Professeur des Universités, Sorbonne Université
Directeur de l’UMR8640
ENS – Département de chimie
24 rue Lhomond, 75005 Paris
Email: rodolphe.vuilleumier@ens.psl.eu
Phone: +33 144323324
Office: E119
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Publications
2018 |
Targeting the Pentose Phosphate Pathway: Characterization of a New 6PGL Inhibitor Article de journal A T Tran; A Sadet; P Calligari; P Lopes; J Ouazzani; M Sollogoub; E Miclet; D Abergel Biophysical Journal, 115 (11), p. 2114–2126, 2018. @article{Tran:2018, title = {Targeting the Pentose Phosphate Pathway: Characterization of a New 6PGL Inhibitor}, author = {A T Tran and A Sadet and P Calligari and P Lopes and J Ouazzani and M Sollogoub and E Miclet and D Abergel}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85056789414&doi=10.1016%2fj.bpj.2018.10.027&partnerID=40&md5=83791c30edf0ef19f0e0bf85e2d86d61}, doi = {10.1016/j.bpj.2018.10.027}, year = {2018}, date = {2018-01-01}, journal = {Biophysical Journal}, volume = {115}, number = {11}, pages = {2114--2126}, abstract = {Human African trypanosomiasis, or sleeping sickness, is a lethal disease caused by the protozoan parasite Trypanosoma brucei. However, although many efforts have been made to understand the biochemistry of this parasite, drug development has led to treatments that are of limited efficiency and of great toxicity. To develop new drugs, new targets must be identified, and among the several metabolic processes of trypanosomes that have been proposed as drug targets, carbohydrate metabolism (glycolysis and the pentose phosphate pathway (PPP)) appears as a promising one. As far as the PPP is concerned, a limited number of studies are related to the glucose-6-phosphate dehydrogenase. In this work, we have focused on the activity of the second PPP enzyme (6-phospho-gluconolactonase (6PGL)) that transforms 6-phosphogluconolactone into 6-phosphogluconic acid. A lactam analog of the natural substrate has been synthesized, and binding of the ligand to 6PGL has been investigated by NMR titration. The ability of this ligand to inhibit 6PGL has also been demonstrated using ultraviolet experiments, and protein-inhibitor interactions have been investigated through docking calculations and molecular dynamics simulations. In addition, a marginal inhibition of the third enzyme of the PPP (6-phosphogluconate dehydrogenase) was also demonstrated. Our results thus open new prospects for targeting T. brucei. © 2018 Biophysical Society}, keywords = {}, pubstate = {published}, tppubtype = {article} } Human African trypanosomiasis, or sleeping sickness, is a lethal disease caused by the protozoan parasite Trypanosoma brucei. However, although many efforts have been made to understand the biochemistry of this parasite, drug development has led to treatments that are of limited efficiency and of great toxicity. To develop new drugs, new targets must be identified, and among the several metabolic processes of trypanosomes that have been proposed as drug targets, carbohydrate metabolism (glycolysis and the pentose phosphate pathway (PPP)) appears as a promising one. As far as the PPP is concerned, a limited number of studies are related to the glucose-6-phosphate dehydrogenase. In this work, we have focused on the activity of the second PPP enzyme (6-phospho-gluconolactonase (6PGL)) that transforms 6-phosphogluconolactone into 6-phosphogluconic acid. A lactam analog of the natural substrate has been synthesized, and binding of the ligand to 6PGL has been investigated by NMR titration. The ability of this ligand to inhibit 6PGL has also been demonstrated using ultraviolet experiments, and protein-inhibitor interactions have been investigated through docking calculations and molecular dynamics simulations. In addition, a marginal inhibition of the third enzyme of the PPP (6-phosphogluconate dehydrogenase) was also demonstrated. Our results thus open new prospects for targeting T. brucei. © 2018 Biophysical Society |
Sample Ripening through Nanophase Separation Influences the Performance of Dynamic Nuclear Polarization Article de journal E M M Weber; G Sicoli; H Vezin; G Frébourg; D Abergel; G Bodenhausen; D Kurzbach Angewandte Chemie - International Edition, 57 (18), p. 5171–5175, 2018. @article{Weber:2018, title = {Sample Ripening through Nanophase Separation Influences the Performance of Dynamic Nuclear Polarization}, author = {E M M Weber and G Sicoli and H Vezin and G Fr\'{e}bourg and D Abergel and G Bodenhausen and D Kurzbach}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85044241782&doi=10.1002%2fanie.201800493&partnerID=40&md5=43bb50812719cf82c566fb0b1e75d97a}, doi = {10.1002/anie.201800493}, year = {2018}, date = {2018-01-01}, journal = {Angewandte Chemie - International Edition}, volume = {57}, number = {18}, pages = {5171--5175}, abstract = {Mixtures of water and glycerol provide popular matrices for low-temperature spectroscopy of vitrified samples. However, they involve counterintuitive physicochemical properties, such as spontaneous nanoscopic phase separations (NPS) in solutions that appear macroscopically homogeneous. We demonstrate that such phenomena can substantially influence the efficiency of dynamic nuclear polarization (DNP) by factors up to 20 % by causing fluctuations in local concentrations of polarization agents (radicals). Thus, a spontaneous NPS of water/glycerol mixtures that takes place on time scales on the order of 30\textendash60 min results in a confinement of polarization agents in nanoscopic water-rich vesicles, which in return affects the DNP. Such effects were found for three common polarization agents, TEMPOL, AMUPol and Trityl. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim}, keywords = {}, pubstate = {published}, tppubtype = {article} } Mixtures of water and glycerol provide popular matrices for low-temperature spectroscopy of vitrified samples. However, they involve counterintuitive physicochemical properties, such as spontaneous nanoscopic phase separations (NPS) in solutions that appear macroscopically homogeneous. We demonstrate that such phenomena can substantially influence the efficiency of dynamic nuclear polarization (DNP) by factors up to 20 % by causing fluctuations in local concentrations of polarization agents (radicals). Thus, a spontaneous NPS of water/glycerol mixtures that takes place on time scales on the order of 30–60 min results in a confinement of polarization agents in nanoscopic water-rich vesicles, which in return affects the DNP. Such effects were found for three common polarization agents, TEMPOL, AMUPol and Trityl. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim |
