Senior Scientist CNRS (DR1)
Associate Professor ENS – PSL
Laboratoire des biomolécules UMR 7203
Office: E117
Short bio
Fabien Ferrage did his undergraduate studies at the Ecole Normale Supérieure and Université Pierre et Marie Curie in Chemistry and Molecular Biophysics. He joined Geoffrey Bodenhausen’s group at ENS for his master thesis and continued with his PhD, which he completed in 2002. He spent.a semester in Art Palmer’s lab at Columbia University in 2001. He joined David Cowburn’s team at the New York Structural Biology Center in 2003 as
a postdoc. He was appointed associate scientist at the Centre National de la Recherche Scientifique (CNRS) in 2005 in Geoffrey Bodenhausen’s group. Between 2007 and 2009, he worked part-time at the New York Structural Biology Center, collaborating with David Cowburn and Ranajeet Ghose. In 2010-1011, he spent two years as a visiting scientist in the team of Aneel Aggarwal at Mount Sinai School of Medicine. He was appointed associate professor at ENS in 2015 and senior scientist at CNRS in 2016.
Research interests
His main focus is on NMR methodology particularly the development of new methods and instruments for the exploration of biomolecular dynamics by NMR relaxation. Among recent developments, he studies protein dynamics from low-magnetic field nuclear spin relaxation, by a technique called high-resolution relaxometry. He introduced recently, in a partnership with Bruker Biospin, two-field NMR spectroscopy, where moderately low and high magnetic fields are coupled in a single experiment. Current investigations shed light on the dynamics of protein side chains in folded proteins as well as motions in intrinsically disordered proteins.
Our research is funded by:
Check out the website of our FET-Open project HIRES-MULTIDYN
Project IMF-NMR
Project CPER PSL-RESOLUTION
Projects 2F-TROSY & DREAMY
MSCA-PF project BiophInLLPSInt
MSCA-DN FC-RELAX, check out the website!
Awards and distinctions
- 2003 PhD prize form the Chemical Physics division from the French Chemical and Physical Societies.
- 2003 Lavoisier fellowship form the French Minister of Foreign Affairs.
- 2003 Nine Choucroun Prize from the Institut de Biologie Physico-Chimique.
- 2004 Raymond Andrew Award from the Groupement Ampère.
- 2011 Starting Grant of the European Research Council (ERC) 2012-2017.
Current Teaching
- Scientific Communication in English (2014-), Master 1, Undergraduate education of the department of Chemistry at ENS, as well as Master Chemistry and Life Sciences.
- Nuclear Magnetic Resonance, First year students in Chemistry, Ecole normale supérieure (2015-pres.).
- Nuclear Magnetic Resonance Spectroscopy (2014-2021), Master 1 Physical, analytical, and theoretical Chemistry, UE M1 4C303, Local Field Spectroscopy and Microscopy: Probes for Structure and Reactivity, Sorbonne Université.
- Molecular Spectroscopies (2020-pres.); Master in Chemistry (M1 Chemistry and Innovation); PSL University.
- Magnetic Resonance (2021-pres.); Master in Integrative Chemistry and Innovation (2nd year); PSL University.
- Dynamics of molecular processes in biological systems (2021-pres.); Master in Integrative Chemistry and Innovation (2nd year); PSL University.
Publications
2012 |
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. |
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. |
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. |
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. |
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. |
2010 |
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. |
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. |
2009 |
Accurate sampling of high-frequency motions in proteins by steady-state 15N- 1H nuclear overhauser effect measurements in the presence of cross-correlated relaxation Article de journal F Ferrage; D Cowburn; R Ghose Journal of the American Chemical Society, 131 (17), p. 6048–6049, 2009. @article{Ferrage:2009, title = {Accurate sampling of high-frequency motions in proteins by steady-state 15N- 1H nuclear overhauser effect measurements in the presence of cross-correlated relaxation}, author = {F Ferrage and D Cowburn and R Ghose}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-70149102207&doi=10.1021%2fja809526q&partnerID=40&md5=e6329f323be9139dc9415da63eaddad2}, doi = {10.1021/ja809526q}, year = {2009}, date = {2009-01-01}, journal = {Journal of the American Chemical Society}, volume = {131}, number = {17}, pages = {6048--6049}, abstract = {The steady-state 1H- 15N NOE experiment is used in most common NMR analyses of backbone dynamics to accurately ascertain the effects of the fast dynamic modes. We demonstrate here that, in its most common implementation, this experiment generates an incorrect steady state in the presence of CSA/dipole cross-correlated relaxation leading to large errors in the characterization of these high-frequency modes. This affects both the quantitative and qualitative interpretation of 15N backbone relaxation in dynamic terms. We demonstrate further that minor changes in the experimental implementation effectively remove these errors and allow a more accurate interpretation of protein backbone dynamics. © 2009 American Chemical Society.