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
2023 |
Efficient 18.8 T MAS-DNP NMR reveals hidden side chains in amyloid fibrils Article de journal Alons Lends; Nicolas Birlirakis; Xinyi Cai; Asen Daskalov; Jayakrishna Shenoy; Muhammed Bilal; Mélanie Berbon; Fabien Ferrage; Yangping Liu; Antoine Loquet; Kong Ooi Tan Journal of Biomolecular NMR, 77 , 2023. @article{Lends2023, title = {Efficient 18.8 T MAS-DNP NMR reveals hidden side chains in amyloid fibrils}, author = {Alons Lends and Nicolas Birlirakis and Xinyi Cai and Asen Daskalov and Jayakrishna Shenoy and Muhammed Bilal and M\'{e}lanie Berbon and Fabien Ferrage and Yangping Liu and Antoine Loquet and Kong Ooi Tan}, url = {https://link.springer.com/article/10.1007/s10858-023-00416-5}, doi = {10.1007/s10858-023-00416-5}, year = {2023}, date = {2023-06-08}, journal = {Journal of Biomolecular NMR}, volume = {77}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
2022 |
Explicit models of motions to understand protein side-chain dynamics Article de journal Nicolas Bolik-Coulon; Olivier Languin-Cattoën; Diego Carnevale; Milan Zachrdla; Damien Laage; Fabio Sterpone; Guillaume Stirnemann; Fabien Ferrage Physical Review Letters, 129 , p. 203001, 2022. @article{Bolik-Coulon2022b, title = {Explicit models of motions to understand protein side-chain dynamics}, author = {Nicolas Bolik-Coulon and Olivier Languin-Catto\"{e}n and Diego Carnevale and Milan Zachrdla and Damien Laage and Fabio Sterpone and Guillaume Stirnemann and Fabien Ferrage }, url = {https://doi.org/10.1103/PhysRevLett.129.203001 }, doi = {10.1103/PhysRevLett.129.203001 }, year = {2022}, date = {2022-11-10}, journal = {Physical Review Letters}, volume = {129 }, pages = {203001}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Convergent Views on Disordered Protein Dynamics From NMR and Computational Approaches Article de journal Nicola Salvi; Vojtěch Zapletal; Zuzana Jaseňáková; Milan Zachrdla; Petr Padrta; Subhash Narasimhan; Thorsten Marquardsen; Jean-Max Tyburn; Lukáš Žídek; Martin Blackledge; Fabien Ferrage; Pavel Kadeřávek Biophysical Journal, 121 , p. 3785, 2022. @article{Salvi2022, title = {Convergent Views on Disordered Protein Dynamics From NMR and Computational Approaches}, author = {Nicola Salvi and Vojtv{e}ch Zapletal and Zuzana Jasev{n}\'{a}kov\'{a} and Milan Zachrdla and Petr Padrta and Subhash Narasimhan and Thorsten Marquardsen and Jean-Max Tyburn and Luk\'{a}\v{s} {\v{Z}}\'{i}dek and Martin Blackledge and Fabien Ferrage and Pavel Kade\v{r}\'{a}vek }, url = {https://doi.org/10.1016/j.bpj.2022.09.016 }, doi = {10.1016/j.bpj.2022.09.016 }, year = {2022}, date = {2022-10-18}, journal = {Biophysical Journal}, volume = {121}, pages = {3785}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Explicit models of motions to analyze NMR relaxation data in proteins Article de journal Nicolas Bolik-Coulon; Fabien Ferrage The Journal of Chemical Physics, 157 , p. 125102, 2022. @article{Bolik-Coulon2022, title = {Explicit models of motions to analyze NMR relaxation data in proteins}, author = {Nicolas Bolik-Coulon and Fabien Ferrage}, url = {https://doi.org/10.1063/5.0095910 }, doi = {10.1063/5.0095910 }, year = {2022}, date = {2022-09-30}, journal = {The Journal of Chemical Physics}, volume = {157}, pages = {125102}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
How does it really move? Recent progress in the investigation of protein nanosecond dynamics by NMR and simulation Article de journal Olof Stenström; Candide Champion; Marc Lehner; Guillaume Bouvignies; Sereina Ringer; Fabien Ferrage Current Opinion in Structural Biology, 77 , p. 102459, 2022. @article{Stenstr\"{o}m2022, title = {How does it really move? Recent progress in the investigation of protein nanosecond dynamics by NMR and simulation}, author = {Olof Stenstr\"{o}m and Candide Champion and Marc Lehner and Guillaume Bouvignies and Sereina Ringer and Fabien Ferrage}, url = {https://doi.org/10.1016/j.sbi.2022.102459 }, doi = {10.1016/j.sbi.2022.102459 }, year = {2022}, date = {2022-09-20}, journal = {Current Opinion in Structural Biology}, volume = {77}, pages = {102459}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
The soft breeze of the cation atmosphere around DNA Article de journal Fabien Ferrage; Damien Laage Biophysical Journal, 121 , p. 3307, 2022. @article{Ferrage2022, title = {The soft breeze of the cation atmosphere around DNA}, author = {Fabien Ferrage and Damien Laage }, url = {https://doi.org/10.1016/j.bpj.2022.08.003 }, doi = {10.1016/j.bpj.2022.08.003 }, year = {2022}, date = {2022-09-20}, journal = {Biophysical Journal}, volume = {121}, pages = {3307}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Explicit models of motions to understand protein side-chain dynamics Article de journal Nicolas Bolik-Coulon; Olivier Languin-Cattoën; Diego Carnevale; Milan Zachrdla; Damien Laage; Fabio Sterpone; Guillaume Stirnemann; Fabien Ferrage Phys Rev Lett, 129 , p. 203001, 2022. @article{, title = {Explicit models of motions to understand protein side-chain dynamics}, author = {Nicolas Bolik-Coulon and Olivier Languin-Catto\"{e}n and Diego Carnevale and Milan Zachrdla and Damien Laage and Fabio Sterpone and Guillaume Stirnemann and Fabien Ferrage}, year = {2022}, date = {2022-01-01}, journal = {Phys Rev Lett}, volume = {129}, pages = {203001}, abstract = {Nuclear magnetic relaxation is widely used to probe protein dynamics. For decades, most analyses of relaxation in proteins have relied successfully on the model-free approach, forgoing mechanistic descriptions of motion. Model-free types of correlation functions cannot describe a large carbon-13 relaxation dataset in protein side chains. Here, we use molecular dynamics simulations to design explicit models of motion and solve Fokker-Planck diffusion equations. These models of motion provide better agreement with relaxation data, mechanistic insight, and a direct link to configuration entropy.