Relaxation of long-lived modes in NMR of deuterated methyl groups Article de journal K L Ivanov; T Kress; M Baudin; D Guarin; D Abergel; G Bodenhausen; D Kurzbach Journal of Chemical Physics, 149 (5), 2018. @article{Ivanov:2018, title = {Relaxation of long-lived modes in NMR of deuterated methyl groups}, author = {K L Ivanov and T Kress and M Baudin and D Guarin and D Abergel and G Bodenhausen and D Kurzbach}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85051239809&doi=10.1063%2f1.5031177&partnerID=40&md5=f335f115812c38354e4239f8c768a44b}, doi = {10.1063/1.5031177}, year = {2018}, date = {2018-01-01}, journal = {Journal of Chemical Physics}, volume = {149}, number = {5}, abstract = {Long-lived imbalances of spin state populations can circumvent fast quadrupolar relaxation by reducing effective longitudinal relaxation rates by about an order of magnitude. This opens new avenues for the study of dynamic processes in deuterated molecules. Here we present an analysis of the relaxation properties of deuterated methyl groups CD3. The number of coupled equations that describe cross-relaxation between the 27 symmetry-adapted spin states of a D3 system can be reduced to only 2 non-trivial "lumped modes" by (i) taking the sums of the populations of all states that equilibrate rapidly within each irreducible representation of the symmetry group, and (ii) by combining populations that have similar relaxation rates although they belong to different irreducible representations. The quadrupolar relaxation rates of the spin state imbalances in CD3 groups are determined not by the correlation time of overall tumbling of the molecule, but by the frequency of jumps of methyl groups about their three-fold symmetry axis. We access these states via dissolution dynamic nuclear polarization (D-DNP), a method that allows one to populate the desired long-lived states at cryogenic temperatures and their subsequent detection at ambient temperatures after rapid dissolution. Experimental examples of DMSO-d6 and ethanol-d6 demonstrate that long-lived deuterium spin states are indeed accessible and that their lifetimes can be determined. Our analysis of the system via "lumped" modes allows us to visualize different possible spin-state populations of symmetry A, B, or E. Thus, we identify a long-lived spin state involving all three deuterons in a CD3 group as an A/E imbalance that can be populated through DNP at low temperatures. © 2018 Author(s).}, keywords = {}, pubstate = {published}, tppubtype = {article} } Long-lived imbalances of spin state populations can circumvent fast quadrupolar relaxation by reducing effective longitudinal relaxation rates by about an order of magnitude. This opens new avenues for the study of dynamic processes in deuterated molecules. Here we present an analysis of the relaxation properties of deuterated methyl groups CD3. The number of coupled equations that describe cross-relaxation between the 27 symmetry-adapted spin states of a D3 system can be reduced to only 2 non-trivial "lumped modes" by (i) taking the sums of the populations of all states that equilibrate rapidly within each irreducible representation of the symmetry group, and (ii) by combining populations that have similar relaxation rates although they belong to different irreducible representations. The quadrupolar relaxation rates of the spin state imbalances in CD3 groups are determined not by the correlation time of overall tumbling of the molecule, but by the frequency of jumps of methyl groups about their three-fold symmetry axis. We access these states via dissolution dynamic nuclear polarization (D-DNP), a method that allows one to populate the desired long-lived states at cryogenic temperatures and their subsequent detection at ambient temperatures after rapid dissolution. Experimental examples of DMSO-d6 and ethanol-d6 demonstrate that long-lived deuterium spin states are indeed accessible and that their lifetimes can be determined. Our analysis of the system via "lumped" modes allows us to visualize different possible spin-state populations of symmetry A, B, or E. Thus, we identify a long-lived spin state involving all three deuterons in a CD3 group as an A/E imbalance that can be populated through DNP at low temperatures. © 2018 Author(s). |
Rates of Chemical Reactions Embedded in a Metabolic Network by Dissolution Dynamic Nuclear Polarisation NMR Article de journal A Sadet; E M M Weber; A Jhajharia; D Kurzbach; G Bodenhausen; E Miclet; D Abergel Chemistry - A European Journal, 24 (21), p. 5456–5461, 2018. @article{Sadet:2018, title = {Rates of Chemical Reactions Embedded in a Metabolic Network by Dissolution Dynamic Nuclear Polarisation NMR}, author = {A Sadet and E M M Weber and A Jhajharia and D Kurzbach and G Bodenhausen and E Miclet and D Abergel}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85044503759&doi=10.1002%2fchem.201705520&partnerID=40&md5=1b9688fdca8e8a72897b2a42cbb1a150}, doi = {10.1002/chem.201705520}, year = {2018}, date = {2018-01-01}, journal = {Chemistry - A European Journal}, volume = {24}, number = {21}, pages = {5456--5461}, abstract = {The isomerisation of 6-phosphogluconolactones and their hydrolyses into 6-phosphogluconic acid form a non enzymatic side cycle of the pentose-phosphate pathway (PPP) in cells. Dissolution dynamic nuclear polarisation can be used for determining the kinetic rates of the involved transformations in real time. It is found that the hydrolysis of both lactones is significantly slower than the isomerisation process, thereby shedding new light onto this subtle chemical process. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim}, keywords = {}, pubstate = {published}, tppubtype = {article} } The isomerisation of 6-phosphogluconolactones and their hydrolyses into 6-phosphogluconic acid form a non enzymatic side cycle of the pentose-phosphate pathway (PPP) in cells. Dissolution dynamic nuclear polarisation can be used for determining the kinetic rates of the involved transformations in real time. It is found that the hydrolysis of both lactones is significantly slower than the isomerisation process, thereby shedding new light onto this subtle chemical process. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim |
2017 |
Decomposition of proteins into dynamic units from atomic cross-correlation functions Article de journal P Calligari; M Gerolin; D Abergel; A Polimeno Journal of Chemical Theory and Computation, 13 (1), p. 309–319, 2017. @article{Calligari:2017, title = {Decomposition of proteins into dynamic units from atomic cross-correlation functions}, author = {P Calligari and M Gerolin and D Abergel and A Polimeno}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85016270051&doi=10.1021%2facs.jctc.6b00702&partnerID=40&md5=ab88646baeb0653b03b259bb4fb41d26}, doi = {10.1021/acs.jctc.6b00702}, year = {2017}, date = {2017-01-01}, journal = {Journal of Chemical Theory and Computation}, volume = {13}, number = {1}, pages = {309--319}, abstract = {In this article, we present a clustering method of atoms in proteins based on the analysis of the correlation times of interatomic distance correlation functions computed from MD simulations. The goal is to provide a coarse-grained description of the protein in terms of fewer elements that can be treated as dynamically independent subunits. Importantly, this domain decomposition method does not take into account structural properties of the protein. Instead, the clustering of protein residues in terms of networks of dynamically correlated domains is defined on the basis of the effective correlation times of the pair distance correlation functions. For these properties, our method stands as a complementary analysis to the customary protein decomposition in terms of quasi-rigid, structure-based domains. Results obtained for a prototypal protein structure illustrate the approach proposed. © 2016 American Chemical Society.}, keywords = {}, pubstate = {published}, tppubtype = {article} } In this article, we present a clustering method of atoms in proteins based on the analysis of the correlation times of interatomic distance correlation functions computed from MD simulations. The goal is to provide a coarse-grained description of the protein in terms of fewer elements that can be treated as dynamically independent subunits. Importantly, this domain decomposition method does not take into account structural properties of the protein. Instead, the clustering of protein residues in terms of networks of dynamically correlated domains is defined on the basis of the effective correlation times of the pair distance correlation functions. For these properties, our method stands as a complementary analysis to the customary protein decomposition in terms of quasi-rigid, structure-based domains. Results obtained for a prototypal protein structure illustrate the approach proposed. © 2016 American Chemical Society. |
Anisotropic longitudinal electronic relaxation affects DNP at cryogenic temperatures Article de journal E M M Weber; H Vezin; J G Kempf; G Bodenhausen; D Abergél; D Kurzbach Physical Chemistry Chemical Physics, 19 (24), p. 16087–16094, 2017. @article{Weber:2017, title = {Anisotropic longitudinal electronic relaxation affects DNP at cryogenic temperatures}, author = {E M M Weber and H Vezin and J G Kempf and G Bodenhausen and D Aberg\'{e}l and D Kurzbach}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85024380057&doi=10.1039%2fc7cp03242k&partnerID=40&md5=9d33aebbe861cd60df34b3c575d7f425}, doi = {10.1039/c7cp03242k}, year = {2017}, date = {2017-01-01}, journal = {Physical Chemistry Chemical Physics}, volume = {19}, number = {24}, pages = {16087--16094}, abstract = {We report the observation of anisotropic longitudinal electronic relaxation in nitroxide radicals under typical dynamic nuclear polarization conditions. This anisotropy affects the efficiency of dynamic nuclear polarization at cryogenic temperatures of 4 K and high magnetic fields of 6.7 T. Under our experimental conditions, the electron paramagnetic resonance spectrum of nitroxides such as TEMPOL (4-hydroxy-2,2,6,6-tetramethylpiperidin-1-oxyl) is only partly averaged by electronic spectral diffusion, so that the relaxation times T1e(ω) vary across the spectrum. We demonstrate how the anisotropy of T1e(ω) can be taken into account in simple DNP models. © the Owner Societies 2017.}, keywords = {}, pubstate = {published}, tppubtype = {article} } We report the observation of anisotropic longitudinal electronic relaxation in nitroxide radicals under typical dynamic nuclear polarization conditions. This anisotropy affects the efficiency of dynamic nuclear polarization at cryogenic temperatures of 4 K and high magnetic fields of 6.7 T. Under our experimental conditions, the electron paramagnetic resonance spectrum of nitroxides such as TEMPOL (4-hydroxy-2,2,6,6-tetramethylpiperidin-1-oxyl) is only partly averaged by electronic spectral diffusion, so that the relaxation times T1e(ω) vary across the spectrum. We demonstrate how the anisotropy of T1e(ω) can be taken into account in simple DNP models. © the Owner Societies 2017. |