}, keywords = {}, pubstate = {published}, tppubtype = {article} } The steady-state 1H- 15N NOE experiment is used in most common NMR analyses of backbone dynamics to accurately ascertain the effects of the fast dynamic modes. We demonstrate here that, in its most common implementation, this experiment generates an incorrect steady state in the presence of CSA/dipole cross-correlated relaxation leading to large errors in the characterization of these high-frequency modes. This affects both the quantitative and qualitative interpretation of 15N backbone relaxation in dynamic terms. We demonstrate further that minor changes in the experimental implementation effectively remove these errors and allow a more accurate interpretation of protein backbone dynamics. © 2009 American Chemical Society. |
2008 |
Single or triple gradients? Article de journal R Sarkar; D Moskau; F Ferrage; P R Vasos; G Bodenhausen Journal of Magnetic Resonance, 193 (1), p. 110–118, 2008. @article{Sarkar:2008a, title = {Single or triple gradients?}, author = {R Sarkar and D Moskau and F Ferrage and P R Vasos and G Bodenhausen}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-44649116396&doi=10.1016%2fj.jmr.2008.04.029&partnerID=40&md5=4f3d92f0bf0f0aaf5cc559e8ffdbf964}, doi = {10.1016/j.jmr.2008.04.029}, year = {2008}, date = {2008-01-01}, journal = {Journal of Magnetic Resonance}, volume = {193}, number = {1}, pages = {110--118}, abstract = {Pulsed Field Gradients (PFGs) have become ubiquitous tools not only for Magnetic Resonance Imaging (MRI), but also for NMR experiments designed to study translational diffusion, for spatial encoding in ultra-fast spectroscopy, for the selection of desirable coherence transfer pathways, for the suppression of solvent signals, and for the elimination of zero-quantum coherences. Some of these experiments can only be carried out if three orthogonal gradients are available, while others can also be implemented using a single gradient, albeit at some expense of performance. This paper discusses some of the advantages of triple- with respect to single-gradient probes. By way of examples we discuss (i) the measurement of small diffusion coefficients making use of the long spin-lattice relaxation times of nuclei with low gyromagnetic ratios γ such as nitrogen-15, and (ii) the elimination of zero-quantum coherences in Exchange or Nuclear Overhauser Spectroscopy (EXSY or NOESY) experiments, as well as in methods relying on long-lived (singlet) states to study very slow exchange or diffusion processes. © 2008 Elsevier Inc. All rights reserved.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Pulsed Field Gradients (PFGs) have become ubiquitous tools not only for Magnetic Resonance Imaging (MRI), but also for NMR experiments designed to study translational diffusion, for spatial encoding in ultra-fast spectroscopy, for the selection of desirable coherence transfer pathways, for the suppression of solvent signals, and for the elimination of zero-quantum coherences. Some of these experiments can only be carried out if three orthogonal gradients are available, while others can also be implemented using a single gradient, albeit at some expense of performance. This paper discusses some of the advantages of triple- with respect to single-gradient probes. By way of examples we discuss (i) the measurement of small diffusion coefficients making use of the long spin-lattice relaxation times of nuclei with low gyromagnetic ratios γ such as nitrogen-15, and (ii) the elimination of zero-quantum coherences in Exchange or Nuclear Overhauser Spectroscopy (EXSY or NOESY) experiments, as well as in methods relying on long-lived (singlet) states to study very slow exchange or diffusion processes. © 2008 Elsevier Inc. All rights reserved. |
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. |
Multiple-timescale dynamics of side-chain carboxyl and carbonyl groups in proteins by 13C nuclear spin relaxation Article de journal R Paquin; F Ferrage; F A A Mulder; M Akke; G Bodenhausen Journal of the American Chemical Society, 130 (47), p. 15805–15807, 2008. @article{Paquin:2008, title = {Multiple-timescale dynamics of side-chain carboxyl and carbonyl groups in proteins by 13C nuclear spin relaxation}, author = {R Paquin and F Ferrage and F A A Mulder and M Akke and G Bodenhausen}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-56749180963&doi=10.1021%2fja803794g&partnerID=40&md5=74ae027f848a9bf016b4b0de7dbc439f}, doi = {10.1021/ja803794g}, year = {2008}, date = {2008-01-01}, journal = {Journal of the American Chemical Society}, volume = {130}, number = {47}, pages = {15805--15807}, abstract = {Side-chain carboxyl and carbonyl groups play a major role in protein interactions and enzyme catalysis. A series of 13C relaxation experiments is introduced to study the dynamics of carboxyl and carbonyl groups in protein side chains on both fast (sub-ns) and slower (μs-ms) time scales. This approach is illustrated on the protein calbindin D9k. Fast dynamics features correlate with hydrogen- and ion-binding patterns. We also identify chemical dynamics on μs time scales in solvent-exposed carboxyl groups, most probably due to exchange between the carboxylate and carboxylic acid forms. Copyright © 2008 American Chemical Society.