd7732e5b242cb16956}, doi = {10.1039/c2cc30578j}, year = {2012}, date = {2012-01-01}, journal = {Chemical Communications}, volume = {48}, number = {43}, pages = {5307--5309}, abstract = {A novel NMR approach allows one to efficiently determine translational diffusion coefficients of macromolecules in solution. This method for Signal Optimization with Recovery in Diffusion Delays (SORDID) monitors transport occurring during the recovery times between consecutive scans so that the duration of the measurements can be reduced approximately by a factor two. © 2012 The Royal Society of Chemistry.}, keywords = {}, pubstate = {published}, tppubtype = {article} } A novel NMR approach allows one to efficiently determine translational diffusion coefficients of macromolecules in solution. This method for Signal Optimization with Recovery in Diffusion Delays (SORDID) monitors transport occurring during the recovery times between consecutive scans so that the duration of the measurements can be reduced approximately by a factor two. © 2012 The Royal Society of Chemistry. |
Restoring symmetry in two-dimensional solid-state NMR correlation spectra Article de journal J -E Herbert-Pucheta; P Pelupessy; G Bodenhausen; P Tekely Chemical Physics Letters, 539-540 , p. 245–251, 2012. @article{Herbert-Pucheta:2012, title = {Restoring symmetry in two-dimensional solid-state NMR correlation spectra}, author = {J -E Herbert-Pucheta and P Pelupessy and G Bodenhausen and P Tekely}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84862659967&doi=10.1016%2fj.cplett.2012.05.030&partnerID=40&md5=5dc708017733276724dc4a288f342f2b}, doi = {10.1016/j.cplett.2012.05.030}, year = {2012}, date = {2012-01-01}, journal = {Chemical Physics Letters}, volume = {539-540}, pages = {245--251}, abstract = {The intrinsic asymmetry of 2D solid-state homonuclear NMR correlation spectra that arises from a non-uniform preparation of the magnetization can be removed by equilibrating the magnetization in the initial stage of the experiments through dipolar recoupling induced by PARIS or PARISxy schemes. Both methods ensure magnetization exchange with modest radio-frequency amplitudes and permit one to create an initial state that restores the symmetry about the main diagonal of 2D spectra of uniformly labeled biomolecules. This improves the determination of structural and kinetic information. Both recoupling schemes may also be used to record nearly quantitative peak amplitudes in 1D cross-polarization magic-angle-spinning spectra. © 2012 Elsevier B.V. All rights reserved.}, keywords = {}, pubstate = {published}, tppubtype = {article} } The intrinsic asymmetry of 2D solid-state homonuclear NMR correlation spectra that arises from a non-uniform preparation of the magnetization can be removed by equilibrating the magnetization in the initial stage of the experiments through dipolar recoupling induced by PARIS or PARISxy schemes. Both methods ensure magnetization exchange with modest radio-frequency amplitudes and permit one to create an initial state that restores the symmetry about the main diagonal of 2D spectra of uniformly labeled biomolecules. This improves the determination of structural and kinetic information. Both recoupling schemes may also be used to record nearly quantitative peak amplitudes in 1D cross-polarization magic-angle-spinning spectra. © 2012 Elsevier B.V. All rights reserved. |
Probing structural and motional features of the c-terminal part of the human Centrin 2/P17-XPC microcrystalline complex by solid-state NMR spectroscopy Article de journal J -E Herbert-Pucheta; M Chan-Huot; L Duma; D Abergel; G Bodenhausen; L Assairi; Y Blouquit; J -B Charbonnier; P Tekely Journal of Physical Chemistry B, 116 (50), p. 14581–14591, 2012. @article{Herbert-Pucheta:2012a, title = {Probing structural and motional features of the c-terminal part of the human Centrin 2/P17-XPC microcrystalline complex by solid-state NMR spectroscopy}, author = {J -E Herbert-Pucheta and M Chan-Huot and L Duma and D Abergel and G Bodenhausen and L Assairi and Y Blouquit and J -B Charbonnier and P Tekely}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84871598384&doi=10.1021%2fjp3099472&partnerID=40&md5=cc0a4b929a6f3bf7085cf90242b4b99a}, doi = {10.1021/jp3099472}, year = {2012}, date = {2012-01-01}, journal = {Journal of Physical Chemistry B}, volume = {116}, number = {50}, pages = {14581--14591}, abstract = {Insight into structural and motional features of the C-terminal part of the Human Centrin 2 in complex with the peptide P17-XPC was obtained by using complementary solid-state NMR methods. We demonstrate that the experimental conditions and procedures of sample crystallization determine the quality of solid-state NMR spectra and the internal mobility of the protein. Two-dimensional (2D) 13C-13C and 15N- 15N correlation spectra reveal intra-and inter-residue dipolar connectivities and provide partial, site-specific assignments of 13C and 15N resonance signals. The secondary structure of the C-ter HsCen2/P17-XPC complex in a microcrystalline state appears similar to that found in solution. Conformational flexibility is probed through relaxation- compensated measurements of dipolar order parameters that exploit the dynamics of cross-polarization in multidimensional experiments. The extracted dipolar coupling constants and relevant order parameters reveal increased backbone flexibility of the loops except for residues involved in coordination with the Ca2+ cation that stabilizes the hydrophobic pocket containing the peptide P17-XPC. © 2012 American Chemical Society.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Insight into structural and motional features of the C-terminal part of the Human Centrin 2 in complex with the peptide P17-XPC was obtained by using complementary solid-state NMR methods. We demonstrate that the experimental conditions and procedures of sample crystallization determine the quality of solid-state NMR spectra and the internal mobility of the protein. Two-dimensional (2D) 13C-13C and 15N- 15N correlation spectra reveal intra-and inter-residue dipolar connectivities and provide partial, site-specific assignments of 13C and 15N resonance signals. The secondary structure of the C-ter HsCen2/P17-XPC complex in a microcrystalline state appears similar to that found in solution. Conformational flexibility is probed through relaxation- compensated measurements of dipolar order parameters that exploit the dynamics of cross-polarization in multidimensional experiments. The extracted dipolar coupling constants and relevant order parameters reveal increased backbone flexibility of the loops except for residues involved in coordination with the Ca2+ cation that stabilizes the hydrophobic pocket containing the peptide P17-XPC. © 2012 American Chemical Society. |
Cross Polarization for Dissolution Dynamic Nuclear Polarization Experiments at Readily Accessible Temperatures 1.2 textless Ŧ textless 4.2 K Article de journal A Bornet; R Melzi; S Jannin; G Bodenhausen Applied Magnetic Resonance, 43 (1-2), p. 107–117, 2012. @article{Bornet:2012, title = {Cross Polarization for Dissolution Dynamic Nuclear Polarization Experiments at Readily Accessible Temperatures 1.2 textless {T} textless 4.2 K}, author = {A Bornet and R Melzi and S Jannin and G Bodenhausen}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84864336115&doi=10.1007%2fs00723-012-0358-1&partnerID=40&md5=2a09b3eadaf0d2129b3afb1d264af607}, doi = {10.1007/s00723-012-0358-1}, year = {2012}, date = {2012-01-01}, journal = {Applied Magnetic Resonance}, volume = {43}, number = {1-2}, pages = {107--117}, abstract = {Cross polarization can provide significant enhancements with respect to direct polarization of low-γ nuclei such as 13C. Substantial gains in sample throughput (shorter polarization times) can be achieved by exploiting shorter build-up times τ DNP( 1H) < τ DNP( 13C). To polarize protons rather than low-γ nuclei, nitroxide radicals with broad ESR resonances such as TEMPO are more appropriate than Trityl and similar carbon-based radicals that have narrow lines. With TEMPO as polarizing agent, the main Dynamic Nuclear Polarization (DNP) mechanism is thermal mixing (TM). Cross polarization makes it possible to attain higher polarization levels at 2.2 K than one can obtain with direct DNP of low-γ nuclei with TEMPO at 1. 2 K, thus avoiding complex cryogenic technology. © 2012 Springer-Verlag.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Cross polarization can provide significant enhancements with respect to direct polarization of low-γ nuclei such as 13C. Substantial gains in sample throughput (shorter polarization times) can be achieved by exploiting shorter build-up times τ DNP( 1H) < τ DNP( 13C). To polarize protons rather than low-γ nuclei, nitroxide radicals with broad ESR resonances such as TEMPO are more appropriate than Trityl and similar carbon-based radicals that have narrow lines. With TEMPO as polarizing agent, the main Dynamic Nuclear Polarization (DNP) mechanism is thermal mixing (TM). Cross polarization makes it possible to attain higher polarization levels at 2.2 K than one can obtain with direct DNP of low-γ nuclei with TEMPO at 1. 2 K, thus avoiding complex cryogenic technology. © 2012 Springer-Verlag. |
Composite pulses for efficient excitation of half-integer quadrupolar nuclei in NMR of static and spinning solid samples Article de journal D Carnevale; G Bodenhausen Chemical Physics Letters, 530 , p. 120–125, 2012. @article{Carnevale:2012, title = {Composite pulses for efficient excitation of half-integer quadrupolar nuclei in NMR of static and spinning solid samples}, author = {D Carnevale and G Bodenhausen}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84858000858&doi=10.1016%2fj.cplett.2012.01.058&partnerID=40&md5=52e3a5fa1b709258fe220a39f91c429d}, doi = {10.1016/j.cplett.2012.01.058}, year = {2012}, date = {2012-01-01}, journal = {Chemical Physics Letters}, volume = {530}, pages = {120--125}, abstract = {Composite pulses of the type ( τp) x(2 τp) -x(3 τp) x allow one to excite the central transition of nuclei with half-integer spin with enhanced efficiency compared to a simple (τpsp) x pulse. The method has been tested on solid samples containing sodium-23 (I = 3/2), aluminium-27 (I = 5/2) and scandium-45 (I = 7/2) under both static and magic-angle spinning conditions. Numerical simulations for I = 3/2 indicate that the enhancement is due to a more efficient conversion of Zeeman population differences associated with the satellite transitions to the central transition. © 2012 Elsevier B.V. All rights reserved.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Composite pulses of the type ( τp) x(2 τp) -x(3 τp) x allow one to excite the central transition of nuclei with half-integer spin with enhanced efficiency compared to a simple (τpsp) x pulse. The method has been tested on solid samples containing sodium-23 (I = 3/2), aluminium-27 (I = 5/2) and scandium-45 (I = 7/2) under both static and magic-angle spinning conditions. Numerical simulations for I = 3/2 indicate that the enhancement is due to a more efficient conversion of Zeeman population differences associated with the satellite transitions to the central transition. © 2012 Elsevier B.V. All rights reserved. |
Broadband excitation in solid-state NMR of paramagnetic samples using Delays Alternating with Nutation for Tailored Excitation ('Para-DANTE') Article de journal D Carnevale; V Vitzthum; O Lafon; J Trébosc; J -P Amoureux; G Bodenhausen Chemical Physics Letters, 553 , p. 68–76, 2012. @article{Carnevale:2012a, title = {Broadband excitation in solid-state NMR of paramagnetic samples using Delays Alternating with Nutation for Tailored Excitation ('Para-DANTE')}, author = {D Carnevale and V Vitzthum and O Lafon and J Tr\'{e}bosc and J -P Amoureux and G Bodenhausen}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84868561166&doi=10.1016%2fj.cplett.2012.09.056&partnerID=40&md5=e3686b49cfe1dac5591574eb541d80c7}, doi = {10.1016/j.cplett.2012.09.056}, year = {2012}, date = {2012-01-01}, journal = {Chemical Physics Letters}, volume = {553}, pages = {68--76}, abstract = {This Letter shows that interleaved sequences of short pulses in the manner of 'Delays Alternating with Nutation for Tailored Excitation' (DANTE) with N = 1, 2, 3 ⋯ equidistant pulses per rotor period extending over K rotor periods can be used to excite, invert or refocus a large number of spinning sidebands of spin-1/2 nuclei in paramagnetic samples where hyperfine couplings lead to very broad spectra that extend over more than 1 MHz. The breadth of the response is maintained for rf-field amplitudes as low as 30 kHz since it results from cumulative effects of individual pulses with very short durations. © 2012 Elsevier B.V. All rights reserved.}, keywords = {}, pubstate = {published}, tppubtype = {article} } This Letter shows that interleaved sequences of short pulses in the manner of 'Delays Alternating with Nutation for Tailored Excitation' (DANTE) with N = 1, 2, 3 ⋯ equidistant pulses per rotor period extending over K rotor periods can be used to excite, invert or refocus a large number of spinning sidebands of spin-1/2 nuclei in paramagnetic samples where hyperfine couplings lead to very broad spectra that extend over more than 1 MHz. The breadth of the response is maintained for rf-field amplitudes as low as 30 kHz since it results from cumulative effects of individual pulses with very short durations. © 2012 Elsevier B.V. All rights reserved. |
Boosting the sensitivity of ligand-protein screening by NMR of long-lived states Article de journal N Salvi; R Buratto; A Bornet; S Ulzega; I Rentero Rebollo; A Angelini; C Heinis; G Bodenhausen Journal of the American Chemical Society, 134 (27), p. 11076–11079, 2012. @article{Salvi:2012a, title = {Boosting the sensitivity of ligand-protein screening by NMR of long-lived states}, author = {N Salvi and R Buratto and A Bornet and S Ulzega and I Rentero Rebollo and A Angelini and C Heinis and G Bodenhausen}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84863856503&doi=10.1021%2fja303301w&partnerID=40&md5=465bbcd1c51b96bf023137318e191631}, doi = {10.1021/ja303301w}, year = {2012}, date = {2012-01-01}, journal = {Journal of the American Chemical Society}, volume = {134}, number = {27}, pages = {11076--11079}, abstract = {A new NMR method for the study of ligand-protein interactions exploits the unusual lifetimes of long-lived states (LLSs). The new method provides better contrast between bound and free ligands and requires a protein-ligand ratio ca. 25 times lower than for established T 1ρ methods, thus saving on costly proteins. The new LLS method was applied to the screening of inhibitors of urokinase-type plasminogen activator (uPA), which is a prototypical target of cancer research. With only 10 μM protein, a dissociation constant (K D) of 180 ± 20 nM was determined for the strong ligand (inhibitor) UK-18, which can be compared with K D = 157 ± 39 nM determined by the established surface plasmon resonance method. © 2012 American Chemical Society.}, keywords = {}, pubstate = {published}, tppubtype = {article} } A new NMR method for the study of ligand-protein interactions exploits the unusual lifetimes of long-lived states (LLSs). The new method provides better contrast between bound and free ligands and requires a protein-ligand ratio ca. 25 times lower than for established T 1ρ methods, thus saving on costly proteins. The new LLS method was applied to the screening of inhibitors of urokinase-type plasminogen activator (uPA), which is a prototypical target of cancer research. With only 10 μM protein, a dissociation constant (K D) of 180 ± 20 nM was determined for the strong ligand (inhibitor) UK-18, which can be compared with K D = 157 ± 39 nM determined by the established surface plasmon resonance method. © 2012 American Chemical Society. |