Characterizing Thermal Mixing Dynamic Nuclear Polarization via Cross-Talk between Spin Reservoirs Article de journal D Guarin; S Marhabaie; A Rosso; D Abergel; G Bodenhausen; K L Ivanov; D Kurzbach Journal of Physical Chemistry Letters, 8 (22), p. 5531–5536, 2017. @article{Guarin:2017, title = {Characterizing Thermal Mixing Dynamic Nuclear Polarization via Cross-Talk between Spin Reservoirs}, author = {D Guarin and S Marhabaie and A Rosso and D Abergel and G Bodenhausen and K L Ivanov and D Kurzbach}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85034211190&doi=10.1021%2facs.jpclett.7b02233&partnerID=40&md5=f1e49f904e8912b8d96da78d3eb1f74a}, doi = {10.1021/acs.jpclett.7b02233}, year = {2017}, date = {2017-01-01}, journal = {Journal of Physical Chemistry Letters}, volume = {8}, number = {22}, pages = {5531--5536}, abstract = {Dynamic nuclear polarization (DNP) embraces a family of methods to increase signal intensities in nuclear magnetic resonance (NMR) spectroscopy. Despite extensive theoretical work that allows one to distinguish at least five distinct mechanisms, it remains challenging to determine the relative weights of the processes that are responsible for DNP in state-of-the-art experiments operating with stable organic radicals like nitroxides at high magnetic fields and low temperatures. Specifically, determining experimental conditions where DNP involves thermal mixing, which denotes a spontaneous heat exchange between different spin reservoirs, remains challenging. We propose an experimental approach to ascertain the prevalence of the thermal mixing regime by monitoring characteristic signature properties of the time evolution of the hyperpolarization. We find that thermal mixing is the dominant DNP mechanism at high nitroxide radical concentrations, while a mixture of different mechanisms prevails at lower concentrations. © 2017 American Chemical Society.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Dynamic nuclear polarization (DNP) embraces a family of methods to increase signal intensities in nuclear magnetic resonance (NMR) spectroscopy. Despite extensive theoretical work that allows one to distinguish at least five distinct mechanisms, it remains challenging to determine the relative weights of the processes that are responsible for DNP in state-of-the-art experiments operating with stable organic radicals like nitroxides at high magnetic fields and low temperatures. Specifically, determining experimental conditions where DNP involves thermal mixing, which denotes a spontaneous heat exchange between different spin reservoirs, remains challenging. We propose an experimental approach to ascertain the prevalence of the thermal mixing regime by monitoring characteristic signature properties of the time evolution of the hyperpolarization. We find that thermal mixing is the dominant DNP mechanism at high nitroxide radical concentrations, while a mixture of different mechanisms prevails at lower concentrations. © 2017 American Chemical Society. |
Communication: Dissolution DNP reveals a long-lived deuterium spin state imbalance in methyl groups Article de journal A Jhajharia; E M M Weber; J G Kempf; D Abergel; G Bodenhausen; D Kurzbach Journal of Chemical Physics, 146 (4), 2017. @article{Jhajharia:2017, title = {Communication: Dissolution DNP reveals a long-lived deuterium spin state imbalance in methyl groups}, author = {A Jhajharia and E M M Weber and J G Kempf and D Abergel and G Bodenhausen and D Kurzbach}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85010822015&doi=10.1063%2f1.4974358&partnerID=40&md5=da0569dbc85b8455d2d0e731c7bcec69}, doi = {10.1063/1.4974358}, year = {2017}, date = {2017-01-01}, journal = {Journal of Chemical Physics}, volume = {146}, number = {4}, abstract = {We report the generation and observation of long-lived spin states in deuterated methyl groups by dissolution DNP. These states are based on population imbalances between manifolds of spin states corresponding to irreducible representations of the C3v point group and feature strongly dampened quadrupolar relaxation. Their lifetime depends on the activation energies of methyl group rotation. With dissolution DNP, we can reduce the deuterium relaxation rate by a factor up to 20, thereby extending the experimentally available time window. The intrinsic limitation of NMR spectroscopy of quadrupolar spins by short relaxation times can thus be alleviated. © 2017 Author(s).}, keywords = {}, pubstate = {published}, tppubtype = {article} } We report the generation and observation of long-lived spin states in deuterated methyl groups by dissolution DNP. These states are based on population imbalances between manifolds of spin states corresponding to irreducible representations of the C3v point group and feature strongly dampened quadrupolar relaxation. Their lifetime depends on the activation energies of methyl group rotation. With dissolution DNP, we can reduce the deuterium relaxation rate by a factor up to 20, thereby extending the experimentally available time window. The intrinsic limitation of NMR spectroscopy of quadrupolar spins by short relaxation times can thus be alleviated. © 2017 Author(s). |