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Side-chain carboxyl and carbonyl groups play a major role in protein interactions and enzyme catalysis. A series of 13C relaxation experiments is introduced to study the dynamics of carboxyl and carbonyl groups in protein side chains on both fast (sub-ns) and slower (μs-ms) time scales. This approach is illustrated on the protein calbindin D9k. Fast dynamics features correlate with hydrogen- and ion-binding patterns. We also identify chemical dynamics on μs time scales in solvent-exposed carboxyl groups, most probably due to exchange between the carboxylate and carboxylic acid forms. Copyright © 2008 American Chemical Society. |
On the measurement of 15N-1H nuclear Overhauser effects Article de journal F Ferrage; A Piserchio; D Cowburn; R Ghose Journal of Magnetic Resonance, 192 (2), p. 302–313, 2008. @article{Ferrage:2008, title = {On the measurement of 15N-1H nuclear Overhauser effects}, author = {F Ferrage and A Piserchio and D Cowburn and R Ghose}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-43949104379&doi=10.1016%2fj.jmr.2008.03.011&partnerID=40&md5=6ab29f9e3c7f7ed1e5f5d0dfe20b7788}, doi = {10.1016/j.jmr.2008.03.011}, year = {2008}, date = {2008-01-01}, journal = {Journal of Magnetic Resonance}, volume = {192}, number = {2}, pages = {302--313}, abstract = {Accurate quantification of the 15N-1H steady-state NOE is central to current methods for the elucidation of protein backbone dynamics on the fast, sub-nanosecond time scale. This experiment is highly susceptible to systematic errors arising from multiple sources. The nature of these errors and their effects on the determined NOE ratio is evaluated by a detailed analysis of the spin dynamics during the pair of experiments used to measure this ratio and possible improvements suggested. The experiment that includes 1H irradiation, is analyzed in the framework of Average Liouvillian Theory and a modified saturation scheme that generates a stable steady-state and eliminates the need to completely saturate 1H nuclei is presented. The largest source of error, however, in 1H-dilute systems at ultra-high fields is found to be an overestimation of the steady-state NOE value as a consequence of the incomplete equilibration of the magnetization in the so-called "reference experiment". The use of very long relaxation delays is usually an effective, but time consuming, solution. Here, we introduce an alternative reference experiment, designed for larger, deuterated systems, that uses the fastest relaxing component of the longitudinal magnetization as a closer approximation to the equilibrium state for shorter relaxation delays. The utility of the modified approach is illustrated through simulations on realistic spin systems over a wide range of time scales and experimentally verified using a perdeuterated sample of human ubiquitin. © 2008 Elsevier Inc. All rights reserved.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Accurate quantification of the 15N-1H steady-state NOE is central to current methods for the elucidation of protein backbone dynamics on the fast, sub-nanosecond time scale. This experiment is highly susceptible to systematic errors arising from multiple sources. The nature of these errors and their effects on the determined NOE ratio is evaluated by a detailed analysis of the spin dynamics during the pair of experiments used to measure this ratio and possible improvements suggested. The experiment that includes 1H irradiation, is analyzed in the framework of Average Liouvillian Theory and a modified saturation scheme that generates a stable steady-state and eliminates the need to completely saturate 1H nuclei is presented. The largest source of error, however, in 1H-dilute systems at ultra-high fields is found to be an overestimation of the steady-state NOE value as a consequence of the incomplete equilibration of the magnetization in the so-called "reference experiment". The use of very long relaxation delays is usually an effective, but time consuming, solution. Here, we introduce an alternative reference experiment, designed for larger, deuterated systems, that uses the fastest relaxing component of the longitudinal magnetization as a closer approximation to the equilibrium state for shorter relaxation delays. The utility of the modified approach is illustrated through simulations on realistic spin systems over a wide range of time scales and experimentally verified using a perdeuterated sample of human ubiquitin. © 2008 Elsevier Inc. All rights reserved. |
2007 |