Dynamic nuclear polarization of quadrupolar nuclei using cross polarization from protons: Surface-enhanced aluminium-27 NMR Article de journal V Vitzthum; P Miéville; D Carnevale; M A Caporini; D Gajan; C Copéret; M Lelli; A Zagdoun; A J Rossini; A Lesage; L Emsley; G Bodenhausen Chemical Communications, 48 (14), p. 1988–1990, 2012. @article{Vitzthum:2012, title = {Dynamic nuclear polarization of quadrupolar nuclei using cross polarization from protons: Surface-enhanced aluminium-27 NMR}, author = {V Vitzthum and P Mi\'{e}ville and D Carnevale and M A Caporini and D Gajan and C Cop\'{e}ret and M Lelli and A Zagdoun and A J Rossini and A Lesage and L Emsley and G Bodenhausen}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84856446761&doi=10.1039%2fc2cc15905h&partnerID=40&md5=36de04d337c8dff29708acb262fed22e}, doi = {10.1039/c2cc15905h}, year = {2012}, date = {2012-01-01}, journal = {Chemical Communications}, volume = {48}, number = {14}, pages = {1988--1990}, abstract = {The surface of γ-alumina nanoparticles can be characterized by dynamic nuclear polarization (DNP) surface-enhanced NMR of 27Al. DNP is combined with cross-polarization and MQ-MAS to determine local symmetries of 27Al sites at the surface. © 2012 The Royal Society of Chemistry.}, keywords = {}, pubstate = {published}, tppubtype = {article} } The surface of γ-alumina nanoparticles can be characterized by dynamic nuclear polarization (DNP) surface-enhanced NMR of 27Al. DNP is combined with cross-polarization and MQ-MAS to determine local symmetries of 27Al sites at the surface. © 2012 The Royal Society of Chemistry. |
Dynamic Nuclear Polarization and other magnetic ideas at EPFL Article de journal A Bornet; J Milani; S Wang; D Mammoli; R Buratto; N Salvi; T F Segawa; V Vitzthum; P Miéville; N Srichinthalapalli; A J Perez-Linde; D Carnevale; S Jannin; M Caporini; S Ulzega; M Rey; G Bodenhausen Chimia, 66 (10), p. 734–740, 2012. @article{Bornet:2012a, title = {Dynamic Nuclear Polarization and other magnetic ideas at EPFL}, author = {A Bornet and J Milani and S Wang and D Mammoli and R Buratto and N Salvi and T F Segawa and V Vitzthum and P Mi\'{e}ville and N Srichinthalapalli and A J Perez-Linde and D Carnevale and S Jannin and M Caporini and S Ulzega and M Rey and G Bodenhausen}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84868593282&doi=10.2533%2fchimia.2012.734&partnerID=40&md5=d4d0c4b9b765db503de5dba2f7ac34d3}, doi = {10.2533/chimia.2012.734}, year = {2012}, date = {2012-01-01}, journal = {Chimia}, volume = {66}, number = {10}, pages = {734--740}, abstract = {Although nuclear magnetic resonance (NMR) can provide a wealth of information, it often suffers from a lack of sensitivity. Dynamic Nuclear Polarization (DNP) provides a way to increase the polarization and hence the signal intensities in NMR spectra by transferring the favourable electron spin polarization of paramagnetic centres to the surrounding nuclear spins through appropriate microwave irradiation. In our group at EPFL, two complementary DNP techniques are under investigation: the combination of DNP with magic angle spinning at temperatures near 100 K ('MAS-DNP'), and the combination of DNP at 1.2 K with rapid heating followed by the transfer of the sample to a high-resolution magnet ('dissolution DNP'). Recent applications of MAS-DNP to surfaces, as well as new developments of magnetization transfer of 1H to 13C at 1.2 K prior to dissolution will illustrate the work performed in our group. A second part of the paper will give an overview of some 'nonenhanced' activities of our laboratory in liquid- and solid-state NMR. © Schweizerische Chemische Gesellschaft.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Although nuclear magnetic resonance (NMR) can provide a wealth of information, it often suffers from a lack of sensitivity. Dynamic Nuclear Polarization (DNP) provides a way to increase the polarization and hence the signal intensities in NMR spectra by transferring the favourable electron spin polarization of paramagnetic centres to the surrounding nuclear spins through appropriate microwave irradiation. In our group at EPFL, two complementary DNP techniques are under investigation: the combination of DNP with magic angle spinning at temperatures near 100 K ('MAS-DNP'), and the combination of DNP at 1.2 K with rapid heating followed by the transfer of the sample to a high-resolution magnet ('dissolution DNP'). Recent applications of MAS-DNP to surfaces, as well as new developments of magnetization transfer of 1H to 13C at 1.2 K prior to dissolution will illustrate the work performed in our group. A second part of the paper will give an overview of some 'nonenhanced' activities of our laboratory in liquid- and solid-state NMR. © Schweizerische Chemische Gesellschaft. |
High field dynamic nuclear polarization at 6.7 Ŧ: Carbon-13 polarization above 70% within 20 min Article de journal S Jannin; A Bornet; R Melzi; G Bodenhausen Chemical Physics Letters, 549 , p. 99–102, 2012. @article{Jannin:2012, title = {High field dynamic nuclear polarization at 6.7 {T}: Carbon-13 polarization above 70% within 20 min}, author = {S Jannin and A Bornet and R Melzi and G Bodenhausen}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84866743552&doi=10.1016%2fj.cplett.2012.08.017&partnerID=40&md5=93f004ce0142a7533a2c141b0dbccbbc}, doi = {10.1016/j.cplett.2012.08.017}, year = {2012}, date = {2012-01-01}, journal = {Chemical Physics Letters}, volume = {549}, pages = {99--102}, abstract = {In most applications of dissolution-DNP, the polarization of nuclei with low gyromagnetic ratios such as 13C is enhanced directly by irradiating the ESR transitions of radicals with narrow ESR lines such as Trityl at low temperatures T = 1.2 K in polarizing fields B 0 ≤ 5 T. In a field B 0 = 6.7 T at T = 1.2 K, DNP with TEMPO leads to a rapid build-up of proton polarization P( 1H) = 91% with τ DNP( 1H) = 150 s. CP at low temperatures yields a polarization P( 1H → 13C) in excess of 70% within 20 min. After rapid dissolution to room temperature, this is 122 000 times larger than the Boltzmann polarization at 300 K and 6.7 T. © 2012 Elsevier B.V. All rights reserved.}, keywords = {}, pubstate = {published}, tppubtype = {article} } In most applications of dissolution-DNP, the polarization of nuclei with low gyromagnetic ratios such as 13C is enhanced directly by irradiating the ESR transitions of radicals with narrow ESR lines such as Trityl at low temperatures T = 1.2 K in polarizing fields B 0 ≤ 5 T. In a field B 0 = 6.7 T at T = 1.2 K, DNP with TEMPO leads to a rapid build-up of proton polarization P( 1H) = 91% with τ DNP( 1H) = 150 s. CP at low temperatures yields a polarization P( 1H → 13C) in excess of 70% within 20 min. After rapid dissolution to room temperature, this is 122 000 times larger than the Boltzmann polarization at 300 K and 6.7 T. © 2012 Elsevier B.V. All rights reserved. |
Insights into internal dynamics of 6-phosphogluconolactonase from Trypanosoma brucei studied by nuclear magnetic resonance and molecular dynamics Article de journal P A Calligari; G F Salgado; P Pelupessy; P Lopes; J Ouazzani; G Bodenhausen; D Abergel Proteins: Structure, Function and Bioinformatics, 80 (4), p. 1196–1210, 2012. @article{Calligari:2012, title = {Insights into internal dynamics of 6-phosphogluconolactonase from Trypanosoma brucei studied by nuclear magnetic resonance and molecular dynamics}, author = {P A Calligari and G F Salgado and P Pelupessy and P Lopes and J Ouazzani and G Bodenhausen and D Abergel}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84857787795&doi=10.1002%2fprot.24019&partnerID=40&md5=ca1fb75cfc050709d9944038cd6dc4d6}, doi = {10.1002/prot.24019}, year = {2012}, date = {2012-01-01}, journal = {Proteins: Structure, Function and Bioinformatics}, volume = {80}, number = {4}, pages = {1196--1210}, abstract = {Nuclear magnetic resonance is used to investigate the backbone dynamics in 6-phosphogluconolactonase from Trypanosoma brucei (Tb6PGL) with (holo-) and without (apo-) 6-phosphogluconic acid as ligand. Relaxation data were analyzed using the model-free approach and reduced spectral density mapping. Comparison of predictions, based on 77 ns molecular dynamics simulations, with the observed relaxation rates gives insight into dynamical properties of the protein and their alteration on ligand binding. Data indicate dynamics changes in the vicinity of the binding site. More interesting is the presence of perturbations located in remote regions of this well-structured globular protein in which no large-amplitude motions are involved. This suggests that delocalized changes in dynamics that occur upon binding could be a general feature of protein-target interactions. © 2012 Wiley Periodicals, Inc.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Nuclear magnetic resonance is used to investigate the backbone dynamics in 6-phosphogluconolactonase from Trypanosoma brucei (Tb6PGL) with (holo-) and without (apo-) 6-phosphogluconic acid as ligand. Relaxation data were analyzed using the model-free approach and reduced spectral density mapping. Comparison of predictions, based on 77 ns molecular dynamics simulations, with the observed relaxation rates gives insight into dynamical properties of the protein and their alteration on ligand binding. Data indicate dynamics changes in the vicinity of the binding site. More interesting is the presence of perturbations located in remote regions of this well-structured globular protein in which no large-amplitude motions are involved. This suggests that delocalized changes in dynamics that occur upon binding could be a general feature of protein-target interactions. © 2012 Wiley Periodicals, Inc. |
Polychromatic decoupling of a manifold of homonuclear scalar interactions in solution-state NMR Article de journal D Carnevale; T F Segawa; G Bodenhausen Chemistry - A European Journal, 18 (37), p. 11573–11576, 2012. @article{Carnevale:2012b, title = {Polychromatic decoupling of a manifold of homonuclear scalar interactions in solution-state NMR}, author = {D Carnevale and T F Segawa and G Bodenhausen}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84865791255&doi=10.1002%2fchem.201200481&partnerID=40&md5=e3fc6c13236638458de22592d7cac757}, doi = {10.1002/chem.201200481}, year = {2012}, date = {2012-01-01}, journal = {Chemistry - A European Journal}, volume = {18}, number = {37}, pages = {11573--11576}, abstract = {Window-acquired tetrachromatic irradiation allows one to decouple simultaneously four amide protons in cyclosporine A (wavy arrows; see figure) leading to simplified multiplets of the alpha protons. By inserting a manifold of polychromatic pulses in each dwell time, several subsystems can be decoupled simultaneously. Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Window-acquired tetrachromatic irradiation allows one to decouple simultaneously four amide protons in cyclosporine A (wavy arrows; see figure) leading to simplified multiplets of the alpha protons. By inserting a manifold of polychromatic pulses in each dwell time, several subsystems can be decoupled simultaneously. Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim. |
2011 |
Control of cross relaxation of multiple-quantum coherences induced by fast chemical exchange under heteronuclear double-resonance irradiation Article de journal S Ulzega; N Salvi; T F Segawa; F Ferrage; G Bodenhausen ChemPhysChem, 12 (2), p. 333–341, 2011. @article{Ulzega:2011, title = {Control of cross relaxation of multiple-quantum coherences induced by fast chemical exchange under heteronuclear double-resonance irradiation}, author = {S Ulzega and N Salvi and T F Segawa and F Ferrage and G Bodenhausen}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-79551483842&doi=10.1002%2fcphc.201000699&partnerID=40&md5=29699f8f0cae7fca8397dc82d7882aae}, doi = {10.1002/cphc.201000699}, year = {2011}, date = {2011-01-01}, journal = {ChemPhysChem}, volume = {12}, number = {2}, pages = {333--341}, abstract = {A fully analytical description of the control of the cross-correlated cross relaxation of multiple-quantum coherences in the presence of local dynamics under heteronuclear double-resonance radio-frequency (RF) irradiation is presented. The contribution of chemical exchange to relaxation can be partly or fully quenched by RF fields. We assume a correlated two-site chemical exchange model with arbitrary populations, and show that in the limit of fast exchange the dependence of the effective multiple-quantum cross-relaxation rate on the applied RF amplitude can be described by a compact analytical expression. Numerical simulations and preliminary experiments support our theoretical results. The relaxation dispersion as a function of RF amplitude can provide accurate information on the kinetics of correlated processes. © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.}, keywords = {}, pubstate = {published}, tppubtype = {article} } A fully analytical description of the control of the cross-correlated cross relaxation of multiple-quantum coherences in the presence of local dynamics under heteronuclear double-resonance radio-frequency (RF) irradiation is presented. The contribution of chemical exchange to relaxation can be partly or fully quenched by RF fields. We assume a correlated two-site chemical exchange model with arbitrary populations, and show that in the limit of fast exchange the dependence of the effective multiple-quantum cross-relaxation rate on the applied RF amplitude can be described by a compact analytical expression. Numerical simulations and preliminary experiments support our theoretical results. The relaxation dispersion as a function of RF amplitude can provide accurate information on the kinetics of correlated processes. © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim. |
1H, 13C and 15N resonance assignment of a 114-residue fragment of Engrailed 2 homeoprotein, a partially disordered protein Article de journal R Augustyniak; S Balayssac; F Ferrage; G Bodenhausen; O Lequin Biomolecular NMR Assignments, 5 (2), p. 229–231, 2011. @article{Augustyniak:2011, title = {1H, 13C and 15N resonance assignment of a 114-residue fragment of Engrailed 2 homeoprotein, a partially disordered protein}, author = {R Augustyniak and S Balayssac and F Ferrage and G Bodenhausen and O Lequin}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84855391140&doi=10.1007%2fs12104-011-9306-5&partnerID=40&md5=415a058e72fb30cb1fa0150ef213bc90}, doi = {10.1007/s12104-011-9306-5}, year = {2011}, date = {2011-01-01}, journal = {Biomolecular NMR Assignments}, volume = {5}, number = {2}, pages = {229--231}, abstract = {Engrailed 2 is a transcription factor belonging to the class of homeoproteins. These proteins possess a 60-residue DNA binding globular domain and play an important role in the early stages of development. We expressed and purified a 13.4 kDa fragment of Engrailed 2, which comprises a 54-residue N-terminal extension in addition to the homeodomain region. Almost all backbone and side-chain resonances have been assigned. The weak dispersion in the proton dimension of the 1H-15N HSQC spectrum indicates the presence of disordered regions that do not belong to the homeodomain. This work is a first step toward the NMR investigation of the structure and dynamics of Engrailed 2 protein that contains a wellstructured globular domain and partially disordered regions. © Springer Science+Business Media B.V. 2011.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Engrailed 2 is a transcription factor belonging to the class of homeoproteins. These proteins possess a 60-residue DNA binding globular domain and play an important role in the early stages of development. We expressed and purified a 13.4 kDa fragment of Engrailed 2, which comprises a 54-residue N-terminal extension in addition to the homeodomain region. Almost all backbone and side-chain resonances have been assigned. The weak dispersion in the proton dimension of the 1H-15N HSQC spectrum indicates the presence of disordered regions that do not belong to the homeodomain. This work is a first step toward the NMR investigation of the structure and dynamics of Engrailed 2 protein that contains a wellstructured globular domain and partially disordered regions. © Springer Science+Business Media B.V. 2011. |