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Nuclear magnetic relaxation is widely used to probe protein dynamics. For decades, most analyses of relaxation in proteins have relied successfully on the model-free approach, forgoing mechanistic descriptions of motion. Model-free types of correlation functions cannot describe a large carbon-13 relaxation dataset in protein side chains. Here, we use molecular dynamics simulations to design explicit models of motion and solve Fokker-Planck diffusion equations. These models of motion provide better agreement with relaxation data, mechanistic insight, and a direct link to configuration entropy. |
2021 |
Detection of Metabolite–Protein Interactions in Complex Biological Samples by High-Resolution Relaxometry: Toward Interactomics by NMR Article de journal Ziqing Wang, Simone Pisano, Veronica Ghini, Pavel Kadeřávek, Milan Zachrdla, Philippe Pelupessy, Morgan Kazmierczak, Thorsten Marquardsen, Jean-Max Tyburn, Guillaume Bouvignies, Giacomo Parigi, Claudio Luchinat,; Fabien Ferrage J. Am. Chem. Soc., 143 , p. 9393–9404, 2021. @article{wang2021, title = {Detection of Metabolite\textendashProtein Interactions in Complex Biological Samples by High-Resolution Relaxometry: Toward Interactomics by NMR}, author = {Ziqing Wang, Simone Pisano, Veronica Ghini, Pavel Kade\v{r}\'{a}vek, Milan Zachrdla, Philippe Pelupessy, Morgan Kazmierczak, Thorsten Marquardsen, Jean-Max Tyburn, Guillaume Bouvignies, Giacomo Parigi, Claudio Luchinat, and Fabien Ferrage}, url = {https://pubs.acs.org/doi/abs/10.1021/jacs.1c01388}, doi = {10.1021/jacs.1c01388}, year = {2021}, date = {2021-06-16}, journal = {J. Am. Chem. Soc.}, volume = {143}, pages = {9393\textendash9404}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Sequential assignment of NMR spectra of peptides at natural isotopic abundance with zero- and ultra-low-field total correlation spectroscopy (ZULF-TOCSY) Article de journal Alexey S. Kiryutin, Ivan V. Zhukov, Fabien Ferrage, Geoffrey Bodenhausen, Alexandra V. Yurkovskaya; Konstantin L. Ivanov Phys. Chem. Chem. Phys., 23 , p. 29715-9720 , 2021. @article{zulfTOCSY2021, title = {Sequential assignment of NMR spectra of peptides at natural isotopic abundance with zero- and ultra-low-field total correlation spectroscopy (ZULF-TOCSY)}, author = {Alexey S. Kiryutin, Ivan V. Zhukov, Fabien Ferrage, Geoffrey Bodenhausen, Alexandra V. Yurkovskaya and Konstantin L. Ivanov}, url = {https://pubs.rsc.org/en/content/articlelanding/2021/cp/d0cp06337a/unauth}, doi = {10.1039/D0CP06337A}, year = {2021}, date = {2021-04-09}, journal = {Phys. Chem. Chem. Phys.}, volume = {23}, pages = {29715-9720 }, keywords = {}, pubstate = {published}, tppubtype = {article} } |
How wide is the window opened by high-resolution relaxometry on the internal dynamics of proteins in solution? Article de journal Albert A. Smith, Nicolas Bolik-Coulon, Matthias Ernst, Beat H. Meier; Fabien Ferrage J. Biomol. NMR, 75 , p. 119–131, 2021. @article{smith2021, title = {How wide is the window opened by high-resolution relaxometry on the internal dynamics of proteins in solution?}, author = {Albert A. Smith, Nicolas Bolik-Coulon, Matthias Ernst, Beat H. Meier and Fabien Ferrage }, url = {https://link.springer.com/article/10.1007/s10858-021-00361-1}, doi = {10.1007/s10858-021-00361-1}, year = {2021}, date = {2021-03-23}, journal = {J. Biomol. NMR}, volume = {75}, pages = {119\textendash131}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
2020 |
Two-field transverse relaxation-optimized spectroscopy for the study of large biomolecules – An in silico investigation Article de journal Nicolas Bolik-Coulon, Philippe Pelupessy, Guillaume Bouvignies; Fabien Ferrage Journal of Magnetic Resonance Open, 4 , p. 100007, 2020. @article{2FTROSY2020, title = {Two-field transverse relaxation-optimized spectroscopy for the study of large biomolecules \textendash An in silico investigation}, author = {Nicolas Bolik-Coulon, Philippe Pelupessy, Guillaume Bouvignies and Fabien Ferrage}, url = {https://www.sciencedirect.com/science/article/pii/S2666441020300078}, doi = {10.1016/j.jmro.2020.100007}, year = {2020}, date = {2020-11-16}, journal = {Journal of Magnetic Resonance Open}, volume = {4}, pages = {100007}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Surprising absence of strong homonuclear coupling at low magnetic field explored by two-field nuclear magnetic resonance spectroscopy Article de journal Ivan V. Zhukov, Alexey S. Kiryutin, Ziqing Wang, Milan Zachrdla, Alexandra V. Yurkovskaya, Konstantin L. Ivanov; Fabien Ferrage Magnetic Resonance, 1 , p. 237–246, 2020. @article{surprising2020, title = {Surprising absence of strong homonuclear coupling at low magnetic field explored by two-field nuclear magnetic resonance spectroscopy}, author = {Ivan V. Zhukov, Alexey S. Kiryutin, Ziqing Wang, Milan Zachrdla, Alexandra V. Yurkovskaya, Konstantin L. Ivanov and Fabien Ferrage}, url = {https://mr.copernicus.org/articles/1/237/2020/}, doi = {10.5194/mr-1-237-2020}, year = {2020}, date = {2020-10-14}, journal = {Magnetic Resonance}, volume = {1}, pages = {237\textendash246}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Total Correlation Spectroscopy across All NMR-Active Nuclei by Mixing at Zero Field Article de journal Ivan V. Zhukov, Alexey S. Kiryutin, Fabien Ferrage, Gerd Buntkowsky, Alexandra V. Yurkovskaya,; Konstantin L. Ivanov J. Phys. Chem. Lett., 11 (17), p. 7291–7296, 2020. @article{zulfTOCSY2020, title = {Total Correlation Spectroscopy across All NMR-Active Nuclei by Mixing at Zero Field}, author = {Ivan V. Zhukov, Alexey S. Kiryutin, Fabien Ferrage, Gerd Buntkowsky, Alexandra V. Yurkovskaya, and Konstantin L. Ivanov}, url = {https://pubs.acs.org/doi/abs/10.1021/acs.jpclett.0c02032}, doi = {10.1021/acs.jpclett.0c02032}, year = {2020}, date = {2020-08-10}, journal = {J. Phys. Chem. Lett.