Changing the lens: Biomolecular NMR experiments at very low and very high resolution Article de journal F Ferrage Actualite Chimique, (314), p. 23–29, 2007. @article{Ferrage:2007, title = {Changing the lens: Biomolecular NMR experiments at very low and very high resolution}, author = {F Ferrage}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-37849015253&partnerID=40&md5=d8d229b3abc672995f7ac0359fa19014}, year = {2007}, date = {2007-01-01}, journal = {Actualite Chimique}, number = {314}, pages = {23--29}, abstract = {Nuclear magnetic resonance is a versatile tool to study biological macromolecules. Several methods are commonly used to characterize the structure and dynamics of biomolecules. Two methodological approaches are reviewed in this paper: the first one, at high resolution, makes it possible to access selectively particular information in a macromolecule. This method is based on the development of a new polarization transfer technique. The second method, at low resolution, is designed to measure the translational diffusion coefficient of a macromolecule or a supramolecular object in order to evaluate its size, even in the presence of poorly resolved spectra. After an introduction of useful concepts, the two methods are presented and illustrated by applications to various proteins.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Nuclear magnetic resonance is a versatile tool to study biological macromolecules. Several methods are commonly used to characterize the structure and dynamics of biomolecules. Two methodological approaches are reviewed in this paper: the first one, at high resolution, makes it possible to access selectively particular information in a macromolecule. This method is based on the development of a new polarization transfer technique. The second method, at low resolution, is designed to measure the translational diffusion coefficient of a macromolecule or a supramolecular object in order to evaluate its size, even in the presence of poorly resolved spectra. After an introduction of useful concepts, the two methods are presented and illustrated by applications to various proteins. |
Joint composite-rotation adiabatic-sweep isotope filtration Article de journal E R Valentine; F Ferrage; F Massi; D Cowburn; A G Palmer III Journal of Biomolecular NMR, 38 (1), p. 11–22, 2007. @article{Valentine:2007, title = {Joint composite-rotation adiabatic-sweep isotope filtration}, author = {E R Valentine and F Ferrage and F Massi and D Cowburn and A G Palmer III}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-34248564601&doi=10.1007%2fs10858-006-9131-9&partnerID=40&md5=75b2a27e660afda66ed3207e4e17a110}, doi = {10.1007/s10858-006-9131-9}, year = {2007}, date = {2007-01-01}, journal = {Journal of Biomolecular NMR}, volume = {38}, number = {1}, pages = {11--22}, abstract = {Joint composite-rotation adiabatic-sweep isotope filters are derived by combining the composite-rotation [Stuart AC et al. (1999) J Am Chem Soc 121: 5346-5347] and adiabatic-sweep [Zwahlen C et al. (1997) J Am Chem Soc 119:6711-6721; Kup̂e E, Freeman R (1997) J Magn Reson 127:36-48] approaches. The joint isotope filters have improved broadband filtration performance, even for extreme values of the one-bond 1H-13C scalar coupling constants in proteins and RNA molecules. An average Hamiltonian analysis is used to describe evolution of the heteronuclear scalar coupling interaction during the adiabatic sweeps within the isotope filter sequences. The new isotope filter elements permit improved selective detection of NMR resonance signals originating from 1H spins attached to an unlabeled natural abundance component of a complex in which the other components are labeled with 13C and 15N isotopes. © Springer Science+Business Media B.V. 2007.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Joint composite-rotation adiabatic-sweep isotope filters are derived by combining the composite-rotation [Stuart AC et al. (1999) J Am Chem Soc 121: 5346-5347] and adiabatic-sweep [Zwahlen C et al. (1997) J Am Chem Soc 119:6711-6721; Kup̂e E, Freeman R (1997) J Magn Reson 127:36-48] approaches. The joint isotope filters have improved broadband filtration performance, even for extreme values of the one-bond 1H-13C scalar coupling constants in proteins and RNA molecules. An average Hamiltonian analysis is used to describe evolution of the heteronuclear scalar coupling interaction during the adiabatic sweeps within the isotope filter sequences. The new isotope filter elements permit improved selective detection of NMR resonance signals originating from 1H spins attached to an unlabeled natural abundance component of a complex in which the other components are labeled with 13C and 15N isotopes. © Springer Science+Business Media B.V. 2007. |
2006 |
Protein backbone dynamics through 13C′-13C α cross-relaxation in NMR spectroscopy Article de journal F Ferrage; P Pelupessy; D Cowburn; G Bodenhausen Journal of the American Chemical Society, 128 (34), p. 11072–11078, 2006. @article{Ferrage:2006, title = {Protein backbone dynamics through 13C′-13C α cross-relaxation in NMR spectroscopy}, author = {F Ferrage and P Pelupessy and D Cowburn and G Bodenhausen}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-33748090298&doi=10.1021%2fja0600577&partnerID=40&md5=3108730b4801207564e4694f629fd277}, doi = {10.1021/ja0600577}, year = {2006}, date = {2006-01-01}, journal = {Journal of the American Chemical Society}, volume = {128}, number = {34}, pages = {11072--11078}, abstract = {Internal dynamics of proteins are usually characterized by the analysis of 15N relaxation rates that reflect the motions of NHN vectors. It was suggested a decade ago that additional information on backbone motions can be obtained by measuring cross-relaxation rates associated with intra-residue C′Cα vectors. Here we propose a new approach to such measurements, based on the observation of the transfer between two-spin orders 2NzC′z and 2NzC z α. This amounts to "anchoring" the C′z and Cz α operators to the N z term from the amide of the next residue. In combination with symmetrical reconversion, this method greatly reduces various artifacts. The experiment is carried out on human ubiquitin at 284.1 K, where the correlation time is 7.1 ns. The motions of the C′Cα vector appear more restricted than those of the NHN vector. © 2006 American Chemical Society.