Methods to determine slow diffusion coefficients of biomolecules. Applications to Engrailed 2, a partially disordered protein Article de journal R Augustyniak; F Ferrage; R Paquin; O Lequin; G Bodenhausen Journal of Biomolecular NMR, 50 (3), p. 209–218, 2011. @article{Augustyniak:2011a, title = {Methods to determine slow diffusion coefficients of biomolecules. Applications to Engrailed 2, a partially disordered protein}, author = {R Augustyniak and F Ferrage and R Paquin and O Lequin and G Bodenhausen}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-80051670410&doi=10.1007%2fs10858-011-9510-8&partnerID=40&md5=a0778c4246c06711c2445ebf4874f6dc}, doi = {10.1007/s10858-011-9510-8}, year = {2011}, date = {2011-01-01}, journal = {Journal of Biomolecular NMR}, volume = {50}, number = {3}, pages = {209--218}, abstract = {We present new NMR methods to measure slow translational diffusion coefficients of biomolecules. Like the heteronuclear stimulated echo experiment (XSTE), these new methods rely on the storage of information about spatial localization during the diffusion delay as longitudinal polarization of nuclei with long T1 such as nitrogen-15. The new BEST-XSTE sequence combines features of Band-selective Excitation Short-Transient (BEST) and XSTE methods. By avoiding the saturation of all protons except those of amide groups, one can increase the sensitivity by 45% in small proteins. The new experiment which combines band-Selective Optimized Flip-Angle Short-Transient with XSTE (SOFAST-XSTE) offers an alternative when very short recovery delays are desired. A modification of the HSQC-edited version of the XSTE experiment offers enhanced sensitivity and access to higher resolution in the indirect dimension. These new methods have been applied to detect changes in diffusion coefficients due to dimerization or proteolysis of Engrailed 2, a partially disordered protein. © 2011 Springer Science+Business Media B.V.}, keywords = {}, pubstate = {published}, tppubtype = {article} } We present new NMR methods to measure slow translational diffusion coefficients of biomolecules. Like the heteronuclear stimulated echo experiment (XSTE), these new methods rely on the storage of information about spatial localization during the diffusion delay as longitudinal polarization of nuclei with long T1 such as nitrogen-15. The new BEST-XSTE sequence combines features of Band-selective Excitation Short-Transient (BEST) and XSTE methods. By avoiding the saturation of all protons except those of amide groups, one can increase the sensitivity by 45% in small proteins. The new experiment which combines band-Selective Optimized Flip-Angle Short-Transient with XSTE (SOFAST-XSTE) offers an alternative when very short recovery delays are desired. A modification of the HSQC-edited version of the XSTE experiment offers enhanced sensitivity and access to higher resolution in the indirect dimension. These new methods have been applied to detect changes in diffusion coefficients due to dimerization or proteolysis of Engrailed 2, a partially disordered protein. © 2011 Springer Science+Business Media B.V. |
A spinning thermometer to monitor microwave heating and glass transitions in dynamic nuclear polarization Article de journal P Miéville; V Vitzthum; M A Caporini; S Jannin; S Gerber-Lemaire; G Bodenhausen Magnetic Resonance in Chemistry, 49 (11), p. 689–692, 2011. @article{Mieville:2011, title = {A spinning thermometer to monitor microwave heating and glass transitions in dynamic nuclear polarization}, author = {P Mi\'{e}ville and V Vitzthum and M A Caporini and S Jannin and S Gerber-Lemaire and G Bodenhausen}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84155170965&doi=10.1002%2fmrc.2811&partnerID=40&md5=f5cdbb1a105f6ef61ff9d9749bdb8877}, doi = {10.1002/mrc.2811}, year = {2011}, date = {2011-01-01}, journal = {Magnetic Resonance in Chemistry}, volume = {49}, number = {11}, pages = {689--692}, abstract = {As previously demonstrated by Thurber and Tycko, the peak position of 79Br in potassium bromide (KBr) allows one to determine the temperature of a spinning sample. We propose to adapt the original design by using a compact KBr tablet placed at the bottom of the magic angle spinning rotor, separated from the sample under investigation by a thin disk made of polytetrafluoroethylene (or 'Teflon' ®). This design allows spinning the sample up to at least 16 kHz. The KBr tablet can remain in the rotor when changing the sample under investigation. Calibration in the range of 98 <T< 320 K has been carried out in a static rotor by inserting a platinum thermometer. The accuracy is better than ± 0.9 K, even in the presence of microwave irradiation. Irradiation with 5W microwaves at 263 GHz leads to a small temperature increase of 3.6 ± 1.4 K in either static or spinning samples. The dynamic nuclear polarization enhancement decreases with increasing temperature, in particular when a frozen glassy sample undergoes a glass transition. Copyright © 2011 John Wiley & Sons, Ltd.}, keywords = {}, pubstate = {published}, tppubtype = {article} } As previously demonstrated by Thurber and Tycko, the peak position of 79Br in potassium bromide (KBr) allows one to determine the temperature of a spinning sample. We propose to adapt the original design by using a compact KBr tablet placed at the bottom of the magic angle spinning rotor, separated from the sample under investigation by a thin disk made of polytetrafluoroethylene (or 'Teflon' ®). This design allows spinning the sample up to at least 16 kHz. The KBr tablet can remain in the rotor when changing the sample under investigation. Calibration in the range of 98 <T< 320 K has been carried out in a static rotor by inserting a platinum thermometer. The accuracy is better than ± 0.9 K, even in the presence of microwave irradiation. Irradiation with 5W microwaves at 263 GHz leads to a small temperature increase of 3.6 ± 1.4 K in either static or spinning samples. The dynamic nuclear polarization enhancement decreases with increasing temperature, in particular when a frozen glassy sample undergoes a glass transition. Copyright © 2011 John Wiley & Sons, Ltd. |
Broadband excitation and indirect detection of nitrogen-14 in rotating solids using Delays Alternating with Nutation (DANTE) Article de journal V Vitzthum; M A Caporini; S Ulzega; G Bodenhausen Journal of Magnetic Resonance, 212 (1), p. 234–239, 2011. @article{Vitzthum:2011, title = {Broadband excitation and indirect detection of nitrogen-14 in rotating solids using Delays Alternating with Nutation (DANTE)}, author = {V Vitzthum and M A Caporini and S Ulzega and G Bodenhausen}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84855407572&doi=10.1016%2fj.jmr.2011.06.013&partnerID=40&md5=056c503ac053c590649306606c26b0bb}, doi = {10.1016/j.jmr.2011.06.013}, year = {2011}, date = {2011-01-01}, journal = {Journal of Magnetic Resonance}, volume = {212}, number = {1}, pages = {234--239}, abstract = {A train of short rotor-synchronized pulses in the manner of Delays Alternating with Nutations for Tailored Excitation (DANTE) applied to nitrogen-14 nuclei (I = 1) in samples spinning at the magic angle at high frequencies (typically νrot = 62.5 kHz so that τrot = 16 μs) allows one to achieve uniform excitation of a great number of spinning sidebands that arise from large first-order quadrupole interactions, as occur for aromatic nitrogen-14 nuclei in histidine. With routine rf amplitudes ω1(14N)/(2π) = 60 kHz and very short pulses of a typical duration 0.5 < τp < 2 μs, efficient excitation can be achieved with 13 rotor-synchronized pulses in 13 srot = 208 ls. Alternatively, with 'overtone' DANTE sequences using 2, 4, or 8 pulses per rotor period one can achieve efficient broadband excitation in fewer rotor periods, typically 2-4 τrot. These principles can be combined with the indirect detection of 14N nuclei via spy nuclei with S = 1/2 such as 1H or 13C in the manner of Dipolar Heteronuclear Multiple-Quantum Correlation (D-HMQC). © 2011 Elsevier Inc. All rights reserved.}, keywords = {}, pubstate = {published}, tppubtype = {article} } A train of short rotor-synchronized pulses in the manner of Delays Alternating with Nutations for Tailored Excitation (DANTE) applied to nitrogen-14 nuclei (I = 1) in samples spinning at the magic angle at high frequencies (typically νrot = 62.5 kHz so that τrot = 16 μs) allows one to achieve uniform excitation of a great number of spinning sidebands that arise from large first-order quadrupole interactions, as occur for aromatic nitrogen-14 nuclei in histidine. With routine rf amplitudes ω1(14N)/(2π) = 60 kHz and very short pulses of a typical duration 0.5 < τp < 2 μs, efficient excitation can be achieved with 13 rotor-synchronized pulses in 13 srot = 208 ls. Alternatively, with 'overtone' DANTE sequences using 2, 4, or 8 pulses per rotor period one can achieve efficient broadband excitation in fewer rotor periods, typically 2-4 τrot. These principles can be combined with the indirect detection of 14N nuclei via spy nuclei with S = 1/2 such as 1H or 13C in the manner of Dipolar Heteronuclear Multiple-Quantum Correlation (D-HMQC). © 2011 Elsevier Inc. All rights reserved. |
Efficiency at high spinning frequencies of heteronuclear decoupling methods designed to quench rotary resonance Article de journal M Weingarth; J Trébosc; J -P Amoureux; G Bodenhausen; P Tekely Solid State Nuclear Magnetic Resonance, 40 (1), p. 21–26, 2011. @article{Weingarth:2011, title = {Efficiency at high spinning frequencies of heteronuclear decoupling methods designed to quench rotary resonance}, author = {M Weingarth and J Tr\'{e}bosc and J -P Amoureux and G Bodenhausen and P Tekely}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-79960305962&doi=10.1016%2fj.ssnmr.2011.03.004&partnerID=40&md5=46dcd6db2e9812d82d89ca2ea11c3458}, doi = {10.1016/j.ssnmr.2011.03.004}, year = {2011}, date = {2011-01-01}, journal = {Solid State Nuclear Magnetic Resonance}, volume = {40}, number = {1}, pages = {21--26}, abstract = {The performance of two recently developed heteronuclear decoupling schemes designed to quench rotary resonance, phase-inverted supercycled sequence for attenuation of rotary resonance (PISSARRO) and high-phase two-pulse phase modulation (high-phase TPPM), are probed at high spinning frequencies. High-phase TPPM may be useful at the n=1 rotary resonance condition while PISSARRO permits efficient decoupling over a broad commonly used range of rf amplitudes, even at very high spinning frequencies. New insights into the response of spin systems to both decoupling schemes have been gained. High-phase TPPM is sensitive to the offsets of remote protons, their chemical shift anisotropies, and the relative orientations of the heteronuclear dipolar and proton chemical shift tensors. Since PISSARRO is virtually immune against such effects, the method is especially suited for very high magnetic fields. © 2011 Elsevier Inc. All rights reserved.}, keywords = {}, pubstate = {published}, tppubtype = {article} } The performance of two recently developed heteronuclear decoupling schemes designed to quench rotary resonance, phase-inverted supercycled sequence for attenuation of rotary resonance (PISSARRO) and high-phase two-pulse phase modulation (high-phase TPPM), are probed at high spinning frequencies. High-phase TPPM may be useful at the n=1 rotary resonance condition while PISSARRO permits efficient decoupling over a broad commonly used range of rf amplitudes, even at very high spinning frequencies. New insights into the response of spin systems to both decoupling schemes have been gained. High-phase TPPM is sensitive to the offsets of remote protons, their chemical shift anisotropies, and the relative orientations of the heteronuclear dipolar and proton chemical shift tensors. Since PISSARRO is virtually immune against such effects, the method is especially suited for very high magnetic fields. © 2011 Elsevier Inc. All rights reserved. |
Disentangling crystallographic inequivalence and crystallographic forms of l-arginine by one- and two-dimensional solid-state NMR spectroscopy Article de journal J -E Herbert-Pucheta; H Colaux; G Bodenhausen; P Tekely Journal of Physical Chemistry B, 115 (51), p. 15415–15421, 2011. @article{Herbert-Pucheta:2011, title = {Disentangling crystallographic inequivalence and crystallographic forms of l-arginine by one- and two-dimensional solid-state NMR spectroscopy}, author = {J -E Herbert-Pucheta and H Colaux and G Bodenhausen and P Tekely}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84255191201&doi=10.1021%2fjp209644k&partnerID=40&md5=1b8ac52ab75ea3e23892eaba35b16fc3}, doi = {10.1021/jp209644k}, year = {2011}, date = {2011-01-01}, journal = {Journal of Physical Chemistry B}, volume = {115}, number = {51}, pages = {15415--15421}, abstract = {Overlapping 13C or 15N solid-state NMR spectra from crystallographically different forms of l-arginine hydrochloride can be separated by exploiting differential proton T1 relaxation in conjunction with cross-polarization. Dipolar 13C-13C and 15N-15N two-dimensional correlation experiments reveal resonances belonging to crystallographically and magnetically inequivalent molecules. © 2011 American Chemical Society.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Overlapping 13C or 15N solid-state NMR spectra from crystallographically different forms of l-arginine hydrochloride can be separated by exploiting differential proton T1 relaxation in conjunction with cross-polarization. Dipolar 13C-13C and 15N-15N two-dimensional correlation experiments reveal resonances belonging to crystallographically and magnetically inequivalent molecules. © 2011 American Chemical Society. |
Fractional spin-labeling of polymers for enhancing NMR sensitivity by solvent-free dynamic nuclear polarization Article de journal V Vitzthum; F Borcard; S Jannin; M Morin; P Miéville; M A Caporini; A Sienkiewicz; S Gerber-Lemaire; G Bodenhausen ChemPhysChem, 12 (16), p. 2929–2932, 2011. @article{Vitzthum:2011a, title = {Fractional spin-labeling of polymers for enhancing NMR sensitivity by solvent-free dynamic nuclear polarization}, author = {V Vitzthum and F Borcard and S Jannin and M Morin and P Mi\'{e}ville and M A Caporini and A Sienkiewicz and S Gerber-Lemaire and G Bodenhausen}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-81255147961&doi=10.1002%2fcphc.201100630&partnerID=40&md5=100bc5710181711390b9b62ca0d77b9f}, doi = {10.1002/cphc.201100630}, year = {2011}, date = {2011-01-01}, journal = {ChemPhysChem}, volume = {12}, number = {16}, pages = {2929--2932}, abstract = {Decapeptides are partly covalently labeled with a polarizing agent (see picture) to enhance NMR signals by dynamic nuclear polarization (DNP). DNP under magic angle spinning conditions at T=100 K was performed directly on these molecules in the absence of any solvent. Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Decapeptides are partly covalently labeled with a polarizing agent (see picture) to enhance NMR signals by dynamic nuclear polarization (DNP). DNP under magic angle spinning conditions at T=100 K was performed directly on these molecules in the absence of any solvent. Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim. |
Fast characterization of functionalized silica materials by silicon-29 surface-enhanced NMR spectroscopy using dynamic nuclear polarization Article de journal M Lelli; D Gajan; A Lesage; M A Caporini; V Vitzthum; P Miéville; F Héroguel; F Rascón; A Roussey; C Thieuleux; M Boualleg; L Veyre; G Bodenhausen; C Copéret; L Emsley Journal of the American Chemical Society, 133 (7), p. 2104–2107, 2011. @article{Lelli:2011, title = {Fast characterization of functionalized silica materials by silicon-29 surface-enhanced NMR spectroscopy using dynamic nuclear polarization}, author = {M Lelli and D Gajan and A Lesage and M A Caporini and V Vitzthum and P Mi\'{e}ville and F H\'{e}roguel and F Rasc\'{o}n and A Roussey and C Thieuleux and M Boualleg and L Veyre and G Bodenhausen and C Cop\'{e}ret and L Emsley}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-79951821785&doi=10.1021%2fja110791d&partnerID=40&md5=d4509aaa93e7a9c7b8ef493e1e7950ab}, doi = {10.1021/ja110791d}, year = {2011}, date = {2011-01-01}, journal = {Journal of the American Chemical Society}, volume = {133}, number = {7}, pages = {2104--2107}, abstract = {We demonstrate fast characterization of the distribution of surface bonding modes and interactions in a series of functionalized materials via surface-enhanced nuclear magnetic resonance spectroscopy using dynamic nuclear polarization (DNP). Surface-enhanced silicon-29 DNP NMR spectra were obtained by using incipient wetness impregnation of the sample with a solution containing a polarizing radical (TOTAPOL). We identify and compare the bonding topology of functional groups in materials obtained via a sol-gel process and in materials prepared by post-grafting reactions. Furthermore, the remarkable gain in time provided by surface-enhanced silicon-29 DNP NMR spectroscopy (typically on the order of a factor 400) allows the facile acquisition of two-dimensional correlation spectra. © 2011 American Chemical Society.}, keywords = {}, pubstate = {published}, tppubtype = {article} } We demonstrate fast characterization of the distribution of surface bonding modes and interactions in a series of functionalized materials via surface-enhanced nuclear magnetic resonance spectroscopy using dynamic nuclear polarization (DNP). Surface-enhanced silicon-29 DNP NMR spectra were obtained by using incipient wetness impregnation of the sample with a solution containing a polarizing radical (TOTAPOL). We identify and compare the bonding topology of functional groups in materials obtained via a sol-gel process and in materials prepared by post-grafting reactions. Furthermore, the remarkable gain in time provided by surface-enhanced silicon-29 DNP NMR spectroscopy (typically on the order of a factor 400) allows the facile acquisition of two-dimensional correlation spectra. © 2011 American Chemical Society. |