Single-Scan 13C Diffusion-Ordered NMR Spectroscopy of DNP-Hyperpolarised Substrates Article de journal L Guduff; D Kurzbach; C van Heijenoort; D Abergel; J -N Dumez Chemistry - A European Journal, 23 (66), p. 16722–16727, 2017. @article{Guduff:2017, title = {Single-Scan 13C Diffusion-Ordered NMR Spectroscopy of DNP-Hyperpolarised Substrates}, author = {L Guduff and D Kurzbach and C van Heijenoort and D Abergel and J -N Dumez}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85030115327&doi=10.1002%2fchem.201703300&partnerID=40&md5=79d87b5569bb4558d83ce5b0ef10f083}, doi = {10.1002/chem.201703300}, year = {2017}, date = {2017-01-01}, journal = {Chemistry - A European Journal}, volume = {23}, number = {66}, pages = {16722--16727}, abstract = {Diffusion-ordered NMR spectroscopy (DOSY) is a powerful approach for the analysis of molecular mixtures, yet its application range is limited by the relatively low sensitivity of NMR. We show here that spectrally resolved 13C DOSY data can be collected, in a single scan, for substrates hyperpolarised by dissolution dynamic nuclear polarisation (D-DNP), which provides signal enhancements of several orders of magnitude. For this we use a convection-compensation pulse scheme, which we also analyse by numerical simulation. The proposed method further allows the acquisition of several consecutive DOSY spectra in a single D-DNP experiment. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim}, keywords = {}, pubstate = {published}, tppubtype = {article} } Diffusion-ordered NMR spectroscopy (DOSY) is a powerful approach for the analysis of molecular mixtures, yet its application range is limited by the relatively low sensitivity of NMR. We show here that spectrally resolved 13C DOSY data can be collected, in a single scan, for substrates hyperpolarised by dissolution dynamic nuclear polarisation (D-DNP), which provides signal enhancements of several orders of magnitude. For this we use a convection-compensation pulse scheme, which we also analyse by numerical simulation. The proposed method further allows the acquisition of several consecutive DOSY spectra in a single D-DNP experiment. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim |
2016 |
Dissolution dynamic nuclear polarization of deuterated molecules enhanced by cross- polarization Article de journal D Kurzbach; E M M Weber; A Jhajharia; S F Cousin; A Sadet; S Marhabaie; E Canet; N Birlirakis; J Milani; S Jannin; D Eshchenko; A Hassan; R Melzi; S Luetolf; M Sacher; M Rossire; J Kempf; J A B Lohman; M Weller; G Bodenhausen; D Abergel Journal of Chemical Physics, 145 (19), 2016. @article{Kurzbach:2016b, title = {Dissolution dynamic nuclear polarization of deuterated molecules enhanced by cross- polarization}, author = {D Kurzbach and E M M Weber and A Jhajharia and S F Cousin and A Sadet and S Marhabaie and E Canet and N Birlirakis and J Milani and S Jannin and D Eshchenko and A Hassan and R Melzi and S Luetolf and M Sacher and M Rossire and J Kempf and J A B Lohman and M Weller and G Bodenhausen and D Abergel}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84998723887&doi=10.1063%2f1.4967402&partnerID=40&md5=5682345f396b249d7aa641f3c27a8850}, doi = {10.1063/1.4967402}, year = {2016}, date = {2016-01-01}, journal = {Journal of Chemical Physics}, volume = {145}, number = {19}, abstract = {We present novel means to hyperpolarize deuterium nuclei in 13CD2 groups at cryogenic temperatures. The method is based on cross-polarization from 1H to 13C and does not require any radio-frequency fields applied to the deuterium nuclei. After rapid dissolution, a new class of long-lived spin states can be detected indirectly by 13C NMR in solution. These long-lived states result from a sextet-triplet imbalance (STI) that involves the two equivalent deuterons with spin I = 1. An STI has similar properties as a triplet-singlet imbalance that can occur in systems with two equivalent I = 1/2 spins. Although the lifetimes TSTI are shorter than T1(Cz), they can exceed the life-time T1(Dz) of deuterium Zeeman magnetization by a factor of more than 20. © 2016 Author(s).}, keywords = {}, pubstate = {published}, tppubtype = {article} } We present novel means to hyperpolarize deuterium nuclei in 13CD2 groups at cryogenic temperatures. The method is based on cross-polarization from 1H to 13C and does not require any radio-frequency fields applied to the deuterium nuclei. After rapid dissolution, a new class of long-lived spin states can be detected indirectly by 13C NMR in solution. These long-lived states result from a sextet-triplet imbalance (STI) that involves the two equivalent deuterons with spin I = 1. An STI has similar properties as a triplet-singlet imbalance that can occur in systems with two equivalent I = 1/2 spins. Although the lifetimes TSTI are shorter than T1(Cz), they can exceed the life-time T1(Dz) of deuterium Zeeman magnetization by a factor of more than 20. © 2016 Author(s). |
2014 |
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. |
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. |
2012 |
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. |
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. |
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. |
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. |
2011 |
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 |
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. |
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. |
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. |
2009 |
Generating spin turbulence through nonlinear excitation in liquid-state NMR Article de journal D Abergel; A Louis-Joseph Journal of Magnetic Resonance, 196 (2), p. 115–118, 2009. @article{Abergel:2009, title = {Generating spin turbulence through nonlinear excitation in liquid-state NMR}, author = {D Abergel and A Louis-Joseph}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-58249142085&doi=10.1016%2fj.jmr.2008.10.016&partnerID=40&md5=5f7fbd1140dbb405ff54068d9123f997}, doi = {10.1016/j.jmr.2008.10.016}, year = {2009}, date = {2009-01-01}, journal = {Journal of Magnetic Resonance}, volume = {196}, number = {2}, pages = {115--118}, abstract = {Chaotic dynamics of a water magnetization in a 600 MHz NMR spectrometer was generated by a radiation damping-based electronic feedback. Erratic induction signal was observed for several tens of seconds. The analysis of the data shows that this chaotic behaviour can be ascribed to spin turbulence in the sample and that a simpler model based on the three-dimensional Bloch equations modified to include a feedback field may not account for the experimental data. © 2008 Elsevier Inc. All rights reserved.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Chaotic dynamics of a water magnetization in a 600 MHz NMR spectrometer was generated by a radiation damping-based electronic feedback. Erratic induction signal was observed for several tens of seconds. The analysis of the data shows that this chaotic behaviour can be ascribed to spin turbulence in the sample and that a simpler model based on the three-dimensional Bloch equations modified to include a feedback field may not account for the experimental data. © 2008 Elsevier Inc. All rights reserved. |