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Internal dynamics of proteins are usually characterized by the analysis of 15N relaxation rates that reflect the motions of NHN vectors. It was suggested a decade ago that additional information on backbone motions can be obtained by measuring cross-relaxation rates associated with intra-residue C′Cα vectors. Here we propose a new approach to such measurements, based on the observation of the transfer between two-spin orders 2NzC′z and 2NzC z α. This amounts to "anchoring" the C′z and Cz α operators to the N z term from the amide of the next residue. In combination with symmetrical reconversion, this method greatly reduces various artifacts. The experiment is carried out on human ubiquitin at 284.1 K, where the correlation time is 7.1 ns. The motions of the C′Cα vector appear more restricted than those of the NHN vector. © 2006 American Chemical Society. |
2005 |
An approach to extract rate constants from reaction-diffusion dynamics in a microchannel Article de journal J -B Salmon; C Dubrocq; P Tabeling; S Charier; D Alcor; L Jullien; F Ferrage Analytical Chemistry, 77 (11), p. 3417–3424, 2005. @article{Salmon:2005, title = {An approach to extract rate constants from reaction-diffusion dynamics in a microchannel}, author = {J -B Salmon and C Dubrocq and P Tabeling and S Charier and D Alcor and L Jullien and F Ferrage}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-20444391378&doi=10.1021%2fac0500838&partnerID=40&md5=069b35f666f1edab8f021528a9616794}, doi = {10.1021/ac0500838}, year = {2005}, date = {2005-01-01}, journal = {Analytical Chemistry}, volume = {77}, number = {11}, pages = {3417--3424}, abstract = {A theoretical model is proposed to extract rate constants of second-order chemical reactions down to the millisecond time scale from the observation of reaction-diffusion processes in a microchannel. We validate this theoretical approach by examining an appropriate model reaction. The measured rate constant is in excellent agreement with this obtained from nuclear magnetic resonance experiments. © 2005 American Chemical Society.}, keywords = {}, pubstate = {published}, tppubtype = {article} } A theoretical model is proposed to extract rate constants of second-order chemical reactions down to the millisecond time scale from the observation of reaction-diffusion processes in a microchannel. We validate this theoretical approach by examining an appropriate model reaction. The measured rate constant is in excellent agreement with this obtained from nuclear magnetic resonance experiments. © 2005 American Chemical Society. |
Stochastic resonance to control diffusive motion in chemistry Article de journal D Alcor; J -F Allemand; E Cogné-Laage; V Croquette; F Ferrage; L Jullien; A Kononov; A Lemarchand Journal of Physical Chemistry B, 109 (3), p. 1318–1328, 2005. @article{Alcor:2005, title = {Stochastic resonance to control diffusive motion in chemistry}, author = {D Alcor and J -F Allemand and E Cogn\'{e}-Laage and V Croquette and F Ferrage and L Jullien and A Kononov and A Lemarchand}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-13444261095&doi=10.1021%2fjp0468307&partnerID=40&md5=16630c2883d35adddf4ee32f3b8185c1}, doi = {10.1021/jp0468307}, year = {2005}, date = {2005-01-01}, journal = {Journal of Physical Chemistry B}, volume = {109}, number = {3}, pages = {1318--1328}, abstract = {This paper reports on a novel procedure to tune the effective diffusion coefficient of a field-sensitive reactant in the presence of a periodic external field. We investigate the motion of two negatively charged azo dyes interacting with α-cyclodextrin (α-CD) upon action of a periodic square wave electrical field. We show that the dyes exhibit an effective diffusion coefficient Deff that depends on the rate constants for dye complexation within α-CD, the period and the amplitude of the field. UV-vis absorption, gradient field 1H NMR, and fluorescence correlation spectroscopy (FCS) after two photon excitation are used to evidence that Deff may be increased far beyond its intrinsic value when specific relations interpreted as a stochastic resonance are fulfilled. The present results may find useful applications in chemical kinetics as well as for molecular sorting.}, keywords = {}, pubstate = {published}, tppubtype = {article} } This paper reports on a novel procedure to tune the effective diffusion coefficient of a field-sensitive reactant in the presence of a periodic external field. We investigate the motion of two negatively charged azo dyes interacting with α-cyclodextrin (α-CD) upon action of a periodic square wave electrical field. We show that the dyes exhibit an effective diffusion coefficient Deff that depends on the rate constants for dye complexation within α-CD, the period and the amplitude of the field. UV-vis absorption, gradient field 1H NMR, and fluorescence correlation spectroscopy (FCS) after two photon excitation are used to evidence that Deff may be increased far beyond its intrinsic value when specific relations interpreted as a stochastic resonance are fulfilled. The present results may find useful applications in chemical kinetics as well as for molecular sorting. |