Extending timescales and narrowing linewidths in NMR Article de journal T F Segawa; A Bornet; N Salvi; P Miéville; V Vitzthum; D Carnevale; S Jannin; M A Caporini; S Ulzega; P R Vasos; M Rey; G Bodenhausen Chimia, 65 (9), p. 652–655, 2011. @article{Segawa:2011, title = {Extending timescales and narrowing linewidths in NMR}, author = {T F Segawa and A Bornet and N Salvi and P Mi\'{e}ville and V Vitzthum and D Carnevale and S Jannin and M A Caporini and S Ulzega and P R Vasos and M Rey and G Bodenhausen}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-80054694151&doi=10.2533%2fchimia.2011.652&partnerID=40&md5=7363e4c293e5356cf205d6d80225155e}, doi = {10.2533/chimia.2011.652}, year = {2011}, date = {2011-01-01}, journal = {Chimia}, volume = {65}, number = {9}, pages = {652--655}, abstract = {Among the different fields of research in nuclear magnetic resonance (NMR) which are currently investigated in the Laboratory of Biomolecular Magnetic Resonance (LRMB), two subjects that are closely related to each other are presented in this article. On the one hand, we show how to populate long-lived states (LLS) that have long lifetimes T LLS which allow one to go beyond the usual limits imposed by the longitudinal relaxation time T 1. This makes it possible to extend NMR experiments to longer time-scales. As an application, we demonstrate the extension of the timescale of diffusion measurements by NMR spectroscopy. On the other hand, we review our work on long-lived coherences (LLC), a particular type of coherence between two spin states that oscillates with the frequency of the scalar coupling constant J IS and decays with a time constant T LLC. Again, this time constant T LLC can be much longer than the transverse relaxation time T 2. By extending the coherence lifetimes, we can narrow the linewidths to an unprecedented extent. J-couplings and residual dipolar couplings (RDCs) in weakly-oriented phases can be measured with the highest precision. © Schweizerische Chemische Gesellschaft.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Among the different fields of research in nuclear magnetic resonance (NMR) which are currently investigated in the Laboratory of Biomolecular Magnetic Resonance (LRMB), two subjects that are closely related to each other are presented in this article. On the one hand, we show how to populate long-lived states (LLS) that have long lifetimes T LLS which allow one to go beyond the usual limits imposed by the longitudinal relaxation time T 1. This makes it possible to extend NMR experiments to longer time-scales. As an application, we demonstrate the extension of the timescale of diffusion measurements by NMR spectroscopy. On the other hand, we review our work on long-lived coherences (LLC), a particular type of coherence between two spin states that oscillates with the frequency of the scalar coupling constant J IS and decays with a time constant T LLC. Again, this time constant T LLC can be much longer than the transverse relaxation time T 2. By extending the coherence lifetimes, we can narrow the linewidths to an unprecedented extent. J-couplings and residual dipolar couplings (RDCs) in weakly-oriented phases can be measured with the highest precision. © Schweizerische Chemische Gesellschaft. |
Low-temperature cross polarization in view of enhancing dissolution Dynamic Nuclear Polarization in NMR Article de journal S Jannin; A Bornet; S Colombo; G Bodenhausen Chemical Physics Letters, 517 (4-6), p. 234–236, 2011. @article{Jannin:2011, title = {Low-temperature cross polarization in view of enhancing dissolution Dynamic Nuclear Polarization in NMR}, author = {S Jannin and A Bornet and S Colombo and G Bodenhausen}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-82455210799&doi=10.1016%2fj.cplett.2011.10.042&partnerID=40&md5=9456f41c4a4f13b3b866551a1bb83662}, doi = {10.1016/j.cplett.2011.10.042}, year = {2011}, date = {2011-01-01}, journal = {Chemical Physics Letters}, volume = {517}, number = {4-6}, pages = {234--236}, abstract = {Dynamic Nuclear Polarization (DNP) induced by saturation of ESR transitions of TEMPO at 1.2 K and 3.35 T is characterized by build-up rates that are typically 5 times faster for protons than for the carboxylic carbon-13 in acetate. We show that cross polarization from protons to carbon-13 allows one to achieve a polarization P(13C) >20% in less than 10 min, twice as much as has been previously reported, in one-fifth of the time. This should open the way to an unprecedented improvement in the efficiency of dissolution DNP. © 2011 Elsevier B.V. All rights reserved.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Dynamic Nuclear Polarization (DNP) induced by saturation of ESR transitions of TEMPO at 1.2 K and 3.35 T is characterized by build-up rates that are typically 5 times faster for protons than for the carboxylic carbon-13 in acetate. We show that cross polarization from protons to carbon-13 allows one to achieve a polarization P(13C) >20% in less than 10 min, twice as much as has been previously reported, in one-fifth of the time. This should open the way to an unprecedented improvement in the efficiency of dissolution DNP. © 2011 Elsevier B.V. All rights reserved. |
Long-lived states to monitor protein unfolding by proton NMR Article de journal A Bornet; P Ahuja; R Sarkar; L Fernandes; S Hadji; S Y Lee; A Haririnia; D Fushman; G Bodenhausen; P R Vasos ChemPhysChem, 12 (15), p. 2729–2734, 2011. @article{Bornet:2011, title = {Long-lived states to monitor protein unfolding by proton NMR}, author = {A Bornet and P Ahuja and R Sarkar and L Fernandes and S Hadji and S Y Lee and A Haririnia and D Fushman and G Bodenhausen and P R Vasos}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-80054747185&doi=10.1002%2fcphc.201100365&partnerID=40&md5=15dbe7707f35478903ca9d92ff179a96}, doi = {10.1002/cphc.201100365}, year = {2011}, date = {2011-01-01}, journal = {ChemPhysChem}, volume = {12}, number = {15}, pages = {2729--2734}, abstract = {The relaxation of long-lived states (LLS) corresponds to the slow return to statistical thermal equilibrium between symmetric and antisymmetric proton spin states. This process is remarkably sensitive to the presence of external spins and can be used to obtain information about partial unfolding of proteins. We detected the appearance of a destabilized conformer of ubiquitin when urea is added to the protein in its native state. This conformer shows increased mobility in the C-terminus, which significantly extends the lifetimes of proton LLS magnetisation in Ser-65. These changes could not be detected by conventional measurements of T 1 and T 2 relaxation times of protons, and would hardly be sensed by carbon-13 or nitrogen-15 relaxation measurements. Conformers with similar dynamic and structural features, as revealed by LLS relaxation times, could be observed, in the absence of urea, in two ubiquitin mutants, L67S and L69S. Sit back, relax...: The relaxation time constants of long-lived states of Gly and Ser residues at specific locations (shown in red along the backbone of ubiquitin) are found to be sensitive to partial unfolding of the protein. Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.}, keywords = {}, pubstate = {published}, tppubtype = {article} } The relaxation of long-lived states (LLS) corresponds to the slow return to statistical thermal equilibrium between symmetric and antisymmetric proton spin states. This process is remarkably sensitive to the presence of external spins and can be used to obtain information about partial unfolding of proteins. We detected the appearance of a destabilized conformer of ubiquitin when urea is added to the protein in its native state. This conformer shows increased mobility in the C-terminus, which significantly extends the lifetimes of proton LLS magnetisation in Ser-65. These changes could not be detected by conventional measurements of T 1 and T 2 relaxation times of protons, and would hardly be sensed by carbon-13 or nitrogen-15 relaxation measurements. Conformers with similar dynamic and structural features, as revealed by LLS relaxation times, could be observed, in the absence of urea, in two ubiquitin mutants, L67S and L69S. Sit back, relax...: The relaxation time constants of long-lived states of Gly and Ser residues at specific locations (shown in red along the backbone of ubiquitin) are found to be sensitive to partial unfolding of the protein. Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim. |
Long-lived coherences for line-narrowing in high-field NMR Article de journal R Sarkar; P Ahuja; P R Vasos; A Bornet; O Wagnires; G Bodenhausen Progress in Nuclear Magnetic Resonance Spectroscopy, 59 (1), p. 83–90, 2011. @article{Sarkar:2011, title = {Long-lived coherences for line-narrowing in high-field NMR}, author = {R Sarkar and P Ahuja and P R Vasos and A Bornet and O Wagnires and G Bodenhausen}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-79956191025&doi=10.1016%2fj.pnmrs.2010.10.002&partnerID=40&md5=8947886d4bf80dbb1015d3ea0f1e9a18}, doi = {10.1016/j.pnmrs.2010.10.002}, year = {2011}, date = {2011-01-01}, journal = {Progress in Nuclear Magnetic Resonance Spectroscopy}, volume = {59}, number = {1}, pages = {83--90}, abstract = {Remarkably narrow lines can be obtained in solution-state NMR spectra in high fields by exploiting the long life-times associated with superpositions of quantum states with different symmetry, known as long-lived coherences (LLCs). These can be compared with coherences that can be excited by extremely low frequency (ELF) irradiation in a vanishing static field. LLCs may be regarded as a special class of zero-quantum coherences (ZQCs). In small molecules in the extreme narrowing limit, the line-widths can be a factor narrower than in spectra of ordinary single-quantum coherences (SQCs), provided relaxation is driven only by the dipole-dipole interaction between the two spins that participate in the LLC. In the slow motion limit for large molecules, the improvement in line-widths can in principle be a factor in favorable cases, provided that extraneous relaxation mechanisms do not operate.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Remarkably narrow lines can be obtained in solution-state NMR spectra in high fields by exploiting the long life-times associated with superpositions of quantum states with different symmetry, known as long-lived coherences (LLCs). These can be compared with coherences that can be excited by extremely low frequency (ELF) irradiation in a vanishing static field. LLCs may be regarded as a special class of zero-quantum coherences (ZQCs). In small molecules in the extreme narrowing limit, the line-widths can be a factor narrower than in spectra of ordinary single-quantum coherences (SQCs), provided relaxation is driven only by the dipole-dipole interaction between the two spins that participate in the LLC. In the slow motion limit for large molecules, the improvement in line-widths can in principle be a factor in favorable cases, provided that extraneous relaxation mechanisms do not operate. |
Reflections of pathways: A short perspective on 'Selection of coherence transfer pathways in NMR pulse experiments Article de journal G Bodenhausen Journal of Magnetic Resonance, 213 (2), p. 295–297, 2011. @article{Bodenhausen:2011, title = {Reflections of pathways: A short perspective on 'Selection of coherence transfer pathways in NMR pulse experiments}, author = {G Bodenhausen}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-83655203531&doi=10.1016%2fj.jmr.2011.08.004&partnerID=40&md5=ca5f018fbfb46f10564efd2559ef0eae}, doi = {10.1016/j.jmr.2011.08.004}, year = {2011}, date = {2011-01-01}, journal = {Journal of Magnetic Resonance}, volume = {213}, number = {2}, pages = {295--297}, abstract = {A short perspective on selection of coherence transfer pathways in NMR pulse experiments is presented. Mukamel has drawn analogies between our modest pathways and the celebrated Feynman diagrams. It is well known that some authors write essentially the same book again and again. Several attempts have been made to generalize pathways to heteronuclear systems, comprising protons I, and, say, carbon-13 nuclei S. It contributed to cleaning up a chaotic field of prescriptions for phase cycles that achieved much the same thing under different guises. But it was hardly written to become a citation classic. It also introduced a rather clumsy notation using bold and lightface characters with and without brackets to distinguish between selected and rejected pathways.}, keywords = {}, pubstate = {published}, tppubtype = {article} } A short perspective on selection of coherence transfer pathways in NMR pulse experiments is presented. Mukamel has drawn analogies between our modest pathways and the celebrated Feynman diagrams. It is well known that some authors write essentially the same book again and again. Several attempts have been made to generalize pathways to heteronuclear systems, comprising protons I, and, say, carbon-13 nuclei S. It contributed to cleaning up a chaotic field of prescriptions for phase cycles that achieved much the same thing under different guises. But it was hardly written to become a citation classic. It also introduced a rather clumsy notation using bold and lightface characters with and without brackets to distinguish between selected and rejected pathways. |
Quenching homonuclear couplings in magnetic resonance by trains of non-refocusing pulses Article de journal B Baishya; T F Segawa; G Bodenhausen Journal of Magnetic Resonance, 211 (2), p. 240–242, 2011. @article{Baishya:2011, title = {Quenching homonuclear couplings in magnetic resonance by trains of non-refocusing pulses}, author = {B Baishya and T F Segawa and G Bodenhausen}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-79960700010&doi=10.1016%2fj.jmr.2011.05.009&partnerID=40&md5=e55ac1a5a37be7c3e614d5294cd49b39}, doi = {10.1016/j.jmr.2011.05.009}, year = {2011}, date = {2011-01-01}, journal = {Journal of Magnetic Resonance}, volume = {211}, number = {2}, pages = {240--242}, abstract = {Trains of 2π or 4π pulses fail to refocus offsets but can suppress the effects of bilinear interactions such as homonuclear scalar couplings. © 2011 Elsevier Inc. All rights reserved.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Trains of 2π or 4π pulses fail to refocus offsets but can suppress the effects of bilinear interactions such as homonuclear scalar couplings. © 2011 Elsevier Inc. All rights reserved. |