2008 |
Proton chemical shift anisotropy measurements of hydrogen-bonded functional groups by fast magic-angle spinning solid-state NMR spectroscopy Article de journal L Duma; D Abergel; P Tekely; G Bodenhausen Chemical Communications, (20), p. 2361–2363, 2008. @article{Duma:2008a, title = {Proton chemical shift anisotropy measurements of hydrogen-bonded functional groups by fast magic-angle spinning solid-state NMR spectroscopy}, author = {L Duma and D Abergel and P Tekely and G Bodenhausen}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-43749121574&doi=10.1039%2fb801154k&partnerID=40&md5=a14d981e87eda5089b4afcd80ee7cfa0}, doi = {10.1039/b801154k}, year = {2008}, date = {2008-01-01}, journal = {Chemical Communications}, number = {20}, pages = {2361--2363}, abstract = {The suitability of fast MAS solid-state NMR spectroscopy for probing 1H chemical shift anisotropy of hydrogen-bonded species has been demonstrated. © The Royal Society of Chemistry.}, keywords = {}, pubstate = {published}, tppubtype = {article} } The suitability of fast MAS solid-state NMR spectroscopy for probing 1H chemical shift anisotropy of hydrogen-bonded species has been demonstrated. © The Royal Society of Chemistry. |
Towards the prediction of NMR relaxation rates in proteins from their structure by a network of coupled rotators Article de journal G Nodet; G Bodenhausen; D Abergel Comptes Rendus Chimie, 11 (4-5), p. 524–529, 2008. @article{Nodet:2008a, title = {Towards the prediction of NMR relaxation rates in proteins from their structure by a network of coupled rotators}, author = {G Nodet and G Bodenhausen and D Abergel}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-41349091032&doi=10.1016%2fj.crci.2007.08.008&partnerID=40&md5=af84035a22030682aa765e8c936643c8}, doi = {10.1016/j.crci.2007.08.008}, year = {2008}, date = {2008-01-01}, journal = {Comptes Rendus Chimie}, volume = {11}, number = {4-5}, pages = {524--529}, abstract = {During the past decades, NMR spectroscopy of isotopically labelled proteins has emerged as a unique tool for the study of internal protein dynamics in solution. The possibility of measuring spin relaxation rates in proteins has motivated numerous theoretical and methodological developments aiming at the interpretation and the prediction of their internal dynamics. In this article, we discuss the possibility of predicting 15N relaxation rates using a Network of Coupled Rotators to describe internal motions of a protein starting from its three-dimensional structure, and illustrate the approach by the example of the protein calbindin. © 2007 Acad\'{e}mie des sciences.}, keywords = {}, pubstate = {published}, tppubtype = {article} } During the past decades, NMR spectroscopy of isotopically labelled proteins has emerged as a unique tool for the study of internal protein dynamics in solution. The possibility of measuring spin relaxation rates in proteins has motivated numerous theoretical and methodological developments aiming at the interpretation and the prediction of their internal dynamics. In this article, we discuss the possibility of predicting 15N relaxation rates using a Network of Coupled Rotators to describe internal motions of a protein starting from its three-dimensional structure, and illustrate the approach by the example of the protein calbindin. © 2007 Académie des sciences. |
Predicting NMR relaxation rates in anisotropically tumbling proteins through networks of coupled rotators Article de journal G Nodet; D Abergel; G Bodenhausen ChemPhysChem, 9 (4), p. 625–633, 2008. @article{Nodet:2008, title = {Predicting NMR relaxation rates in anisotropically tumbling proteins through networks of coupled rotators}, author = {G Nodet and D Abergel and G Bodenhausen}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-41149168620&doi=10.1002%2fcphc.200700732&partnerID=40&md5=83bcc0378e6083dd0ae8e51f15bd915b}, doi = {10.1002/cphc.200700732}, year = {2008}, date = {2008-01-01}, journal = {ChemPhysChem}, volume = {9}, number = {4}, pages = {625--633}, abstract = {We show that the prediction of 15N relaxation rates in proteins can be extended to systems with anisotropic global rotational diffusion by using a network of coupled rotators (NCR), starting from a three-dimensional structure. The relaxation rates predicted by this method are confronted in several examples with experiments performed by other groups. The NCR spectral density functions are compared with the results obtained from reduced spectral density mapping. The consequence of the timescales of inter-nal motions on the predicted relaxation rates and the effects of the predicted local anisotropy - present only in the case of anisotropic overall tumbling - on dynamic parameters, are discussed. © 2008 Wiley-VCH Verlag GmbH & Co. KGaA.}, keywords = {}, pubstate = {published}, tppubtype = {article} } We show that the prediction of 15N relaxation rates in proteins can be extended to systems with anisotropic global rotational diffusion by using a network of coupled rotators (NCR), starting from a three-dimensional structure. The relaxation rates predicted by this method are confronted in several examples with experiments performed by other groups. The NCR spectral density functions are compared with the results obtained from reduced spectral density mapping. The consequence of the timescales of inter-nal motions on the predicted relaxation rates and the effects of the predicted local anisotropy - present only in the case of anisotropic overall tumbling - on dynamic parameters, are discussed. © 2008 Wiley-VCH Verlag GmbH & Co. KGaA. |