}, volume = {11}, number = {17}, pages = {7291\textendash7296}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Theoretical and computational framework for the analysis of the relaxation properties of arbitrary spin systems. Application to high-resolution relaxometry Article de journal Nicolas Bolik-Coulon; Pavel Kadeřávek; Philippe Pelupessy; Jean-Nicolas Dumez; Fabien Ferrage; Samuel F Cousin Journal of Magnetic Resonance, 313 , p. 106718, 2020, ISSN: 10907807. @article{Bolik-Coulon2020b, title = {Theoretical and computational framework for the analysis of the relaxation properties of arbitrary spin systems. Application to high-resolution relaxometry}, author = {Nicolas Bolik-Coulon and Pavel Kade\v{r}\'{a}vek and Philippe Pelupessy and Jean-Nicolas Dumez and Fabien Ferrage and Samuel F Cousin}, url = {https://linkinghub.elsevier.com/retrieve/pii/S1090780720300367}, doi = {10.1016/j.jmr.2020.106718}, issn = {10907807}, year = {2020}, date = {2020-04-01}, journal = {Journal of Magnetic Resonance}, volume = {313}, pages = {106718}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Theoretical and computational framework for the analysis of the relaxation properties of arbitrary spin systems. Application to high-resolution relaxometry Article de journal N Bolik-Coulon; P Kadeřávek; P Pelupessy; J-N Dumez; F Ferrage; S F Cousin Journal of Magnetic Resonance, 313 , p. 106718, 2020. @article{Bolik-Coulon2020, title = {Theoretical and computational framework for the analysis of the relaxation properties of arbitrary spin systems. Application to high-resolution relaxometry}, author = {N Bolik-Coulon and P Kade\v{r}\'{a}vek and P Pelupessy and J-N Dumez and F Ferrage and S F Cousin}, doi = {10.1016/j.jmr.2020.106718}, year = {2020}, date = {2020-03-16}, journal = {Journal of Magnetic Resonance}, volume = {313}, pages = {106718}, abstract = {A wide variety of nuclear magnetic resonance experiments rely on the prediction and analysis of relax- ation processes. Recently, innovative approaches have been introduced where the sample travels through a broad range of magnetic fields in the course of the experiment, such as dissolution dynamic nuclear polarization or high-resolution relaxometry. Understanding the relaxation properties of nuclear spin systems over orders of magnitude of magnetic fields is essential to rationalize the results of these exper- iments. For example, during a high-resolution relaxometry experiment, the absence of control of nuclear spin relaxation pathways during the sample transfers and relaxation delays leads to systematic devia- tions of polarization decays from an ideal mono-exponential decay with the pure longitudinal relaxation rate. These deviations have to be taken into account to describe quantitatively the dynamics of the sys- tem. Here, we present computational tools to (1) calculate analytical expressions of relaxation rates for a broad variety of spin systems and (2) use these analytical expressions to correct the deviations arising in high-resolution relaxometry experiments. These tools lead to a better understanding of nuclear spin relaxation, which is required to improve the sensitivity of many pulse sequences, and to better charac- terize motions in macromolecules.}, keywords = {}, pubstate = {published}, tppubtype = {article} } A wide variety of nuclear magnetic resonance experiments rely on the prediction and analysis of relax- ation processes. Recently, innovative approaches have been introduced where the sample travels through a broad range of magnetic fields in the course of the experiment, such as dissolution dynamic nuclear polarization or high-resolution relaxometry. Understanding the relaxation properties of nuclear spin systems over orders of magnitude of magnetic fields is essential to rationalize the results of these exper- iments. For example, during a high-resolution relaxometry experiment, the absence of control of nuclear spin relaxation pathways during the sample transfers and relaxation delays leads to systematic devia- tions of polarization decays from an ideal mono-exponential decay with the pure longitudinal relaxation rate. These deviations have to be taken into account to describe quantitatively the dynamics of the sys- tem. Here, we present computational tools to (1) calculate analytical expressions of relaxation rates for a broad variety of spin systems and (2) use these analytical expressions to correct the deviations arising in high-resolution relaxometry experiments. These tools lead to a better understanding of nuclear spin relaxation, which is required to improve the sensitivity of many pulse sequences, and to better charac- terize motions in macromolecules. |