Probing the quenching of rotary resonance by PISSARRO decoupling Article de journal M Weingarth; G Bodenhausen; P Tekely Chemical Physics Letters, 502 (4-6), p. 259–265, 2011. @article{Weingarth:2011a, title = {Probing the quenching of rotary resonance by PISSARRO decoupling}, author = {M Weingarth and G Bodenhausen and P Tekely}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-78751642377&doi=10.1016%2fj.cplett.2010.12.040&partnerID=40&md5=813652e0804bfd9f4076bb1431c2227c}, doi = {10.1016/j.cplett.2010.12.040}, year = {2011}, date = {2011-01-01}, journal = {Chemical Physics Letters}, volume = {502}, number = {4-6}, pages = {259--265}, abstract = {Solid-state NMR experiments may suffer from rotary resonance recoupling (R3) due to the interference between sample spinning at a frequency νrot and rf irradiation with an amplitude ν1 H in the vicinity of harmonic relationships ν 1 H=nνrot where n = 1 or 2. Until recently, only the use of very high rf amplitudes (e.g., ν1 H≫2ν rot) made it possible to avoid such interference effects. With the advent of PISSARRO decoupling, the deleterious effects of rotary resonance recoupling can be quenched, notably for ν1 H= 2νrot, so that demands on the rf amplitude ν1 H are relaxed. Here, we discuss how PISSARRO decoupling benefits from mirror symmetry and phase-shifting. We also show that PISSARRO can cope with the chemical shift anisotropy of protons and with proton-proton dipolar interactions. PISSARRO is most effective for very fast spinning at very high static fields. © 2010 Elsevier B.V. All rights reserved.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Solid-state NMR experiments may suffer from rotary resonance recoupling (R3) due to the interference between sample spinning at a frequency νrot and rf irradiation with an amplitude ν1 H in the vicinity of harmonic relationships ν 1 H=nνrot where n = 1 or 2. Until recently, only the use of very high rf amplitudes (e.g., ν1 H≫2ν rot) made it possible to avoid such interference effects. With the advent of PISSARRO decoupling, the deleterious effects of rotary resonance recoupling can be quenched, notably for ν1 H= 2νrot, so that demands on the rf amplitude ν1 H are relaxed. Here, we discuss how PISSARRO decoupling benefits from mirror symmetry and phase-shifting. We also show that PISSARRO can cope with the chemical shift anisotropy of protons and with proton-proton dipolar interactions. PISSARRO is most effective for very fast spinning at very high static fields. © 2010 Elsevier B.V. All rights reserved. |
Sensitive 13C-13C correlation spectra of amyloid fibrils at very high spinning frequencies and magnetic fields Article de journal M Weingarth; Y Masuda; K Takegoshi; G Bodenhausen; P Tekely Journal of Biomolecular NMR, 50 (2), p. 129–136, 2011. @article{Weingarth:2011b, title = {Sensitive 13C-13C correlation spectra of amyloid fibrils at very high spinning frequencies and magnetic fields}, author = {M Weingarth and Y Masuda and K Takegoshi and G Bodenhausen and P Tekely}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-80051692551&doi=10.1007%2fs10858-011-9501-9&partnerID=40&md5=deac8184cb3d290eb80ab0c9644c5340}, doi = {10.1007/s10858-011-9501-9}, year = {2011}, date = {2011-01-01}, journal = {Journal of Biomolecular NMR}, volume = {50}, number = {2}, pages = {129--136}, abstract = {Sensitive 2D solid-state 13C-13C correlation spectra of amyloid β fibrils have been recorded at very fast spinning frequencies and very high magnetic fields. It is demonstrated that PARIS-xy recoupling using moderate rf amplitudes can provide structural information by promoting efficient magnetization transfer even under such challenging experimental conditions. Furthermore, it has been shown both experimentally and by numerical simulations that the method is not very sensitive to dipolar truncation effects and can reveal direct transfer across distances of about 3.5-4r{A} . © 2011 Springer Science+Business Media B.V.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Sensitive 2D solid-state 13C-13C correlation spectra of amyloid β fibrils have been recorded at very fast spinning frequencies and very high magnetic fields. It is demonstrated that PARIS-xy recoupling using moderate rf amplitudes can provide structural information by promoting efficient magnetization transfer even under such challenging experimental conditions. Furthermore, it has been shown both experimentally and by numerical simulations that the method is not very sensitive to dipolar truncation effects and can reveal direct transfer across distances of about 3.5-4Å . © 2011 Springer Science+Business Media B.V. |
Relaxometry of insensitive nuclei: Optimizing dissolution dynamic nuclear polarization Article de journal P Miéville; S Jannin; G Bodenhausen Journal of Magnetic Resonance, 210 (1), p. 137–140, 2011. @article{Mieville:2011a, title = {Relaxometry of insensitive nuclei: Optimizing dissolution dynamic nuclear polarization}, author = {P Mi\'{e}ville and S Jannin and G Bodenhausen}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-79955070834&doi=10.1016%2fj.jmr.2011.02.006&partnerID=40&md5=b2abce41b1e9bc98ebe6db014971e555}, doi = {10.1016/j.jmr.2011.02.006}, year = {2011}, date = {2011-01-01}, journal = {Journal of Magnetic Resonance}, volume = {210}, number = {1}, pages = {137--140}, abstract = {We report measurements of spin-lattice relaxation of carbon-13 as a function of the magnetic field ('relaxometry') in view of optimizing dissolution-DNP. The sample is temporarily lifted into the stray field above a high-resolution magnet using a simple and inexpensive 'shuttle'. The signals of arbitrary molecules can be observed at high field with high-resolution and sensitivity. During the dissolution process and subsequent 'voyage' from the polarizer to the NMR magnet, relaxation is accelerated by paramagnetic polarizing agents, but it can be quenched by using scavengers. © 2011 Elsevier Inc. All rights reserved.}, keywords = {}, pubstate = {published}, tppubtype = {article} } We report measurements of spin-lattice relaxation of carbon-13 as a function of the magnetic field ('relaxometry') in view of optimizing dissolution-DNP. The sample is temporarily lifted into the stray field above a high-resolution magnet using a simple and inexpensive 'shuttle'. The signals of arbitrary molecules can be observed at high field with high-resolution and sensitivity. During the dissolution process and subsequent 'voyage' from the polarizer to the NMR magnet, relaxation is accelerated by paramagnetic polarizing agents, but it can be quenched by using scavengers. © 2011 Elsevier Inc. All rights reserved. |
The kinship or k-index as an antidote against the toxic effects of h-indices Article de journal A Molinié; G Bodenhausen Chimia, 65 (6), p. 433–436, 2011. @article{Molinie:2011, title = {The kinship or k-index as an antidote against the toxic effects of h-indices}, author = {A Molini\'{e} and G Bodenhausen}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-79960367219&doi=10.2533%2fchimia.2011.433&partnerID=40&md5=c12ff5abe46d89fd7fde8c26803a02d6}, doi = {10.2533/chimia.2011.433}, year = {2011}, date = {2011-01-01}, journal = {Chimia}, volume = {65}, number = {6}, pages = {433--436}, abstract = {In a bilingual paper entitled 'Bibliometrics as weapons of mass citation - La bibliom\'{e}trie comme arme de citation massive', [1] recently translated into English, [2] we have argued that the current fashion of ranking people, papers and journals is anything but harmless. The point was forcefully supported by Richard Ernst in a post-face entitled The Follies of Citation Indices and Academic Ranking Lists.'[34] We received a surprising number of passionate responses, such as 'It's written out of my heart' (TH); 'Je soutiens cette entreprise courageuse de tout coeur' (VT); 'Impact Faktoren sind ein Marktinstrument gewisser Verlage (FS);' Il y a un combat \`{a} mener' (SB). Some thoughtful responses have been incorporated into this Essay, albeit in attenuated form. We suggest that the 'fertility' of individual scientists be appreciated in terms of kinship rather than through personalized indices. © Schweizerische Chemische Gesellschaft.}, keywords = {}, pubstate = {published}, tppubtype = {article} } In a bilingual paper entitled 'Bibliometrics as weapons of mass citation - La bibliométrie comme arme de citation massive', [1] recently translated into English, [2] we have argued that the current fashion of ranking people, papers and journals is anything but harmless. The point was forcefully supported by Richard Ernst in a post-face entitled The Follies of Citation Indices and Academic Ranking Lists.'[34] We received a surprising number of passionate responses, such as 'It's written out of my heart' (TH); 'Je soutiens cette entreprise courageuse de tout coeur' (VT); 'Impact Faktoren sind ein Marktinstrument gewisser Verlage (FS);' Il y a un combat à mener' (SB). Some thoughtful responses have been incorporated into this Essay, albeit in attenuated form. We suggest that the 'fertility' of individual scientists be appreciated in terms of kinship rather than through personalized indices. © Schweizerische Chemische Gesellschaft. |
Ultra high-resolution NMR: Sustained induction decays of long-lived coherences Article de journal A Bornet; S Jannin; J A Konter; P Hautle; B Van Den Brandt; G Bodenhausen Journal of the American Chemical Society, 133 (39), p. 15644–15649, 2011. @article{Bornet:2011a, title = {Ultra high-resolution NMR: Sustained induction decays of long-lived coherences}, author = {A Bornet and S Jannin and J A Konter and P Hautle and B Van Den Brandt and G Bodenhausen}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-80053337062&doi=10.1021%2fja2052792&partnerID=40&md5=0838a7ef35bdd2c6755bd93095b73664}, doi = {10.1021/ja2052792}, year = {2011}, date = {2011-01-01}, journal = {Journal of the American Chemical Society}, volume = {133}, number = {39}, pages = {15644--15649}, abstract = {Long-lived coherences (LLCs) in homonuclear pairs of chemically inequivalent spins can be excited and sustained during protracted radio frequency irradiation periods that alternate with brief windows for signal observation. Fourier transformation of the sustained induction decays recorded in a single scan yields NMR spectra with line-widths in the range 10 textless δν textless 100 mHz, even in moderately inhomogeneous magnetic fields. The resulting doublets, which are reminiscent of J-spectra, allow one to determine the sum of scalar and residual dipolar interactions in partly oriented media. The signal intensity can be boosted by several orders of magnitude by "dissolution" dynamic nuclear polarization (DNP). © 2011 American Chemical Society.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Long-lived coherences (LLCs) in homonuclear pairs of chemically inequivalent spins can be excited and sustained during protracted radio frequency irradiation periods that alternate with brief windows for signal observation. Fourier transformation of the sustained induction decays recorded in a single scan yields NMR spectra with line-widths in the range 10 textless δν textless 100 mHz, even in moderately inhomogeneous magnetic fields. The resulting doublets, which are reminiscent of J-spectra, allow one to determine the sum of scalar and residual dipolar interactions in partly oriented media. The signal intensity can be boosted by several orders of magnitude by "dissolution" dynamic nuclear polarization (DNP). © 2011 American Chemical Society. |
Three-field NMR to preserve hyperpolarized proton magnetization as long-lived states in moderate magnetic fields Article de journal A Bornet; S Jannin; G Bodenhausen Chemical Physics Letters, 512 (4-6), p. 151–154, 2011. @article{Bornet:2011b, title = {Three-field NMR to preserve hyperpolarized proton magnetization as long-lived states in moderate magnetic fields}, author = {A Bornet and S Jannin and G Bodenhausen}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-80051800293&doi=10.1016%2fj.cplett.2011.07.015&partnerID=40&md5=ea0d4fbce59da63a692680a6c88e669a}, doi = {10.1016/j.cplett.2011.07.015}, year = {2011}, date = {2011-01-01}, journal = {Chemical Physics Letters}, volume = {512}, number = {4-6}, pages = {151--154}, abstract = {This communication describes a three-field experiment where inequivalent scalar coupled spin pairs are hyperpolarized at 3.35 T and 1.2 K by dynamic nuclear polarization (DNP), rapidly transferred to high field (7 T) to prepare a suitable initial condition that is converted adiabatically into a long-lived state (LLS) by shuttling to a 'low' magnetic field (2 mT-7 T). Even without applying any rf irradiation to sustain the LLS, it has a lifetime T LLS ≫ T1 in low fields. Finally, the sample is shuttled back to high field for observation under high-resolution conditions. © 2011 Elsevier B.V. All rights reserved.}, keywords = {}, pubstate = {published}, tppubtype = {article} } This communication describes a three-field experiment where inequivalent scalar coupled spin pairs are hyperpolarized at 3.35 T and 1.2 K by dynamic nuclear polarization (DNP), rapidly transferred to high field (7 T) to prepare a suitable initial condition that is converted adiabatically into a long-lived state (LLS) by shuttling to a 'low' magnetic field (2 mT-7 T). Even without applying any rf irradiation to sustain the LLS, it has a lifetime T LLS ≫ T1 in low fields. Finally, the sample is shuttled back to high field for observation under high-resolution conditions. © 2011 Elsevier B.V. All rights reserved. |
From NMR relaxation to fractional brownian dynamics in proteins: Results from a virtual experiment Article de journal P Calligari; V Calandrini; G R Kneller; D Abergel Journal of Physical Chemistry B, 115 (43), p. 12370–12379, 2011. @article{Calligari:2011, title = {From NMR relaxation to fractional brownian dynamics in proteins: Results from a virtual experiment}, author = {P Calligari and V Calandrini and G R Kneller and D Abergel}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-80054991123&doi=10.1021%2fjp205380f&partnerID=40&md5=ec8b4f518bdf41ab81b7018fc6eeb136}, doi = {10.1021/jp205380f}, year = {2011}, date = {2011-01-01}, journal = {Journal of Physical Chemistry B}, volume = {115}, number = {43}, pages = {12370--12379}, abstract = {In a recent simulation study [ J. Chem. Phys. 2010, 133, 145101 ], it has been shown that the time correlation functions probed by nuclear magnetic resonance (NMR) relaxation spectroscopy of proteins are well described by a fractional Brownian dynamics model, which accounts for the wide spectrum of relaxation rates characterizing their internal dynamics. Here, we perform numerical experiments to explore the possibility of using this model directly in the analysis of experimental NMR relaxation data. Starting from a molecular dynamics simulation of the 266 residue protein 6PGL in explicit water, we construct virtual 15N R1, R2, and NOE relaxation rates at two different magnetic fields, including artificial noise, and test how far the parameters obtained from a fit of the model to the virtual experimental data coincide with those obtained from an analysis of the MD time correlation functions that have been used to construct these data. We show that in most cases, close agreement is found. Acceptance or rejection of parameter values obtained from relaxation rates are discussed on a physical basis, therefore avoiding overfitting. © 2011 American Chemical Society.}, keywords = {}, pubstate = {published}, tppubtype = {article} } In a recent simulation study [ J. Chem. Phys. 2010, 133, 145101 ], it has been shown that the time correlation functions probed by nuclear magnetic resonance (NMR) relaxation spectroscopy of proteins are well described by a fractional Brownian dynamics model, which accounts for the wide spectrum of relaxation rates characterizing their internal dynamics. Here, we perform numerical experiments to explore the possibility of using this model directly in the analysis of experimental NMR relaxation data. Starting from a molecular dynamics simulation of the 266 residue protein 6PGL in explicit water, we construct virtual 15N R1, R2, and NOE relaxation rates at two different magnetic fields, including artificial noise, and test how far the parameters obtained from a fit of the model to the virtual experimental data coincide with those obtained from an analysis of the MD time correlation functions that have been used to construct these data. We show that in most cases, close agreement is found. Acceptance or rejection of parameter values obtained from relaxation rates are discussed on a physical basis, therefore avoiding overfitting. © 2011 American Chemical Society. |
2010 |