Broadband dipolar recoupling for magnetization transfer in solid-state NMR correlation spectroscopy Article de journal L Duma; D Abergel; F Ferrage; P Pelupessy; P Tekely; G Bodenhausen ChemPhysChem, 9 (8), p. 1104–1106, 2008. @article{Duma:2008, title = {Broadband dipolar recoupling for magnetization transfer in solid-state NMR correlation spectroscopy}, author = {L Duma and D Abergel and F Ferrage and P Pelupessy and P Tekely and G Bodenhausen}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-45249097635&doi=10.1002%2fcphc.200800053&partnerID=40&md5=66d336ed908539f86a0a55977ae0ed7c}, doi = {10.1002/cphc.200800053}, year = {2008}, date = {2008-01-01}, journal = {ChemPhysChem}, volume = {9}, number = {8}, pages = {1104--1106}, abstract = {Efficient recoupling: A new experimental procedure using a broadband variant of rotary resonance recoupling (B2R3, see figure) improves 13C-13C transfer of magnetization in biological molecules. (Chemical Equation Presented) The robustness of the method, combined with its simplicity, results in improved structural analysis of crystalline and non-crystalline systems. © 2008 Wiley-VCH Verlag GmbH & Co. KGaA.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Efficient recoupling: A new experimental procedure using a broadband variant of rotary resonance recoupling (B2R3, see figure) improves 13C-13C transfer of magnetization in biological molecules. (Chemical Equation Presented) The robustness of the method, combined with its simplicity, results in improved structural analysis of crystalline and non-crystalline systems. © 2008 Wiley-VCH Verlag GmbH & Co. KGaA. |
2007 |
Weak calcium-mediated interactions between Lewis X-related trisaccharides studied by NMR measurements of residual dipolar couplings Article de journal G Nodet; L Poggi; D Abergel; C Gourmala; D Dong; Y Zhang; J -M Mallet; G Bodenhausen Journal of the American Chemical Society, 129 (29), p. 9080–9085, 2007. @article{Nodet:2007a, title = {Weak calcium-mediated interactions between Lewis X-related trisaccharides studied by NMR measurements of residual dipolar couplings}, author = {G Nodet and L Poggi and D Abergel and C Gourmala and D Dong and Y Zhang and J -M Mallet and G Bodenhausen}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-34547539474&doi=10.1021%2fja0711056&partnerID=40&md5=53aca08b440b69755694551b321f0625}, doi = {10.1021/ja0711056}, year = {2007}, date = {2007-01-01}, journal = {Journal of the American Chemical Society}, volume = {129}, number = {29}, pages = {9080--9085}, abstract = {The Lewis X (LeX) determinant, a trisaccharide with the carbohydrate sequence Galβ(1→4)-[Fucα(1→3)]GlcNAcβ, is believed to be responsible for Ca2+-mediated cell-cell interactions. In partly oriented phases composed of mixtures of penta(ethyleneglycol) monododecyl ether HO(CH2CH2O)5C 12H25 and n-hexanol in the presence of Ca2+ ions, the variation of the residual dipolar couplings 1DCH of various CiHi vectors in LeX as a function of the concentration of the trisaccharide demonstrates the existence of very weak LeX-Ca2+-LeX complexes in solution. Synthetic 3-, 4-, and 6-deoxy-LeX variants were also shown to form complexes in the presence of calcium ions, despite the replacement of one of their hydroxyl groups by hydrogen atoms. This is the first direct observation in solution of a calcium-mediated interaction between LeX molecules. © 2007 American Chemical Society.}, keywords = {}, pubstate = {published}, tppubtype = {article} } The Lewis X (LeX) determinant, a trisaccharide with the carbohydrate sequence Galβ(1→4)-[Fucα(1→3)]GlcNAcβ, is believed to be responsible for Ca2+-mediated cell-cell interactions. In partly oriented phases composed of mixtures of penta(ethyleneglycol) monododecyl ether HO(CH2CH2O)5C 12H25 and n-hexanol in the presence of Ca2+ ions, the variation of the residual dipolar couplings 1DCH of various CiHi vectors in LeX as a function of the concentration of the trisaccharide demonstrates the existence of very weak LeX-Ca2+-LeX complexes in solution. Synthetic 3-, 4-, and 6-deoxy-LeX variants were also shown to form complexes in the presence of calcium ions, despite the replacement of one of their hydroxyl groups by hydrogen atoms. This is the first direct observation in solution of a calcium-mediated interaction between LeX molecules. © 2007 American Chemical Society. |
An overview of recent developments in the interpretation and prediction of fast internal protein dynamics Article de journal G Nodet; D Abergel European Biophysics Journal, 36 (8), p. 985–993, 2007. @article{Nodet:2007, title = {An overview of recent developments in the interpretation and prediction of fast internal protein dynamics}, author = {G Nodet and D Abergel}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-35748939712&doi=10.1007%2fs00249-007-0167-x&partnerID=40&md5=b03987136664528d090ec89ed6e35bc8}, doi = {10.1007/s00249-007-0167-x}, year = {2007}, date = {2007-01-01}, journal = {European Biophysics Journal}, volume = {36}, number = {8}, pages = {985--993}, abstract = {During the past decades, NMR spectroscopy has emerged as a unique tool for the study of protein dynamics. Indeed, relaxation studies on isotopically labeled proteins can provide information on the overall motions as well as the internal fast, sub-nanosecond, dynamics. Therefore, the interpretation and the prediction of spin relaxation rates in proteins are important issues that have motivated numerous theoretical and methodological developments, including the description of overall dynamics and its possible coupling to internal mobility, the introduction of models of internal dynamics, the determination of correlation functions from experimental data, and the relationship between relaxation and thermodynamical quantities. A brief account of recent developments that have proven useful in this domain are presented. © 2007 EBSA.}, keywords = {}, pubstate = {published}, tppubtype = {article} } During the past decades, NMR spectroscopy has emerged as a unique tool for the study of protein dynamics. Indeed, relaxation studies on isotopically labeled proteins can provide information on the overall motions as well as the internal fast, sub-nanosecond, dynamics. Therefore, the interpretation and the prediction of spin relaxation rates in proteins are important issues that have motivated numerous theoretical and methodological developments, including the description of overall dynamics and its possible coupling to internal mobility, the introduction of models of internal dynamics, the determination of correlation functions from experimental data, and the relationship between relaxation and thermodynamical quantities. A brief account of recent developments that have proven useful in this domain are presented. © 2007 EBSA. |