2004 |
Frequency-switched single-transition cross-polarization: A tool for selective experiments in biomolecular NMR Article de journal F Ferrage; T R Eykyn; G Bodenhausen ChemPhysChem, 5 (1), p. 76–84, 2004. @article{Ferrage:2004, title = {Frequency-switched single-transition cross-polarization: A tool for selective experiments in biomolecular NMR}, author = {F Ferrage and T R Eykyn and G Bodenhausen}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-2442499080&doi=10.1002%2fcphc.200300905&partnerID=40&md5=15bb7fd42f64fc588cdfaf1de3a4fc23}, doi = {10.1002/cphc.200300905}, year = {2004}, date = {2004-01-01}, journal = {ChemPhysChem}, volume = {5}, number = {1}, pages = {76--84}, abstract = {Frequency-switched single-transition cross-polarization (FS-ST-CP) provides a versatile tool for selective coherence transfer in heteronuclear NMR of biomolecules such as proteins and nucleic acids. This types of coherence transfer is spin-state-selective and can therefore benefit from the extension of the life-times of selected coherences due to partial cancellation of interfering relaxation mechanisms. The limits of the selectivity of the transfer are discussed by theory and illustrated by experiment. The methods are particularly efficient to obtain quantitative structural and dynamic information for selected residues in medium-sized nitrogen-15 or carbon-13 labeled macromolecules.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Frequency-switched single-transition cross-polarization (FS-ST-CP) provides a versatile tool for selective coherence transfer in heteronuclear NMR of biomolecules such as proteins and nucleic acids. This types of coherence transfer is spin-state-selective and can therefore benefit from the extension of the life-times of selected coherences due to partial cancellation of interfering relaxation mechanisms. The limits of the selectivity of the transfer are discussed by theory and illustrated by experiment. The methods are particularly efficient to obtain quantitative structural and dynamic information for selected residues in medium-sized nitrogen-15 or carbon-13 labeled macromolecules. |
2003 |
Slow diffusion of macromolecular assemblies by a new pulsed field gradient NMR method Article de journal F Ferrage; M Zoonens; D E Warschawski; J -L Popot; G Bodenhausen Journal of the American Chemical Society, 125 (9), p. 2541–2545, 2003. @article{Ferrage:2003, title = {Slow diffusion of macromolecular assemblies by a new pulsed field gradient NMR method}, author = {F Ferrage and M Zoonens and D E Warschawski and J -L Popot and G Bodenhausen}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-0242669339&doi=10.1021%2fja0211407&partnerID=40&md5=754f14f13b7ab39866044af53f46b0ae}, doi = {10.1021/ja0211407}, year = {2003}, date = {2003-01-01}, journal = {Journal of the American Chemical Society}, volume = {125}, number = {9}, pages = {2541--2545}, abstract = {The translational diffusion coefficient of an integral membrane protein/surfactant complex has been measured using a novel pulsed field gradient NMR method. In this new approach, the information about the localization of the molecules is temporarily stored in the form of longitudinal magnetization of isotopes with long spin-lattice relaxation times. This allows one to increase the duration of the diffusion interval by about 1 order of magnitude. Unlike standard proton NMR methods using pulsed field gradients and stimulated echoes, the new method can be applied to macromolecular assemblies with diffusion coefficients well below 10-10 m2 s-1, corresponding to masses in excess of 25 kDa in aqueous solution at room temperature. The method was illustrated by application to a water-soluble complex of tOmpA, the hydrophobic transmembrane domain of bacterial outer membrane protein A, with the detergent octyl-tetraoxyethylene (C8E4; overall mass of complex ∼45 kDa). The diffusion coefficient was found to be D = (4.99 ± 0.07) × 10-11 m2 s-1, consistent with measurements by size exclusion chromatography and by ultracentrifugation. The method has also been applied to a solution of recombinant human tRNA3Lys, which has a molecular mass of 24 kDa, and the diffusion coefficient D = (1.05 ± 0.015) × 10-10 m2 s-1.