Surface enhanced NMR spectroscopy by dynamic nuclear polarization Article de journal A Lesage; M Lelli; D Gajan; M A Caporini; V Vitzthum; P Miéville; J Alauzun; A Roussey; C Thieuleux; A Mehdi; G Bodenhausen; C Copéret; L Emsley Journal of the American Chemical Society, 132 (44), p. 15459–15461, 2010. @article{Lesage:2010, title = {Surface enhanced NMR spectroscopy by dynamic nuclear polarization}, author = {A Lesage and M Lelli and D Gajan and M A Caporini and V Vitzthum and P Mi\'{e}ville and J Alauzun and A Roussey and C Thieuleux and A Mehdi and G Bodenhausen and C Cop\'{e}ret and L Emsley}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-78149232356&doi=10.1021%2fja104771z&partnerID=40&md5=7268a2bf68b78babc48d4548ad831aea}, doi = {10.1021/ja104771z}, year = {2010}, date = {2010-01-01}, journal = {Journal of the American Chemical Society}, volume = {132}, number = {44}, pages = {15459--15461}, abstract = {It is shown that surface NMR spectra can be greatly enhanced using dynamic nuclear polarization. Polarization is transferred from the protons of the solvent to the rare nuclei (here carbon-13 at natural isotopic abundance) at the surface, yielding at least a 50-fold signal enhancement for surface species covalently incorporated into a silica framework. © 2010 American Chemical Society.}, keywords = {}, pubstate = {published}, tppubtype = {article} } It is shown that surface NMR spectra can be greatly enhanced using dynamic nuclear polarization. Polarization is transferred from the protons of the solvent to the rare nuclei (here carbon-13 at natural isotopic abundance) at the surface, yielding at least a 50-fold signal enhancement for surface species covalently incorporated into a silica framework. © 2010 American Chemical Society. |
Speeding up nuclear magnetic resonance spectroscopy by the use of SMAll Recovery Times - SMART NMR Article de journal B Vitorge; G Bodenhausen; P Pelupessy Journal of Magnetic Resonance, 207 (1), p. 149–152, 2010. @article{Vitorge:2010, title = {Speeding up nuclear magnetic resonance spectroscopy by the use of SMAll Recovery Times - SMART NMR}, author = {B Vitorge and G Bodenhausen and P Pelupessy}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-77957956758&doi=10.1016%2fj.jmr.2010.07.017&partnerID=40&md5=96a330db0ba19ecd1c33735714573144}, doi = {10.1016/j.jmr.2010.07.017}, year = {2010}, date = {2010-01-01}, journal = {Journal of Magnetic Resonance}, volume = {207}, number = {1}, pages = {149--152}, abstract = {A drastic reduction of the time required for two-dimensional NMR experiments can be achieved by reducing or skipping the recovery delay between successive experiments. Novel SMAll Recovery Times (SMART) methods use orthogonal pulsed field gradients in three spatial directions to select the desired pathways and suppress interference effects. Two-dimensional spectra of dilute amino acids with concentrations as low as 2 mM can be recorded in about 0.1 s per increment in the indirect domain. © 2010 Elsevier Inc. All rights reserved.}, keywords = {}, pubstate = {published}, tppubtype = {article} } A drastic reduction of the time required for two-dimensional NMR experiments can be achieved by reducing or skipping the recovery delay between successive experiments. Novel SMAll Recovery Times (SMART) methods use orthogonal pulsed field gradients in three spatial directions to select the desired pathways and suppress interference effects. Two-dimensional spectra of dilute amino acids with concentrations as low as 2 mM can be recorded in about 0.1 s per increment in the indirect domain. © 2010 Elsevier Inc. All rights reserved. |
Solid-state nitrogen-14 nuclear magnetic resonance enhanced by dynamic nuclear polarization using a gyrotron Article de journal V Vitzthum; M A Caporini; G Bodenhausen Journal of Magnetic Resonance, 205 (1), p. 177–179, 2010. @article{Vitzthum:2010, title = {Solid-state nitrogen-14 nuclear magnetic resonance enhanced by dynamic nuclear polarization using a gyrotron}, author = {V Vitzthum and M A Caporini and G Bodenhausen}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-77955332613&doi=10.1016%2fj.jmr.2010.04.014&partnerID=40&md5=7347bc9f9c9e752b606deeda96c56e77}, doi = {10.1016/j.jmr.2010.04.014}, year = {2010}, date = {2010-01-01}, journal = {Journal of Magnetic Resonance}, volume = {205}, number = {1}, pages = {177--179}, abstract = {By combining indirect detection of 14N with dynamic nuclear polarization (DNP) using a gyrotron, the signal-to-noise ratio can be dramatically improved and the recovery delay between subsequent experiments can be shortened. Spectra of glassy samples of the amino acid proline doped with the stable bi-radical TOTAPOL rotating at 15.625 kHz at 110 K were obtained in a 400 MHz solid-state NMR spectrometer equipped with a gyrotron for microwave irradiation at 263 GHz. DNP enhancement factors on the order of ∼ 40 were achieved. The recovery delays can be reduced from 60 s without radicals at 300 K to 6 s with radicals at 110 K. In the absence of radicals at room temperature, the proton relaxation in proline is inefficient due to the absence of rotating methyl groups and other heat sinks, thus making long recovery delays mandatory. DNP allows one to reduce the acquisition times of 13C-detected 14N spectra from several days to a few hours. © 2010 Elsevier Inc. All rights reserved.}, keywords = {}, pubstate = {published}, tppubtype = {article} } By combining indirect detection of 14N with dynamic nuclear polarization (DNP) using a gyrotron, the signal-to-noise ratio can be dramatically improved and the recovery delay between subsequent experiments can be shortened. Spectra of glassy samples of the amino acid proline doped with the stable bi-radical TOTAPOL rotating at 15.625 kHz at 110 K were obtained in a 400 MHz solid-state NMR spectrometer equipped with a gyrotron for microwave irradiation at 263 GHz. DNP enhancement factors on the order of ∼ 40 were achieved. The recovery delays can be reduced from 60 s without radicals at 300 K to 6 s with radicals at 110 K. In the absence of radicals at room temperature, the proton relaxation in proline is inefficient due to the absence of rotating methyl groups and other heat sinks, thus making long recovery delays mandatory. DNP allows one to reduce the acquisition times of 13C-detected 14N spectra from several days to a few hours. © 2010 Elsevier Inc. All rights reserved. |
Transverse Relaxation of Scalar-Coupled Protons Article de journal T F Segawa; B Baishya; G Bodenhausen ChemPhysChem, 11 (15), p. 3343–3354, 2010. @article{Segawa:2010a, title = {Transverse Relaxation of Scalar-Coupled Protons}, author = {T F Segawa and B Baishya and G Bodenhausen}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-77958544375&doi=10.1002%2fcphc.201000350&partnerID=40&md5=33ee98fa5c6afbb092531189671458b5}, doi = {10.1002/cphc.201000350}, year = {2010}, date = {2010-01-01}, journal = {ChemPhysChem}, volume = {11}, number = {15}, pages = {3343--3354}, abstract = {In a preliminary communication (B. Baishya, T. F. Segawa, G. Bodenhausen, J. Am. Chem. Soc. 2009, 131, 17538-17539), we recently demonstrated that it is possible to obtain clean echo decays of protons in biomolecules despite the presence of homonuclear scalar couplings. These unmodulated decays allow one to determine apparent transverse relaxation rates R2 app of individual protons. Herein, we report the observation of R2 app for three methyl protons, four amide HN protons, and all 11 backbone Hα protons in cyclosporin A. If the proton resonances overlap, their R2 app rates can be measured by transferring their magnetization to neighboring 13C nuclei, which are less prone to overlap. The R2 app rates of protons attached to 13C are faster than those attached to 12C because of 13C-1H dipolar interactions. The differences of these rates allow the determination of local correlation functions. Backbone HN and Hα protons that have fast decay rates R2 app also feature fast longitudinal relaxation rates R1 and intense NOESY cross peaks that are typical of crowded environments. Variations of R2 app rates of backbone Hα protons in similar amino acids reflect differences in local environments. Time to relax: The transverse relaxation rates of protons in peptides can be measured using multiple refocusing with moderate pulse amplitudes and suitable interpulse delays. Decays of overlapping protons can be obtained by transfer to 13C. These rates are enhanced (see faster decays in figures) by the dipolar 1H-13C interaction. Copyright © 2010 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.}, keywords = {}, pubstate = {published}, tppubtype = {article} } In a preliminary communication (B. Baishya, T. F. Segawa, G. Bodenhausen, J. Am. Chem. Soc. 2009, 131, 17538-17539), we recently demonstrated that it is possible to obtain clean echo decays of protons in biomolecules despite the presence of homonuclear scalar couplings. These unmodulated decays allow one to determine apparent transverse relaxation rates R2 app of individual protons. Herein, we report the observation of R2 app for three methyl protons, four amide HN protons, and all 11 backbone Hα protons in cyclosporin A. If the proton resonances overlap, their R2 app rates can be measured by transferring their magnetization to neighboring 13C nuclei, which are less prone to overlap. The R2 app rates of protons attached to 13C are faster than those attached to 12C because of 13C-1H dipolar interactions. The differences of these rates allow the determination of local correlation functions. Backbone HN and Hα protons that have fast decay rates R2 app also feature fast longitudinal relaxation rates R1 and intense NOESY cross peaks that are typical of crowded environments. Variations of R2 app rates of backbone Hα protons in similar amino acids reflect differences in local environments. Time to relax: The transverse relaxation rates of protons in peptides can be measured using multiple refocusing with moderate pulse amplitudes and suitable interpulse delays. Decays of overlapping protons can be obtained by transfer to 13C. These rates are enhanced (see faster decays in figures) by the dipolar 1H-13C interaction. Copyright © 2010 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim. |
Structure, Dynamics and Thermodynamics of the Human Centrin 2/hSfi1 Complex Article de journal J Martinez-Sanz; F Kateb; L Assairi; Y Blouquit; G Bodenhausen; D Abergel; L Mouawad; C T Craescu Journal of Molecular Biology, 395 (1), p. 191–204, 2010. @article{Martinez-Sanz:2010, title = {Structure, Dynamics and Thermodynamics of the Human Centrin 2/hSfi1 Complex}, author = {J Martinez-Sanz and F Kateb and L Assairi and Y Blouquit and G Bodenhausen and D Abergel and L Mouawad and C T Craescu}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-70450224069&doi=10.1016%2fj.jmb.2009.10.041&partnerID=40&md5=a950ce9b6ab90aa3304874c76efa658f}, doi = {10.1016/j.jmb.2009.10.041}, year = {2010}, date = {2010-01-01}, journal = {Journal of Molecular Biology}, volume = {395}, number = {1}, pages = {191--204}, abstract = {Centrin, an EF-hand calcium-binding protein, has been shown to be involved in the duplication of centrosomes, and Sfi1 (Suppressor of fermentation-induced loss of stress resistance protein 1) is one of its centrosomal targets. There are three isoforms of human centrin, but here we only considered centrin 2 (HsCen2). This protein has the ability to bind to any of the ∼ 25 repeats of human Sfi1 (hSfi1) with more or less affinity. In this study, we mainly focused on the 17th repeat (R17-hSfi1-20), which presents the highest level of similarity with a well-studied 17-residue peptide (P17-XPC) from human xeroderma pigmentosum complementation group C protein, another centrin target for DNA repair. The only known structure of HsCen2 was resolved in complex with P17-XPC. The 20-residue peptide R17-hSfi1-20 exhibits the motif L8L4W1, which is the reverse of the XPC motif, W1L4L8. Consequently, the dipole of the helix formed by this motif has a reverse orientation. We wished to ascertain the impact of this reversal on the structure, dynamics and affinity of centrin. To address this question, we determined the structure of C-HsCen2 [the C-terminal domain of HsCen2 (T94-Y172)] in complex with R17-hSfi1-20 and monitored its dynamics by NMR, after having verified that the N-terminal domain of HsCen2 does not interact with the peptide. The structure shows that the binding mode is similar to that of P17-XPC. However, we observed a 2 -r{A} translation of the R17-hSfi1-20 helix along its axis, inducing less anchorage in the protein and the disruption of a hydrogen bond between a tryptophan residue in the peptide and a well-conserved nearby glutamate in C-HsCen2. NMR dynamic studies of the complex strongly suggested the existence of an unusual calcium secondary binding mode in calcium-binding loop III, made possible by the uncommon residue composition of this loop. The secondary metal site is only populated at high calcium concentration and depends on the type of bound ligand. © 2009 Elsevier Ltd. All rights reserved.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Centrin, an EF-hand calcium-binding protein, has been shown to be involved in the duplication of centrosomes, and Sfi1 (Suppressor of fermentation-induced loss of stress resistance protein 1) is one of its centrosomal targets. There are three isoforms of human centrin, but here we only considered centrin 2 (HsCen2). This protein has the ability to bind to any of the ∼ 25 repeats of human Sfi1 (hSfi1) with more or less affinity. In this study, we mainly focused on the 17th repeat (R17-hSfi1-20), which presents the highest level of similarity with a well-studied 17-residue peptide (P17-XPC) from human xeroderma pigmentosum complementation group C protein, another centrin target for DNA repair. The only known structure of HsCen2 was resolved in complex with P17-XPC. The 20-residue peptide R17-hSfi1-20 exhibits the motif L8L4W1, which is the reverse of the XPC motif, W1L4L8. Consequently, the dipole of the helix formed by this motif has a reverse orientation. We wished to ascertain the impact of this reversal on the structure, dynamics and affinity of centrin. To address this question, we determined the structure of C-HsCen2 [the C-terminal domain of HsCen2 (T94-Y172)] in complex with R17-hSfi1-20 and monitored its dynamics by NMR, after having verified that the N-terminal domain of HsCen2 does not interact with the peptide. The structure shows that the binding mode is similar to that of P17-XPC. However, we observed a 2 -Å translation of the R17-hSfi1-20 helix along its axis, inducing less anchorage in the protein and the disruption of a hydrogen bond between a tryptophan residue in the peptide and a well-conserved nearby glutamate in C-HsCen2. NMR dynamic studies of the complex strongly suggested the existence of an unusual calcium secondary binding mode in calcium-binding loop III, made possible by the uncommon residue composition of this loop. The secondary metal site is only populated at high calcium concentration and depends on the type of bound ligand. © 2009 Elsevier Ltd. All rights reserved. |