Networks of coupled rotators: Relationship between structures and internal dynamics in metal-binding proteins. Applications to apo- and holo-calbindin Article de journal A Dhulesia; D Abergel; G Bodenhausen Journal of the American Chemical Society, 129 (16), p. 4998–5006, 2007. @article{Dhulesia:2007, title = {Networks of coupled rotators: Relationship between structures and internal dynamics in metal-binding proteins. Applications to apo- and holo-calbindin}, author = {A Dhulesia and D Abergel and G Bodenhausen}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-34247515255&doi=10.1021%2fja067429w&partnerID=40&md5=3251f3cd503a2a506d34abf755bdcdfe}, doi = {10.1021/ja067429w}, year = {2007}, date = {2007-01-01}, journal = {Journal of the American Chemical Society}, volume = {129}, number = {16}, pages = {4998--5006}, abstract = {This article presents an analysis of the internal dynamics of the Ca 2+-binding protein calbindin, based on the Networks of Coupled Rotators (NCRs) introduced recently. Several fundamental and practical issues raised by this approach are investigated. The roles of various parameters of the model are examined. The NCR model is shown to account for the modifications of the internal dynamics upon Ca2+ binding by calbindin. Two alternative strategies to estimate local internal effective correlation times of the protein are proposed, which offer good agreement between predictions and experiment. © 2007 American Chemical Society.}, keywords = {}, pubstate = {published}, tppubtype = {article} } This article presents an analysis of the internal dynamics of the Ca 2+-binding protein calbindin, based on the Networks of Coupled Rotators (NCRs) introduced recently. Several fundamental and practical issues raised by this approach are investigated. The roles of various parameters of the model are examined. The NCR model is shown to account for the modifications of the internal dynamics upon Ca2+ binding by calbindin. Two alternative strategies to estimate local internal effective correlation times of the protein are proposed, which offer good agreement between predictions and experiment. © 2007 American Chemical Society. |
2006 |
F Kateb; D Abergel; Y Blouquit; P Duchambon; C T Craescu; G Bodenhausen Biochemistry, 45 (50), p. 15011–15019, 2006. @article{Kateb:2006, title = {Slow backbone dynamics of the C-terminal fragment of human centrin 2 in complex with a target peptide probed by cross-correlated relaxation in multiple-quantum NMR spectroscopy}, author = {F Kateb and D Abergel and Y Blouquit and P Duchambon and C T Craescu and G Bodenhausen}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-33845575989&doi=10.1021%2fbi061469v&partnerID=40&md5=cb9dd24328030efe21f5a95dba7e6bb1}, doi = {10.1021/bi061469v}, year = {2006}, date = {2006-01-01}, journal = {Biochemistry}, volume = {45}, number = {50}, pages = {15011--15019}, abstract = {The C-terminal domain of human centrin 2 (C-HsCen2) strongly binds to P1-XPC, a peptide comprising 17 amino acids with a NWKLLAKGLLIRERLKR sequence. This peptide corresponds to residues N847-R863 of XPC, a protein involved in the recognition of damaged DNA during the initial step of the nucleotide excision repair pathway. The slow internal dynamics of the protein backbone in the C-HsCen-P1-XPC complex was studied by measuring the relaxation rates of zero- and double-quantum coherences involving neighboring pairs of carbonyl 13C and amide 15N nuclei. These relaxation rates, which reflect dynamics on time scales in the range of micro- to milliseconds, vary significantly along the protein backbone. Analysis of the relaxation rates at different CaCl2 concentrations and ionic strengths shows that these slow motions are mainly affected by the binding of a Ca2+ ion to the lower-affinity EF-hand III. Moreover, we discuss the possible functional role of residues that undergo differential exchange in the formation of HsCen homodimers. © 2006 American Chemical Society.}, keywords = {}, pubstate = {published}, tppubtype = {article} } The C-terminal domain of human centrin 2 (C-HsCen2) strongly binds to P1-XPC, a peptide comprising 17 amino acids with a NWKLLAKGLLIRERLKR sequence. This peptide corresponds to residues N847-R863 of XPC, a protein involved in the recognition of damaged DNA during the initial step of the nucleotide excision repair pathway. The slow internal dynamics of the protein backbone in the C-HsCen-P1-XPC complex was studied by measuring the relaxation rates of zero- and double-quantum coherences involving neighboring pairs of carbonyl 13C and amide 15N nuclei. These relaxation rates, which reflect dynamics on time scales in the range of micro- to milliseconds, vary significantly along the protein backbone. Analysis of the relaxation rates at different CaCl2 concentrations and ionic strengths shows that these slow motions are mainly affected by the binding of a Ca2+ ion to the lower-affinity EF-hand III. Moreover, we discuss the possible functional role of residues that undergo differential exchange in the formation of HsCen homodimers. © 2006 American Chemical Society. |