Boosting the resolution of low-field $$^15hbox N$$ relaxation experiments on intrinsically disordered proteins with triple-resonance NMR Article de journal Zuzana Jaseňáková; Vojtěch Zapletal; Petr Padrta; Milan Zachrdla; Nicolas Bolik-Coulon; Thorsten Marquardsen; Jean-Max Tyburn; Lukáš Žídek; Fabien Ferrage; Pavel Kadeřávek Journal of Biomolecular NMR, 74 (2-3), p. 139–145, 2020, ISSN: 0925-2738. @article{Jasenakova2020b, title = {Boosting the resolution of low-field $$^15hbox N$$ relaxation experiments on intrinsically disordered proteins with triple-resonance NMR}, author = {Zuzana Jasev{n}\'{a}kov\'{a} and Vojt{v{e}}ch Zapletal and Petr Padrta and Milan Zachrdla and Nicolas Bolik-Coulon and Thorsten Marquardsen and Jean-Max Tyburn and Luk\'{a}\v{s} {\v{Z}}\'{i}dek and Fabien Ferrage and Pavel Kade\v{r}\'{a}vek}, url = {http://link.springer.com/10.1007/s10858-019-00298-6}, doi = {10.1007/s10858-019-00298-6}, issn = {0925-2738}, year = {2020}, date = {2020-03-01}, journal = {Journal of Biomolecular NMR}, volume = {74}, number = {2-3}, pages = {139--145}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Sensitivity-enhanced three-dimensional and carbon-detected two-dimensional NMR of proteins using hyperpolarized water Article de journal Gregory L Olsen; Or Szekely; Borja Mateos; Pavel Kadeřávek; Fabien Ferrage; Robert Konrat; Roberta Pierattelli; Isabella C Felli; Geoffrey Bodenhausen; Dennis Kurzbach; Lucio Frydman Journal of Biomolecular NMR, 74 (2-3), p. 161–171, 2020, ISSN: 0925-2738. @article{Olsen2020, title = {Sensitivity-enhanced three-dimensional and carbon-detected two-dimensional NMR of proteins using hyperpolarized water}, author = {Gregory L Olsen and Or Szekely and Borja Mateos and Pavel Kade\v{r}\'{a}vek and Fabien Ferrage and Robert Konrat and Roberta Pierattelli and Isabella C Felli and Geoffrey Bodenhausen and Dennis Kurzbach and Lucio Frydman}, url = {http://link.springer.com/10.1007/s10858-020-00301-5}, doi = {10.1007/s10858-020-00301-5}, issn = {0925-2738}, year = {2020}, date = {2020-03-01}, journal = {Journal of Biomolecular NMR}, volume = {74}, number = {2-3}, pages = {161--171}, abstract = {Signal enhancements of up to two orders of magnitude in protein NMR can be achieved by employing HDO as a vector to introduce hyperpolarization into folded or intrinsically disordered proteins. In this approach, hyperpolarized HDO produced by dissolution-dynamic nuclear polarization (D-DNP) is mixed with a protein solution waiting in a high-field NMR spectrometer, whereupon amide proton exchange and nuclear Overhauser effects (NOE) transfer hyperpolarization to the protein and enable acquisition of a signal-enhanced high-resolution spectrum. To date, the use of this strategy has been limited to 1D and 1 H- 15 N 2D correlation experiments. Here we introduce 2D 13 C-detected D-DNP, to reduce exchange-induced broadening and other relaxation penalties that can adversely affect proton-detected D-DNP experiments. We also introduce hyperpolarized 3D spectroscopy, opening the possibility of D-DNP studies of larger proteins and IDPs, where assignment and residue-specific investigation may be impeded by spectral crowding. The signal enhancements obtained depend in particular on the rates of chemical and magnetic exchange of the observed residues, thus resulting in non-uniform ‘hyperpolarization-selective' signal enhancements. The resulting spectral sparsity, however, makes it possible to resolve and monitor individual amino acids in IDPs of over 200 residues at acquisition times of just over a minute. We apply the proposed experiments to two model systems: the compactly folded protein ubiquitin, and the intrinsically disordered protein (IDP) osteopontin (OPN).}, keywords = {}, pubstate = {published}, tppubtype = {article} } Signal enhancements of up to two orders of magnitude in protein NMR can be achieved by employing HDO as a vector to introduce hyperpolarization into folded or intrinsically disordered proteins. In this approach, hyperpolarized HDO produced by dissolution-dynamic nuclear polarization (D-DNP) is mixed with a protein solution waiting in a high-field NMR spectrometer, whereupon amide proton exchange and nuclear Overhauser effects (NOE) transfer hyperpolarization to the protein and enable acquisition of a signal-enhanced high-resolution spectrum. To date, the use of this strategy has been limited to 1D and 1 H- 15 N 2D correlation experiments. Here we introduce 2D 13 C-detected D-DNP, to reduce exchange-induced broadening and other relaxation penalties that can adversely affect proton-detected D-DNP experiments. We also introduce hyperpolarized 3D spectroscopy, opening the possibility of D-DNP studies of larger proteins and IDPs, where assignment and residue-specific investigation may be impeded by spectral crowding. The signal enhancements obtained depend in particular on the rates of chemical and magnetic exchange of the observed residues, thus resulting in non-uniform ‘hyperpolarization-selective' signal enhancements. The resulting spectral sparsity, however, makes it possible to resolve and monitor individual amino acids in IDPs of over 200 residues at acquisition times of just over a minute. We apply the proposed experiments to two model systems: the compactly folded protein ubiquitin, and the intrinsically disordered protein (IDP) osteopontin (OPN). |