Toward structural dynamics: Protein motions viewed by chemical shift modulations and direct detection of CŃ multiple-quantum relaxation Article de journal M Mori; F Kateb; G Bodenhausen; M Piccioli; D Abergel Journal of the American Chemical Society, 132 (10), p. 3594–3600, 2010. @article{Mori:2010, title = {Toward structural dynamics: Protein motions viewed by chemical shift modulations and direct detection of C\'{N} multiple-quantum relaxation}, author = {M Mori and F Kateb and G Bodenhausen and M Piccioli and D Abergel}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-77949360195&doi=10.1021%2fja9103556&partnerID=40&md5=4bccb7cc8f93b7ad6ba3ab7272c1f30c}, doi = {10.1021/ja9103556}, year = {2010}, date = {2010-01-01}, journal = {Journal of the American Chemical Society}, volume = {132}, number = {10}, pages = {3594--3600}, abstract = {Multiple quantum relaxation in proteins reveals unexpected relationships between correlated or anti-correlated conformational backbone dynamics in α-helices or β-sheets. The contributions of conformational exchange to the relaxation rates of C'N coherences (i.e., double- and zero-quantum coherences involving backbone carbonyl 13C and neighboring amide 15N nuclei) depend on the kinetics of slow exchange processes, as well as on the populations of the conformations and chemical shift differences of 13C' and 15N nuclei. The relaxation rates of C'N coherences, which reflect concerted fluctuations due to slow chemical shift modulations (CSMs), were determined by direct 13C detection in diamagnetic and paramagnetic proteins. In well-folded proteins such as lanthanide-substituted calbindin (CaLnCb), copper, zinc superoxide dismutase (Cu,Zn SOD), and matrix metalloproteinase (MMP12), slow conformational exchange occurs along the entire backbone. Our observations demonstrate that relaxation rates of CN coherences arising from slow backbone dynamics have positive signs (characteristic of correlated fluctuations) in β-sheets and negative signs (characteristic of anti-correlated fluctuations) in α-helices. This extends the prospects of structuredynamics relationships to slow time scales that are relevant for protein function and enzymatic activity. © 2010 American Chemical Society.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Multiple quantum relaxation in proteins reveals unexpected relationships between correlated or anti-correlated conformational backbone dynamics in α-helices or β-sheets. The contributions of conformational exchange to the relaxation rates of C'N coherences (i.e., double- and zero-quantum coherences involving backbone carbonyl 13C and neighboring amide 15N nuclei) depend on the kinetics of slow exchange processes, as well as on the populations of the conformations and chemical shift differences of 13C' and 15N nuclei. The relaxation rates of C'N coherences, which reflect concerted fluctuations due to slow chemical shift modulations (CSMs), were determined by direct 13C detection in diamagnetic and paramagnetic proteins. In well-folded proteins such as lanthanide-substituted calbindin (CaLnCb), copper, zinc superoxide dismutase (Cu,Zn SOD), and matrix metalloproteinase (MMP12), slow conformational exchange occurs along the entire backbone. Our observations demonstrate that relaxation rates of CN coherences arising from slow backbone dynamics have positive signs (characteristic of correlated fluctuations) in β-sheets and negative signs (characteristic of anti-correlated fluctuations) in α-helices. This extends the prospects of structuredynamics relationships to slow time scales that are relevant for protein function and enzymatic activity. © 2010 American Chemical Society. |
Fractional protein dynamics seen by nuclear magnetic resonance spectroscopy: Relating molecular dynamics simulation and experiment Article de journal V Calandrini; D Abergel; G R Kneller Journal of Chemical Physics, 133 (14), 2010. @article{Calandrini:2010, title = {Fractional protein dynamics seen by nuclear magnetic resonance spectroscopy: Relating molecular dynamics simulation and experiment}, author = {V Calandrini and D Abergel and G R Kneller}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-77958097500&doi=10.1063%2f1.3486195&partnerID=40&md5=5bc86479657b553dc7e2deb097bc2f96}, doi = {10.1063/1.3486195}, year = {2010}, date = {2010-01-01}, journal = {Journal of Chemical Physics}, volume = {133}, number = {14}, abstract = {We propose a fractional Brownian dynamics model for time correlation functions characterizing the internal dynamics of proteins probed by NMR relaxation spectroscopy. The time correlation functions are represented by a broad distribution of exponential functions which are characterized by two parameters. We show that the model describes well the restricted rotational motion of N-H vectors in the amide groups of lysozyme obtained from molecular dynamics simulation and that reliable predictions of experimental relaxation rates can be obtained on that basis. © 2010 American Institute of Physics.}, keywords = {}, pubstate = {published}, tppubtype = {article} } We propose a fractional Brownian dynamics model for time correlation functions characterizing the internal dynamics of proteins probed by NMR relaxation spectroscopy. The time correlation functions are represented by a broad distribution of exponential functions which are characterized by two parameters. We show that the model describes well the restricted rotational motion of N-H vectors in the amide groups of lysozyme obtained from molecular dynamics simulation and that reliable predictions of experimental relaxation rates can be obtained on that basis. © 2010 American Institute of Physics. |
On the measurement of 15N-1H nuclear Overhauser effects. 2. Effects of the saturation scheme and water signal suppression Article de journal F Ferrage; A Reichel; S Battacharya; D Cowburn; R Ghose Journal of Magnetic Resonance, 207 (2), p. 294–303, 2010. @article{Ferrage:2010, title = {On the measurement of 15N-1H nuclear Overhauser effects. 2. Effects of the saturation scheme and water signal suppression}, author = {F Ferrage and A Reichel and S Battacharya and D Cowburn and R Ghose}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-78649444679&doi=10.1016%2fj.jmr.2010.09.014&partnerID=40&md5=db597511840e8b5ab12b990ca7da6096}, doi = {10.1016/j.jmr.2010.09.014}, year = {2010}, date = {2010-01-01}, journal = {Journal of Magnetic Resonance}, volume = {207}, number = {2}, pages = {294--303}, abstract = {Measurement of steady-state 15N-1H nuclear Overhauser effects forms a cornerstone of most methods to determine protein backbone dynamics from spin-relaxation data, since it is the most reliable probe of very fast motions on the ps-ns timescale. We have, in two previous publications (J. Magn. Reson. 192 (2008) 302-313; J. Am. Chem. Soc. 131 (2009) 6048-6049) reevaluated spin-dynamics during steady-state (or "saturated") and reference experiments, both of which are required to determine the NOE ratio. Here we assess the performance of several windowed and windowless sequences to achieve effective saturation of protons in steady-state experiments. We also evaluate the influence of the residual water signal due to radiation damping on the NOE ratio. We suggest a recipe that allows one to determine steady-state 15N-1H NOE's without artifacts and with the highest possible accuracy. © 2010 Elsevier Inc. All rights reserved.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Measurement of steady-state 15N-1H nuclear Overhauser effects forms a cornerstone of most methods to determine protein backbone dynamics from spin-relaxation data, since it is the most reliable probe of very fast motions on the ps-ns timescale. We have, in two previous publications (J. Magn. Reson. 192 (2008) 302-313; J. Am. Chem. Soc. 131 (2009) 6048-6049) reevaluated spin-dynamics during steady-state (or "saturated") and reference experiments, both of which are required to determine the NOE ratio. Here we assess the performance of several windowed and windowless sequences to achieve effective saturation of protons in steady-state experiments. We also evaluate the influence of the residual water signal due to radiation damping on the NOE ratio. We suggest a recipe that allows one to determine steady-state 15N-1H NOE's without artifacts and with the highest possible accuracy. © 2010 Elsevier Inc. All rights reserved. |
Nuclear spin relaxation in isotropic and anisotropic media Article de journal M P Nicholas; E Eryilmaz; F Ferrage; D Cowburn; R Ghose Progress in Nuclear Magnetic Resonance Spectroscopy, 57 (2), p. 111–158, 2010. @article{Nicholas:2010, title = {Nuclear spin relaxation in isotropic and anisotropic media}, author = {M P Nicholas and E Eryilmaz and F Ferrage and D Cowburn and R Ghose}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-77954083765&doi=10.1016%2fj.pnmrs.2010.04.003&partnerID=40&md5=de258d5454f8fddf7681eaab8e411ca6}, doi = {10.1016/j.pnmrs.2010.04.003}, year = {2010}, date = {2010-01-01}, journal = {Progress in Nuclear Magnetic Resonance Spectroscopy}, volume = {57}, number = {2}, pages = {111--158}, abstract = {A unified, self-consistent description of the microscopic interactions that influence dynamics in spin-space for an ensemble of spin-1/2 particles, as well as the real-space effects of the macroscopic (classical) global rotational diffusion determined both by molecular shape and the nature of the solvent is studied. The combined effects of the two on the spin-relaxation rates measured by NMR spectroscopists is also studied. The measurement of amide 15N spin-lattice (R1), spin spin (R2) and the steady-state NOE with the attached hydrogen has become routine for practitioners of biomolecular NMR spectroscopy. These rates can be used to determine the underlying spectral density functions and to interpret them using the Lipari-Szabo formalism that relies on the separation of the global rotational diffusion and local dynamics on single or multiple timescales. All spectral density functions in this review have been derived assuming that the spin-system under consideration is rigidly attached to the biomolecule and that the only motion results from the overall rotational diffusion.}, keywords = {}, pubstate = {published}, tppubtype = {article} } A unified, self-consistent description of the microscopic interactions that influence dynamics in spin-space for an ensemble of spin-1/2 particles, as well as the real-space effects of the macroscopic (classical) global rotational diffusion determined both by molecular shape and the nature of the solvent is studied. The combined effects of the two on the spin-relaxation rates measured by NMR spectroscopists is also studied. The measurement of amide 15N spin-lattice (R1), spin spin (R2) and the steady-state NOE with the attached hydrogen has become routine for practitioners of biomolecular NMR spectroscopy. These rates can be used to determine the underlying spectral density functions and to interpret them using the Lipari-Szabo formalism that relies on the separation of the global rotational diffusion and local dynamics on single or multiple timescales. All spectral density functions in this review have been derived assuming that the spin-system under consideration is rigidly attached to the biomolecule and that the only motion results from the overall rotational diffusion. |
Structural determination of biomolecular interfaces by nuclear magnetic resonance of proteins with reduced proton density Article de journal F Ferrage; K Dutta; A Shekhtman; D Cowburn Journal of Biomolecular NMR, 47 (1), p. 41–54, 2010. @article{Ferrage:2010a, title = {Structural determination of biomolecular interfaces by nuclear magnetic resonance of proteins with reduced proton density}, author = {F Ferrage and K Dutta and A Shekhtman and D Cowburn}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-77951665540&doi=10.1007%2fs10858-010-9409-9&partnerID=40&md5=eb764751ab931c0e15662159b96c61cd}, doi = {10.1007/s10858-010-9409-9}, year = {2010}, date = {2010-01-01}, journal = {Journal of Biomolecular NMR}, volume = {47}, number = {1}, pages = {41--54}, abstract = {Protein interactions are important for understanding many molecular mechanisms underlying cellular processes. So far, interfaces between interacting proteins have been characterized by NMR spectroscopy mostly by using chemical shift perturbations and cross-saturation via intermolecular cross-relaxation. Although powerful, these techniques cannot provide unambiguous estimates of intermolecular distances between interacting proteins. Here, we present an alternative approach, called REDSPRINT (REDduced/Standard PRoton density INTerface identification), to map protein interfaces with greater accuracy by using multiple NMR probes. Our approach is based on monitoring the cross-relaxation from a source protein (or from an arbitrary ligand that need not be a protein) with high proton density to a target protein (or other biomolecule) with low proton density by using isotope-filtered nuclear Overhauser spectroscopy (NOESY). This methodology uses different isotropic labeling for the source and target proteins to identify the source-target interface and also determine the proton density of the source protein at the interface for protein-protein or protein-ligand docking. Simulation indicates significant gains in sensitivity because of the resultant relaxation properties, and the utility of this technique, including a method for direct determination of the protein interface, is demonstrated for two different protein-protein complexes. © 2010 Springer Science+Business Media B.V.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Protein interactions are important for understanding many molecular mechanisms underlying cellular processes. So far, interfaces between interacting proteins have been characterized by NMR spectroscopy mostly by using chemical shift perturbations and cross-saturation via intermolecular cross-relaxation. Although powerful, these techniques cannot provide unambiguous estimates of intermolecular distances between interacting proteins. Here, we present an alternative approach, called REDSPRINT (REDduced/Standard PRoton density INTerface identification), to map protein interfaces with greater accuracy by using multiple NMR probes. Our approach is based on monitoring the cross-relaxation from a source protein (or from an arbitrary ligand that need not be a protein) with high proton density to a target protein (or other biomolecule) with low proton density by using isotope-filtered nuclear Overhauser spectroscopy (NOESY). This methodology uses different isotropic labeling for the source and target proteins to identify the source-target interface and also determine the proton density of the source protein at the interface for protein-protein or protein-ligand docking. Simulation indicates significant gains in sensitivity because of the resultant relaxation properties, and the utility of this technique, including a method for direct determination of the protein interface, is demonstrated for two different protein-protein complexes. © 2010 Springer Science+Business Media B.V. |
Broadband magnetization transfer using moderate radio-frequency fields for NMR with very high static fields and spinning speeds Article de journal M Weingarth; G Bodenhausen; P Tekely Chemical Physics Letters, 488 (1-3), p. 10–16, 2010. @article{Weingarth:2010, title = {Broadband magnetization transfer using moderate radio-frequency fields for NMR with very high static fields and spinning speeds}, author = {M Weingarth and G Bodenhausen and P Tekely}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-77950520342&doi=10.1016%2fj.cplett.2010.01.072&partnerID=40&md5=8d4c87b61b3c0084f56fa1bbc0222687}, doi = {10.1016/j.cplett.2010.01.072}, year = {2010}, date = {2010-01-01}, journal = {Chemical Physics Letters}, volume = {488}, number = {1-3}, pages = {10--16}, abstract = {We introduce a new dipolar recoupling scheme, dubbed PARIS-xy (phase-alternated recoupling irradiation scheme using orthogonal radio-frequency phases), to promote efficient broadband magnetization exchange between 13C nuclei using moderate radio-frequency amplitudes at very high magnetic field strengths and spinning speeds. Experimental observations for a wide range of spinning frequencies 30 ≤ νrot ≤ 60 kHz and magnetic field strengths (B0 = 9.4, 17.6 and 21.2 T) are backed up by numerical simulations. © 2010 Elsevier B.V. All rights reserved.}, keywords = {}, pubstate = {published}, tppubtype = {article} } We introduce a new dipolar recoupling scheme, dubbed PARIS-xy (phase-alternated recoupling irradiation scheme using orthogonal radio-frequency phases), to promote efficient broadband magnetization exchange between 13C nuclei using moderate radio-frequency amplitudes at very high magnetic field strengths and spinning speeds. Experimental observations for a wide range of spinning frequencies 30 ≤ νrot ≤ 60 kHz and magnetic field strengths (B0 = 9.4, 17.6 and 21.2 T) are backed up by numerical simulations. © 2010 Elsevier B.V. All rights reserved. |