}, keywords = {}, pubstate = {published}, tppubtype = {article} } The translational diffusion coefficient of an integral membrane protein/surfactant complex has been measured using a novel pulsed field gradient NMR method. In this new approach, the information about the localization of the molecules is temporarily stored in the form of longitudinal magnetization of isotopes with long spin-lattice relaxation times. This allows one to increase the duration of the diffusion interval by about 1 order of magnitude. Unlike standard proton NMR methods using pulsed field gradients and stimulated echoes, the new method can be applied to macromolecular assemblies with diffusion coefficients well below 10-10 m2 s-1, corresponding to masses in excess of 25 kDa in aqueous solution at room temperature. The method was illustrated by application to a water-soluble complex of tOmpA, the hydrophobic transmembrane domain of bacterial outer membrane protein A, with the detergent octyl-tetraoxyethylene (C8E4; overall mass of complex ∼45 kDa). The diffusion coefficient was found to be D = (4.99 ± 0.07) × 10-11 m2 s-1, consistent with measurements by size exclusion chromatography and by ultracentrifugation. The method has also been applied to a solution of recombinant human tRNA3Lys, which has a molecular mass of 24 kDa, and the diffusion coefficient D = (1.05 ± 0.015) × 10-10 m2 s-1. |
2002 |
Highly selective excitation in biomolecular NMR by frequency-switched single-transition cross-polarization Article de journal F Ferrage; T R Eykyn; G Bodenhausen Journal of the American Chemical Society, 124 (10), p. 2076–2077, 2002. @article{Ferrage:2002, title = {Highly selective excitation in biomolecular NMR by frequency-switched single-transition cross-polarization}, author = {F Ferrage and T R Eykyn and G Bodenhausen}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-0037070539&doi=10.1021%2fja012452x&partnerID=40&md5=09679a64024130c23edb55660347b015}, doi = {10.1021/ja012452x}, year = {2002}, date = {2002-01-01}, journal = {Journal of the American Chemical Society}, volume = {124}, number = {10}, pages = {2076--2077}, abstract = {A new method for selective excitation in biomolecular NMR uses two-fold single-transition cross-polarization between protons and nitrogen-15 or carbon-13 nuclei. Switching the frequencies between the forward and backward transfer steps allows one to select a multiplet pattern that is associated with a single pair of spins in a medium-size protein. The efficiency of the transfer benefits from so-called TROSY line-narrowing effects which arise from interference between relaxation mechanisms. Copyright © 2002 American Chemical Society.}, keywords = {}, pubstate = {published}, tppubtype = {article} } A new method for selective excitation in biomolecular NMR uses two-fold single-transition cross-polarization between protons and nitrogen-15 or carbon-13 nuclei. Switching the frequencies between the forward and backward transfer steps allows one to select a multiplet pattern that is associated with a single pair of spins in a medium-size protein. The efficiency of the transfer benefits from so-called TROSY line-narrowing effects which arise from interference between relaxation mechanisms. Copyright © 2002 American Chemical Society. |
Synthesis and properties of water-soluble gold colloids covalently derivatized with neutral polymer monolayers Article de journal C Mangeney; F Ferrage; I Aujard; V Artzner; L Jullien; O Ouari; E Djouhar Rékai; A Laschewsky; I Vikholm; J W Sadowski Journal of the American Chemical Society, 124 (20), p. 5811–5821, 2002. @article{Mangeney:2002, title = {Synthesis and properties of water-soluble gold colloids covalently derivatized with neutral polymer monolayers}, author = {C Mangeney and F Ferrage and I Aujard and V Artzner and L Jullien and O Ouari and E Djouhar R\'{e}kai and A Laschewsky and I Vikholm and J W Sadowski}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-0037157185&doi=10.1021%2fja010796h&partnerID=40&md5=0866a4217a986ce8c43d1a84df5645a0}, doi = {10.1021/ja010796h}, year = {2002}, date = {2002-01-01}, journal = {Journal of the American Chemical Society}, volume = {124}, number = {20}, pages = {5811--5821}, abstract = {Citrate-capped gold nanoparticles as well as planar gold surfaces can be efficiently grafted with a covalently attached polymer monolayer a few nanometers thick, by simple contact of the metal surface with dilute aqueous solutions of hydrophilic polymers that are end-capped with disulfide moieties, as shown by UV/vis absorption, dynamic light scattering, and surface plasmon resonance studies. The hydrophilic polymer-coated gold colloids can be freeze-dried and stored as powders that can be subsequently dissolved to yield stable aqueous dispersions, even at very large concentrations. They allow for applying filtrations, gel permeation chromatography, or centrifugation. They do not suffer from undesirable nonspecific adsorption of proteins while allowing the diffusion of small species within the hydrogel surface coating. In addition, specific properties of the original hydrophilic polymers are retained such as a lower critical solution temperature. The latter feature could be useful to enhance optical responses of functionalized gold surfaces toward interaction with various substrates.