Boosting the resolution of low‐field 15N relaxation experiments on intrinsically disordered proteins with triple‐resonance NMR Article de journal Z Jasenáková; V Zapletal; P Padrta; M Zachrdla; N Bolik-Coulon; T Marquardsen; J-M Tyburn; L Zidek; F Ferrage Journal of Biomolecular NMR, 74 , p. 139, 2020. @article{Jasen\'{a}kov\'{a}2020, title = {Boosting the resolution of low‐field 15N relaxation experiments on intrinsically disordered proteins with triple‐resonance NMR}, author = {Z Jasen\'{a}kov\'{a} and V Zapletal and P Padrta and M Zachrdla and N Bolik-Coulon and T Marquardsen and J-M Tyburn and L Zidek and F Ferrage }, doi = {10.1007/s10858-019-00298-6}, year = {2020}, date = {2020-01-20}, journal = {Journal of Biomolecular NMR}, volume = {74}, pages = {139}, abstract = {Improving our understanding of nanosecond motions in disordered proteins requires the enhanced sampling of the spectral density function obtained from relaxation at low magnetic fields. High-resolution relaxometry and two-field NMR meas- urements of relaxation have, so far, only been based on the recording of one- or two-dimensional spectra, which provide insufficient resolution for challenging disordered proteins. Here, we introduce a 3D-HNCO-based two-field NMR experi- ment for measurements of protein backbone 15N amide longitudinal relaxation rates. The experiment provides accurate longitudinal relaxation rates at low field (0.33 T in our case) preserving the resolution and sensitivity typical for high-field NMR spectroscopy. Radiofrequency pulses applied on six different radiofrequency channels are used to manipulate the spin system at both fields. The experiment was demonstrated on the C-terminal domain of ???? subunit of RNA polymerase from Bacillus subtilis, a protein with highly repetitive amino-acid sequence and very low dispersion of backbone chemical shifts.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Improving our understanding of nanosecond motions in disordered proteins requires the enhanced sampling of the spectral density function obtained from relaxation at low magnetic fields. High-resolution relaxometry and two-field NMR meas- urements of relaxation have, so far, only been based on the recording of one- or two-dimensional spectra, which provide insufficient resolution for challenging disordered proteins. Here, we introduce a 3D-HNCO-based two-field NMR experi- ment for measurements of protein backbone 15N amide longitudinal relaxation rates. The experiment provides accurate longitudinal relaxation rates at low field (0.33 T in our case) preserving the resolution and sensitivity typical for high-field NMR spectroscopy. Radiofrequency pulses applied on six different radiofrequency channels are used to manipulate the spin system at both fields. The experiment was demonstrated on the C-terminal domain of ???? subunit of RNA polymerase from Bacillus subtilis, a protein with highly repetitive amino-acid sequence and very low dispersion of backbone chemical shifts. |
2019 |
Protein Dynamics from Accurate Low-Field Site-Specific Longitudinal and Transverse Nuclear Spin Relaxation Article de journal P Kadeřávek; N Bolik-Coulon; S F Cousin; T Marquardsen; J-M Tyburn; J-N Dumez; F Ferrage The Journal of Physical Chemistry Letters, 10 , p. 5917, 2019. @article{Kade\v{r}\'{a}vek2019, title = {Protein Dynamics from Accurate Low-Field Site-Specific Longitudinal and Transverse Nuclear Spin Relaxation}, author = {P Kade\v{r}\'{a}vek and N Bolik-Coulon and S F Cousin and T Marquardsen and J-M Tyburn and J-N Dumez and F Ferrage}, url = {https://pubs.acs.org/doi/10.1021/acs.jpclett.9b02233}, doi = {10.1021/acs.jpclett.9b02233}, year = {2019}, date = {2019-09-11}, journal = {The Journal of Physical Chemistry Letters}, volume = {10}, pages = {5917}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Reducing bias in the analysis of solution-state NMR data with dynamics detectors Article de journal Albert A. Smith; Matthias Ernst; Beat H. Meier; Fabien Ferrage Journal of Chemical Physics, 151 , p. 034102, 2019. @article{Smith2019b, title = {Reducing bias in the analysis of solution-state NMR data with dynamics detectors}, author = {Albert A. Smith and Matthias Ernst and Beat H. Meier and Fabien Ferrage}, url = {https://aip.scitation.org/doi/full/10.1063/1.5111081 https://arxiv.org/abs/1812.01890}, doi = {https://doi.org/10.1063/1.5111081}, year = {2019}, date = {2019-07-15}, journal = {Journal of Chemical Physics}, volume = {151}, pages = {034102}, keywords = {}, pubstate = {published}, tppubtype = {article} } |
Experimental characterization of the dynamics of IDPs and IDRs by NMR Livre N Bolik-Coulon; G Bouvignies; L Carlier; F Ferrage 2019, ISBN: 9780128163481. @book{Bolik-Coulon2019b, title = {Experimental characterization of the dynamics of IDPs and IDRs by NMR}, author = {N Bolik-Coulon and G Bouvignies and L Carlier and F Ferrage}, editor = {N Salvi}, url = {http://www.sciencedirect.com/science/article/pii/B978012816348100003X}, doi = {10.1016/B978-0-12-816348-1.00003-X}, isbn = {9780128163481}, year = {2019}, date = {2019-07-01}, series = {Intrinsically Disordered Proteins}, keywords = {}, pubstate = {published}, tppubtype = {book} } |
Understanding the methyl-TROSY effect over a wide range of magnetic fields Article de journal N Bolik-Coulon; S F Cousin; P Kadeřávek; J-N Dumez; F Ferrage The Journal of Chemical Physics, 150 , p. 224202, 2019. @article{Bolik-Coulon2019, title = {Understanding the methyl-TROSY effect over a wide range of magnetic fields}, author = {N Bolik-Coulon and S F Cousin and P Kade\v{r}\'{a}vek and J-N Dumez and F Ferrage}, url = {https://aip.scitation.org/doi/10.1063/1.5095757}, doi = {10.1063/1.5095757}, year = {2019}, date = {2019-06-14}, journal = {The Journal of Chemical Physics}, volume = {150}, pages = {224202}, abstract = {The use of relaxation interference in the methyl Transverse Relaxation-Optimized SpectroscopY (TROSY) experiment has opened new avenues for the study of large proteins and protein assemblies in nuclear magnetic resonance. So far, the theoretical description of the methyl- TROSY experiment has been limited to the slow-tumbling approximation, which is correct for large proteins on high-field spectrometers. In a recent paper, favorable relaxation interference was observed in the methyl groups of a small protein at a magnetic field as low as 0.33 T, well outside the slow-tumbling regime. Here, we present a model to describe relaxation interference in methyl groups over a broad range of magnetic fields, not limited to the slow-tumbling regime. We predict that the type of multiple-quantum transition that shows favorable relaxation properties change with the magnetic field. Under the condition of fast methyl-group rotation, methyl-TROSY experiments can be recorded over the entire range of magnetic fields from a fraction of 1 T up to 100 T.