Bibliometrics as Weapons of Mass Citation La bibliométrie comme arme de citation massive Article de journal A Molinié; G Bodenhausen Chimia, 64 (1-2), p. 78–89, 2010. @article{Molinie:2010, title = {Bibliometrics as Weapons of Mass Citation La bibliom\'{e}trie comme arme de citation massive}, author = {A Molini\'{e} and G Bodenhausen}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-77949373211&doi=10.2533%2fchimia.2010.78&partnerID=40&md5=fc1243cc9f0fb5b93b269852e4228d46}, doi = {10.2533/chimia.2010.78}, year = {2010}, date = {2010-01-01}, journal = {Chimia}, volume = {64}, number = {1-2}, pages = {78--89}, abstract = {The allocation of resources for research is increasingly based on so-called 'bibliometrics'. Scientists are now deemed to be successful on the sole condition that their work be abundantly cited. This world-wide trend appears to enjoy support not only by granting agencies (whose task is obviously simplified by extensive recourse to bibliometrics), but also by the scientists themselves (who seem to enjoy their status of celebrities). This trend appears to be fraught with dangers, particularly in the area of social sciences, where bibliometrics are less developed, and where monographs (which are not taken into account in citation indexes) are often more important than articles published in journals. We argue in favour of a return to the values of 'real science', in analogy to the much-promised return to a 'real economy'. While economists may strive towards a more objective evaluation of the prospects of a company, a market, or an industrial sector, we scientists can only base our appraisal on a responsible practice of peer review. Since we fear that decision-takers of granting agencies such as the FNRS, CTI, EPFL, ETHZ, ANR, CNRS, NIH, NSF, DOE,[1] etc. will be too busy to read our humble paper in Chimia, we appeal to scientists of all countries and disciplines to unite against the tyranny of bibliometrics. © Schweizerische Chemische Gesellschaft.}, keywords = {}, pubstate = {published}, tppubtype = {article} } The allocation of resources for research is increasingly based on so-called 'bibliometrics'. Scientists are now deemed to be successful on the sole condition that their work be abundantly cited. This world-wide trend appears to enjoy support not only by granting agencies (whose task is obviously simplified by extensive recourse to bibliometrics), but also by the scientists themselves (who seem to enjoy their status of celebrities). This trend appears to be fraught with dangers, particularly in the area of social sciences, where bibliometrics are less developed, and where monographs (which are not taken into account in citation indexes) are often more important than articles published in journals. We argue in favour of a return to the values of 'real science', in analogy to the much-promised return to a 'real economy'. While economists may strive towards a more objective evaluation of the prospects of a company, a market, or an industrial sector, we scientists can only base our appraisal on a responsible practice of peer review. Since we fear that decision-takers of granting agencies such as the FNRS, CTI, EPFL, ETHZ, ANR, CNRS, NIH, NSF, DOE,[1] etc. will be too busy to read our humble paper in Chimia, we appeal to scientists of all countries and disciplines to unite against the tyranny of bibliometrics. © Schweizerische Chemische Gesellschaft. |
Apparent transverse relaxation rates in systems with coupled carbon-13 spins Article de journal T F Segawa; N Aeby; G Bodenhausen Physical Chemistry Chemical Physics, 12 (33), p. 9772–9776, 2010. @article{Segawa:2010, title = {Apparent transverse relaxation rates in systems with coupled carbon-13 spins}, author = {T F Segawa and N Aeby and G Bodenhausen}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-77955911529&doi=10.1039%2fc004293e&partnerID=40&md5=1575cf7239ef87a20182ffb70cc7de1b}, doi = {10.1039/c004293e}, year = {2010}, date = {2010-01-01}, journal = {Physical Chemistry Chemical Physics}, volume = {12}, number = {33}, pages = {9772--9776}, abstract = {In systems with homonuclear scalar couplings, the envelopes of spin echoes obtained with simple refocusing pulses or trains of such pulses are normally modulated so that it is difficult to extract transverse relaxation rates. It has been shown recently that echo modulations can be quenched by cumulative pulse errors that arise after applying a large number of refocusing pulses with moderate rf amplitudes. The resulting unmodulated decays allow one to extract apparent transverse relaxation rates. Early work on systems comprising only two nitrogen-15 nuclei or two carbon-13 spins has recently been extended to systems with coupled protons. This work focuses on systems with three coupled carbon-13 spins, which in turn are coupled to several neighbouring protons. Unmodulated echo trains can be obtained by optimizing the pulse interval, the carrier frequency and the rf amplitude of the refocusing pulses. © the Owner Societies.}, keywords = {}, pubstate = {published}, tppubtype = {article} } In systems with homonuclear scalar couplings, the envelopes of spin echoes obtained with simple refocusing pulses or trains of such pulses are normally modulated so that it is difficult to extract transverse relaxation rates. It has been shown recently that echo modulations can be quenched by cumulative pulse errors that arise after applying a large number of refocusing pulses with moderate rf amplitudes. The resulting unmodulated decays allow one to extract apparent transverse relaxation rates. Early work on systems comprising only two nitrogen-15 nuclei or two carbon-13 spins has recently been extended to systems with coupled protons. This work focuses on systems with three coupled carbon-13 spins, which in turn are coupled to several neighbouring protons. Unmodulated echo trains can be obtained by optimizing the pulse interval, the carrier frequency and the rf amplitude of the refocusing pulses. © the Owner Societies. |
Improving the quality of 2D solid-state NMR spectra of microcrystalline proteins by covariance analysis Article de journal M Weingarth; P Tekely; R Brüschweiler; G Bodenhausen Chemical Communications, 46 (6), p. 952–954, 2010. @article{Weingarth:2010a, title = {Improving the quality of 2D solid-state NMR spectra of microcrystalline proteins by covariance analysis}, author = {M Weingarth and P Tekely and R Br\"{u}schweiler and G Bodenhausen}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-75649087355&doi=10.1039%2fb920844e&partnerID=40&md5=9e52ce334ae044b6a51cb673eb31468c}, doi = {10.1039/b920844e}, year = {2010}, date = {2010-01-01}, journal = {Chemical Communications}, volume = {46}, number = {6}, pages = {952--954}, abstract = {Gaining time, resolution and sensitivity at the same time: covariance processing of two-dimensional NMR spectra of microcrystalline proteins improves spectral quality over conventional Fourier transformation despite a significant reduction of the experimental time. © The Royal Society of Chemistry 2010.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Gaining time, resolution and sensitivity at the same time: covariance processing of two-dimensional NMR spectra of microcrystalline proteins improves spectral quality over conventional Fourier transformation despite a significant reduction of the experimental time. © The Royal Society of Chemistry 2010. |
Long-lived coherences for homogeneous line narrowing in spectroscopy Article de journal R Sarkar; P Ahuja; P R Vasos; G Bodenhausen Physical Review Letters, 104 (5), 2010. @article{Sarkar:2010, title = {Long-lived coherences for homogeneous line narrowing in spectroscopy}, author = {R Sarkar and P Ahuja and P R Vasos and G Bodenhausen}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-75849157852&doi=10.1103%2fPhysRevLett.104.053001&partnerID=40&md5=565b33ab3b93649984c5f0a75eea5f5c}, doi = {10.1103/PhysRevLett.104.053001}, year = {2010}, date = {2010-01-01}, journal = {Physical Review Letters}, volume = {104}, number = {5}, abstract = {Line broadening, which can arise from inhomogeneities or homogeneous relaxation effects that lead to finite lifetimes of quantum states, is the Achilles' heel of many forms of spectroscopy. We show that line broadening may be considerably reduced by exploiting long lifetimes associated with superpositions of quantum states with different symmetry, termed long-lived coherences. In proton NMR of arbitrary molecules (including proteins) in isotropic solution, the slow oscillatory decays of long-lived coherences can yield spectra with very high resolution. This improvement opens the way to high-field magnetic resonance of molecular assemblies that are almost an order of magnitude larger than could be hitherto studied. Coherences between states of different symmetry may be useful in other forms of spectroscopy to cancel unwanted line broadening effects. © 2010 The American Physical Society.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Line broadening, which can arise from inhomogeneities or homogeneous relaxation effects that lead to finite lifetimes of quantum states, is the Achilles' heel of many forms of spectroscopy. We show that line broadening may be considerably reduced by exploiting long lifetimes associated with superpositions of quantum states with different symmetry, termed long-lived coherences. In proton NMR of arbitrary molecules (including proteins) in isotropic solution, the slow oscillatory decays of long-lived coherences can yield spectra with very high resolution. This improvement opens the way to high-field magnetic resonance of molecular assemblies that are almost an order of magnitude larger than could be hitherto studied. Coherences between states of different symmetry may be useful in other forms of spectroscopy to cancel unwanted line broadening effects. © 2010 The American Physical Society. |
Line-narrowing in proton-detected nitrogen-14 NMR Article de journal S Cavadini; V Vitzthum; S Ulzega; A Abraham; G Bodenhausen Journal of Magnetic Resonance, 202 (1), p. 57–63, 2010. @article{Cavadini:2010, title = {Line-narrowing in proton-detected nitrogen-14 NMR}, author = {S Cavadini and V Vitzthum and S Ulzega and A Abraham and G Bodenhausen}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-72149114876&doi=10.1016%2fj.jmr.2009.09.018&partnerID=40&md5=0453427382327b5d54022b23a7e14ff9}, doi = {10.1016/j.jmr.2009.09.018}, year = {2010}, date = {2010-01-01}, journal = {Journal of Magnetic Resonance}, volume = {202}, number = {1}, pages = {57--63}, abstract = {In solids spinning at the magic angle, the indirect detection of single-quantum (SQ) and double-quantum (DQ) 14N spectra (I = 1) via spy nuclei S = 1/2 such as protons can be achieved in the manner of heteronuclear single- or multiple-quantum correlation (HSQC or HMQC) spectroscopy. The HMQC method relies on the excitation of two-spin coherences of the type T11I T11S and T21I T11S at the beginning of the evolution interval t1. The spectra obtained by Fourier transformation from t1 to ω1 may be broadened by the homogenous decay of the transverse terms of the spy nuclei S. This broadening is mostly due to homonuclear dipolar S-S′ interactions between the proton spy nuclei. In this work we have investigated the possibility of inserting rotor-synchronized symmetry-based C or R sequences and decoupling schemes such as Phase-Modulated Lee-Goldburg (PMLG) sequences in the evolution period. These schemes reduce the homonuclear proton-proton interactions and lead to an enhancement of the resolution of both SQ and DQ proton-detected 14N HMQC spectra. In addition, we have investigated the combination of HSQC with symmetry-based sequences and PMLG and shown that the highest resolution in the 14N dimension is achieved by using HSQC in combination with symmetry-based sequences of the R-type. We show improvements in resolution in samples of l-alanine and the tripeptide ala-ala-gly (AAG). In particular, for l-alanine the width of the 14N SQ peak is reduced from 2 to 1.2 kHz, in agreement with simulations. We report accurate measurements of quadrupolar coupling constants and asymmetry parameters for amide 14N in AAG peptide bonds. © 2009 Elsevier Inc. All rights reserved.}, keywords = {}, pubstate = {published}, tppubtype = {article} } In solids spinning at the magic angle, the indirect detection of single-quantum (SQ) and double-quantum (DQ) 14N spectra (I = 1) via spy nuclei S = 1/2 such as protons can be achieved in the manner of heteronuclear single- or multiple-quantum correlation (HSQC or HMQC) spectroscopy. The HMQC method relies on the excitation of two-spin coherences of the type T11I T11S and T21I T11S at the beginning of the evolution interval t1. The spectra obtained by Fourier transformation from t1 to ω1 may be broadened by the homogenous decay of the transverse terms of the spy nuclei S. This broadening is mostly due to homonuclear dipolar S-S′ interactions between the proton spy nuclei. In this work we have investigated the possibility of inserting rotor-synchronized symmetry-based C or R sequences and decoupling schemes such as Phase-Modulated Lee-Goldburg (PMLG) sequences in the evolution period. These schemes reduce the homonuclear proton-proton interactions and lead to an enhancement of the resolution of both SQ and DQ proton-detected 14N HMQC spectra. In addition, we have investigated the combination of HSQC with symmetry-based sequences and PMLG and shown that the highest resolution in the 14N dimension is achieved by using HSQC in combination with symmetry-based sequences of the R-type. We show improvements in resolution in samples of l-alanine and the tripeptide ala-ala-gly (AAG). In particular, for l-alanine the width of the 14N SQ peak is reduced from 2 to 1.2 kHz, in agreement with simulations. We report accurate measurements of quadrupolar coupling constants and asymmetry parameters for amide 14N in AAG peptide bonds. © 2009 Elsevier Inc. All rights reserved. |
Life-times of long-lived coherences under different motional regimes Article de journal A Bornet; R Sarkar; G Bodenhausen Journal of Magnetic Resonance, 206 (1), p. 154–156, 2010. @article{Bornet:2010, title = {Life-times of long-lived coherences under different motional regimes}, author = {A Bornet and R Sarkar and G Bodenhausen}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-77955925395&doi=10.1016%2fj.jmr.2010.06.004&partnerID=40&md5=ee250cbde689349a996b83aff14a3501}, doi = {10.1016/j.jmr.2010.06.004}, year = {2010}, date = {2010-01-01}, journal = {Journal of Magnetic Resonance}, volume = {206}, number = {1}, pages = {154--156}, abstract = {The transverse relaxation rate R2 of single quantum coherences, the relaxation rate RLLC of long-lived coherences (LLC), and the ratio R2/RLLC have been studied by experiment, simulation and theory in the two-spin system formed by the Glycine aliphatic protons of the dipeptide Alanine-Glycine as a function of the correlation time of rotational diffusion. © 2010 Elsevier Inc. All rights reserved.}, keywords = {}, pubstate = {published}, tppubtype = {article} } The transverse relaxation rate R2 of single quantum coherences, the relaxation rate RLLC of long-lived coherences (LLC), and the ratio R2/RLLC have been studied by experiment, simulation and theory in the two-spin system formed by the Glycine aliphatic protons of the dipeptide Alanine-Glycine as a function of the correlation time of rotational diffusion. © 2010 Elsevier Inc. All rights reserved. |
Kinetics of yttrium-Ligand complexation monitored using hyperpolarized 89Y as a model for gadolinium in contrast agents Article de journal P Miéville; S Jannin; L Helm; G Bodenhausen Journal of the American Chemical Society, 132 (14), p. 5006–5007, 2010. @article{Mieville:2010, title = {Kinetics of yttrium-Ligand complexation monitored using hyperpolarized 89Y as a model for gadolinium in contrast agents}, author = {P Mi\'{e}ville and S Jannin and L Helm and G Bodenhausen}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-77950839844&doi=10.1021%2fja1013954&partnerID=40&md5=db658620716fae1b1f0bc20998b6f74c}, doi = {10.1021/ja1013954}, year = {2010}, date = {2010-01-01}, journal = {Journal of the American Chemical Society}, volume = {132}, number = {14}, pages = {5006--5007}, abstract = {Hyperpolarization by dissolution dynamic nuclear polarization (DNP) enhances 89Y spin magnetization by 3 to 4 orders of magnitude and provides a way to monitor yttrium?ligand complexation on the fly by means of 89Y NMR. In this communication, we show an example of free yttrium Y3+ being complexed with 1,4,7,10-tetrakis(acetamido)-1,4,7,10- tetraazacyclododecane (DOTAM) to form [Y(DOTAM)(H2O)]3+ as a model for gadolinium in contrast agents. © 2010 American Chemical Society.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Hyperpolarization by dissolution dynamic nuclear polarization (DNP) enhances 89Y spin magnetization by 3 to 4 orders of magnitude and provides a way to monitor yttrium?ligand complexation on the fly by means of 89Y NMR. In this communication, we show an example of free yttrium Y3+ being complexed with 1,4,7,10-tetrakis(acetamido)-1,4,7,10- tetraazacyclododecane (DOTAM) to form [Y(DOTAM)(H2O)]3+ as a model for gadolinium in contrast agents. © 2010 American Chemical Society. |