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Citrate-capped gold nanoparticles as well as planar gold surfaces can be efficiently grafted with a covalently attached polymer monolayer a few nanometers thick, by simple contact of the metal surface with dilute aqueous solutions of hydrophilic polymers that are end-capped with disulfide moieties, as shown by UV/vis absorption, dynamic light scattering, and surface plasmon resonance studies. The hydrophilic polymer-coated gold colloids can be freeze-dried and stored as powders that can be subsequently dissolved to yield stable aqueous dispersions, even at very large concentrations. They allow for applying filtrations, gel permeation chromatography, or centrifugation. They do not suffer from undesirable nonspecific adsorption of proteins while allowing the diffusion of small species within the hydrogel surface coating. In addition, specific properties of the original hydrophilic polymers are retained such as a lower critical solution temperature. The latter feature could be useful to enhance optical responses of functionalized gold surfaces toward interaction with various substrates. |
Quasi-isotropic single-transition cross-polarization in nuclear magnetic resonance Article de journal T R Eykyn; F Ferrage; G Bodenhausen Journal of Chemical Physics, 116 (23), p. 10041–10050, 2002. @article{Eykyn:2002, title = {Quasi-isotropic single-transition cross-polarization in nuclear magnetic resonance}, author = {T R Eykyn and F Ferrage and G Bodenhausen}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-0037162260&doi=10.1063%2f1.1477176&partnerID=40&md5=fb47c40fc7f3bf8f438fcd34eeaf7ec8}, doi = {10.1063/1.1477176}, year = {2002}, date = {2002-01-01}, journal = {Journal of Chemical Physics}, volume = {116}, number = {23}, pages = {10041--10050}, abstract = {An investigation of the theory of single-transition (ST) cross-polarization (CP) in nuclear magnetic resonance (NMR) was presented and verified by experimental evidence. Investigation was done under the influence of two extremely weak constant-amplitude radio frequency (rf) fields applied to two connected single-transition coherences which shared a common eigenstate. The results showed that ST-CP was quasi-isotropic in the sense that all three components, Sx, Sy and Sz, of the angular momentum of a spin were transfered simultaneously to all three components Ix, Iy and Iz.}, keywords = {}, pubstate = {published}, tppubtype = {article} } An investigation of the theory of single-transition (ST) cross-polarization (CP) in nuclear magnetic resonance (NMR) was presented and verified by experimental evidence. Investigation was done under the influence of two extremely weak constant-amplitude radio frequency (rf) fields applied to two connected single-transition coherences which shared a common eigenstate. The results showed that ST-CP was quasi-isotropic in the sense that all three components, Sx, Sy and Sz, of the angular momentum of a spin were transfered simultaneously to all three components Ix, Iy and Iz. |
2000 |
Coherence transfer by single-transition cross-polarization: quantitation of cross-correlation effects in nuclear magnetic resonance Article de journal F Ferrage; T R Eykyn; G Bodenhausen Journal of Chemical Physics, 113 (3), p. 1081–1087, 2000. @article{Ferrage:2000, title = {Coherence transfer by single-transition cross-polarization: quantitation of cross-correlation effects in nuclear magnetic resonance}, author = {F Ferrage and T R Eykyn and G Bodenhausen}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-0034229257&doi=10.1063%2f1.481958&partnerID=40&md5=ee6ea9fd6547a382a516fbf30e871949}, doi = {10.1063/1.481958}, year = {2000}, date = {2000-01-01}, journal = {Journal of Chemical Physics}, volume = {113}, number = {3}, pages = {1081--1087}, abstract = {A study was carried out to demonstrate the possibility of transferring coherence by selective cross-polarization between two transitions in a four-level system consisting of scalar coupled spins I = 1/2 and S = 1/2 in isotropic solution. Cross-polarization provided the selectivity to confine the evolution of the single-transition coherence within two mutually exclusive subspaces of the Liouville space.}, keywords = {}, pubstate = {published}, tppubtype = {article} } A study was carried out to demonstrate the possibility of transferring coherence by selective cross-polarization between two transitions in a four-level system consisting of scalar coupled spins I = 1/2 and S = 1/2 in isotropic solution. Cross-polarization provided the selectivity to confine the evolution of the single-transition coherence within two mutually exclusive subspaces of the Liouville space. |
Single-transition coherence transfer by adiabatic cross polarization in NMR Article de journal T R Eykyn; F Ferrage; E Winterfors; G Bodenhausen ChemPhysChem, 1 (4), p. 217–221, 2000. @article{Eykyn:2000, title = {Single-transition coherence transfer by adiabatic cross polarization in NMR}, author = {T R Eykyn and F Ferrage and E Winterfors and G Bodenhausen}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-0000511343&partnerID=40&md5=f3592a241ff561508eeb7f9082d7beef}, year = {2000}, date = {2000-01-01}, journal = {ChemPhysChem}, volume = {1}, number = {4}, pages = {217--221}, keywords = {}, pubstate = {published}, tppubtype = {article} } |