}, keywords = {}, pubstate = {published}, tppubtype = {article} } The use of relaxation interference in the methyl Transverse Relaxation-Optimized SpectroscopY (TROSY) experiment has opened new avenues for the study of large proteins and protein assemblies in nuclear magnetic resonance. So far, the theoretical description of the methyl- TROSY experiment has been limited to the slow-tumbling approximation, which is correct for large proteins on high-field spectrometers. In a recent paper, favorable relaxation interference was observed in the methyl groups of a small protein at a magnetic field as low as 0.33 T, well outside the slow-tumbling regime. Here, we present a model to describe relaxation interference in methyl groups over a broad range of magnetic fields, not limited to the slow-tumbling regime. We predict that the type of multiple-quantum transition that shows favorable relaxation properties change with the magnetic field. Under the condition of fast methyl-group rotation, methyl-TROSY experiments can be recorded over the entire range of magnetic fields from a fraction of 1 T up to 100 T. |
2018 |
Determination of protein ps-ns motions by high-resolution relaxometry Livre S F Cousin; P Kadeřávek; N Bolik-Coulon; F Ferrage 2018. @book{Cousin:2018a, title = {Determination of protein ps-ns motions by high-resolution relaxometry}, author = {S F Cousin and P Kade\v{r}\'{a}vek and N Bolik-Coulon and F Ferrage}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85034820210&doi=10.1007%2f978-1-4939-7386-6_9&partnerID=40&md5=acb0426074b113adef7f6c89e86d7340}, doi = {10.1007/978-1-4939-7386-6_9}, year = {2018}, date = {2018-01-01}, volume = {1688}, series = {Methods in Molecular Biology}, abstract = {Many of the functions of biomacromolecules can be rationalized by the characterization of their conformational energy landscapes: the structures of the dominant states, transitions between states and motions within states. Nuclear magnetic resonance (NMR) spectroscopy is the technique of choice to study internal motions in proteins. The determination of motions on picosecond to nanosecond timescales requires the measurement of nuclear spin relaxation rates at multiple magnetic fields. High sensitivity and resolution are obtained only at high magnetic fields, so that, until recently, site-specific relaxation rates in biomolecules were only measured over a narrow range of high magnetic fields. This limitation was particularly striking for the quantification of motions on nanosecond timescales, close to the correlation time for overall rotational diffusion. High-resolution relaxometry is an emerging technique to investigate picosecond\textemdashnanosecond motions of proteins. This approach uses a high-field NMR spectrometer equipped with a sample shuttle device, which allows for the measurement of the relaxation rate constants at low magnetic fields, while preserving the sensitivity and resolution of a high-field NMR spectrometer. The combined analysis of high-resolution relaxometry and standard high-field relaxation data provides a more accurate description of the dynamics of proteins, in particular in the nanosecond range. The purpose of this chapter is to describe how to perform high-resolution relaxometry experiments and how to analyze the rates measured with this technique. © 2018, Springer Science+Business Media LLC.}, keywords = {}, pubstate = {published}, tppubtype = {book} } Many of the functions of biomacromolecules can be rationalized by the characterization of their conformational energy landscapes: the structures of the dominant states, transitions between states and motions within states. Nuclear magnetic resonance (NMR) spectroscopy is the technique of choice to study internal motions in proteins. The determination of motions on picosecond to nanosecond timescales requires the measurement of nuclear spin relaxation rates at multiple magnetic fields. High sensitivity and resolution are obtained only at high magnetic fields, so that, until recently, site-specific relaxation rates in biomolecules were only measured over a narrow range of high magnetic fields. This limitation was particularly striking for the quantification of motions on nanosecond timescales, close to the correlation time for overall rotational diffusion. High-resolution relaxometry is an emerging technique to investigate picosecond—nanosecond motions of proteins. This approach uses a high-field NMR spectrometer equipped with a sample shuttle device, which allows for the measurement of the relaxation rate constants at low magnetic fields, while preserving the sensitivity and resolution of a high-field NMR spectrometer. The combined analysis of high-resolution relaxometry and standard high-field relaxation data provides a more accurate description of the dynamics of proteins, in particular in the nanosecond range. The purpose of this chapter is to describe how to perform high-resolution relaxometry experiments and how to analyze the rates measured with this technique. © 2018, Springer Science+Business Media LLC. |
Measuring Solvent Hydrogen Exchange Rates by Multifrequency Excitation 15N CEST: Application to Protein Phase Separation Article de journal T Yuwen; A Bah; J P Brady; F Ferrage; G Bouvignies; L E Kay Journal of Physical Chemistry B, 122 (49), p. 11206–11217, 2018. @article{Yuwen:2018, title = {Measuring Solvent Hydrogen Exchange Rates by Multifrequency Excitation 15N CEST: Application to Protein Phase Separation}, author = {T Yuwen and A Bah and J P Brady and F Ferrage and G Bouvignies and L E Kay}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85053865280&doi=10.1021%2facs.jpcb.8b06820&partnerID=40&md5=a061f9c2e15482bd5d837067aeb2551b}, doi = {10.1021/acs.jpcb.8b06820}, year = {2018}, date = {2018-01-01}, journal = {Journal of Physical Chemistry B}, volume = {122}, number = {49}, pages = {11206--11217}, abstract = {Solvent exchange rates provide important information about the structural and dynamical properties of biomolecules. A large number of NMR experiments have been developed to measure such rates in proteins, the great majority of which quantify the buildup of signals from backbone amides after initial perturbation of water magnetization. Here we present a different approach that circumvents the main limitations that result from these classical hydrogen exchange NMR experiments. Building on recent developments that enable rapid recording of chemical exchange saturation transfer (CEST) pseudo-3D data sets, we describe a 15N-based CEST scheme for measurement of solvent exchange in proteins that exploits the one-bond 15N deuterium isotope shift. The utility of the approach is verified with an application to a 236 residue intrinsically disordered protein domain under conditions where it phase separates and a second application involving a mutated form of the domain that does not phase separate, establishing very similar hydrogen exchange rates for both samples. The methodology is well suited for studies of hydrogen exchange in any 15N-labeled biomolecule. A discussion of the merits of the CEST experiment in relation to the popular CLEANEX-PM scheme is presented. © 2018 American Chemical Society.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Solvent exchange rates provide important information about the structural and dynamical properties of biomolecules. A large number of NMR experiments have been developed to measure such rates in proteins, the great majority of which quantify the buildup of signals from backbone amides after initial perturbation of water magnetization. Here we present a different approach that circumvents the main limitations that result from these classical hydrogen exchange NMR experiments. Building on recent developments that enable rapid recording of chemical exchange saturation transfer (CEST) pseudo-3D data sets, we describe a 15N-based CEST scheme for measurement of solvent exchange in proteins that exploits the one-bond 15N deuterium isotope shift. The utility of the approach is verified with an application to a 236 residue intrinsically disordered protein domain under conditions where it phase separates and a second application involving a mutated form of the domain that does not phase separate, establishing very similar hydrogen exchange rates for both samples. The methodology is well suited for studies of hydrogen exchange in any 15N-labeled biomolecule. A discussion of the merits of the CEST experiment in relation to the popular CLEANEX-PM scheme is presented. © 2018 American Chemical Society. |
Analysis of NMR Spin-Relaxation Data Using an Inverse Gaussian Distribution Function Article de journal A Hsu; F Ferrage; A G Palmer III Biophysical Journal, 115 (12), p. 2301–2309, 2018. @article{Hsu:2018, title = {Analysis of NMR Spin-Relaxation Data Using an Inverse Gaussian Distribution Function}, author = {A Hsu and F Ferrage and A G Palmer III}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85057226262&doi=10.1016%2fj.bpj.2018.10.030&partnerID=40&md5=eab8de988f2c698fae81d4860dcddc7b}, doi = {10.1016/j.bpj.2018.10.030}, year = {2018}, date = {2018-01-01}, journal = {Biophysical Journal}, volume = {115}, number = {12}, pages = {2301--2309}, abstract = {Spin relaxation in solution-state NMR spectroscopy is a powerful approach to explore the conformational dynamics of biological macromolecules. Probability distribution functions for overall or internal correlation times have been used previously to model spectral density functions central to spin-relaxation theory. Applications to biological macromolecules rely on transverse relaxation rate constants, and when studying nanosecond timescale motions, sampling at ultralow frequencies is often necessary. Consequently, appropriate distribution functions necessitate spectral density functions that are accurate and convergent as frequencies approach zero. In this work, the inverse Gaussian probability distribution function is derived from general properties of spectral density functions at low and high frequencies for macromolecules in solution, using the principle of maximal entropy. This normalized distribution function is first used to calculate the correlation function, followed by the spectral density function. The resulting model-free spectral density functions are finite at a frequency of zero and can be used to describe distributions of either overall or internal correlation times using the model-free ansatz. To validate the approach, 15N spin-relaxation data for the bZip transcription factor domain of the Saccharomyces cerevisiae protein GCN4, in the absence of cognate DNA, were analyzed using the inverse Gaussian probability distribution for intramolecular correlation times. The results extend previous models for the conformational dynamics of the intrinsically disordered, DNA-binding region of the bZip transcription factor domain. © 2018 Biophysical Society}, keywords = {}, pubstate = {published}, tppubtype = {article} } Spin relaxation in solution-state NMR spectroscopy is a powerful approach to explore the conformational dynamics of biological macromolecules. Probability distribution functions for overall or internal correlation times have been used previously to model spectral density functions central to spin-relaxation theory. Applications to biological macromolecules rely on transverse relaxation rate constants, and when studying nanosecond timescale motions, sampling at ultralow frequencies is often necessary. Consequently, appropriate distribution functions necessitate spectral density functions that are accurate and convergent as frequencies approach zero. In this work, the inverse Gaussian probability distribution function is derived from general properties of spectral density functions at low and high frequencies for macromolecules in solution, using the principle of maximal entropy. This normalized distribution function is first used to calculate the correlation function, followed by the spectral density function. The resulting model-free spectral density functions are finite at a frequency of zero and can be used to describe distributions of either overall or internal correlation times using the model-free ansatz. To validate the approach, 15N spin-relaxation data for the bZip transcription factor domain of the Saccharomyces cerevisiae protein GCN4, in the absence of cognate DNA, were analyzed using the inverse Gaussian probability distribution for intramolecular correlation times. The results extend previous models for the conformational dynamics of the intrinsically disordered, DNA-binding region of the bZip transcription factor domain. © 2018 Biophysical Society |
Time-Resolved Protein Side-Chain Motions Unraveled by High-Resolution Relaxometry and Molecular Dynamics Simulations Article de journal S F Cousin; P Kadeřávek; N Bolik-Coulon; Y Gu; C Charlier; L Carlier; L Bruschweiler-Li; T Marquardsen; J -M Tyburn; R Brüschweiler; F Ferrage Journal of the American Chemical Society, 140 (41), p. 13456–13465, 2018. @article{Cousin:2018, title = {Time-Resolved Protein Side-Chain Motions Unraveled by High-Resolution Relaxometry and Molecular Dynamics Simulations}, author = {S F Cousin and P Kade\v{r}\'{a}vek and N Bolik-Coulon and Y Gu and C Charlier and L Carlier and L Bruschweiler-Li and T Marquardsen and J -M Tyburn and R Br\"{u}schweiler and F Ferrage}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85054139114&doi=10.1021%2fjacs.8b09107&partnerID=40&md5=e619ef5070ec06092676f682c2c6cd3d}, doi = {10.1021/jacs.8b09107}, year = {2018}, date = {2018-01-01}, journal = {Journal of the American Chemical Society}, volume = {140}, number = {41}, pages = {13456--13465}, abstract = {Motions of proteins are essential for the performance of their functions. Aliphatic protein side chains and their motions play critical roles in protein interactions: for recognition and binding of partner molecules at the surface or serving as an entropy reservoir within the hydrophobic core. Here, we present a new NMR method based on high-resolution relaxometry and high-field relaxation to determine quantitatively both motional amplitudes and time scales of methyl-bearing side chains in the picosecond-to-nanosecond range. We detect a wide variety of motions in isoleucine side chains in the protein ubiquitin. We unambiguously identify slow motions in the low nanosecond range, which, in conjunction with molecular dynamics computer simulations, could be assigned to transitions between rotamers. Our approach provides unmatched detailed insight into the motions of aliphatic side chains in proteins and provides a better understanding of the nature and functional role of protein side-chain motions. © Copyright 2018 American Chemical Society.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Motions of proteins are essential for the performance of their functions. Aliphatic protein side chains and their motions play critical roles in protein interactions: for recognition and binding of partner molecules at the surface or serving as an entropy reservoir within the hydrophobic core. Here, we present a new NMR method based on high-resolution relaxometry and high-field relaxation to determine quantitatively both motional amplitudes and time scales of methyl-bearing side chains in the picosecond-to-nanosecond range. We detect a wide variety of motions in isoleucine side chains in the protein ubiquitin. We unambiguously identify slow motions in the low nanosecond range, which, in conjunction with molecular dynamics computer simulations, could be assigned to transitions between rotamers. Our approach provides unmatched detailed insight into the motions of aliphatic side chains in proteins and provides a better understanding of the nature and functional role of protein side-chain motions. © Copyright 2018 American Chemical Society. |
High-Resolution NMR of Folded Proteins in Hyperpolarized Physiological Solvents Article de journal P Kadeřávek; F Ferrage; G Bodenhausen; D Kurzbach Chemistry - A European Journal, 24 (51), p. 13418–13423, 2018. @article{Kaderavek:2018, title = {High-Resolution NMR of Folded Proteins in Hyperpolarized Physiological Solvents}, author = {P Kade\v{r}\'{a}vek and F Ferrage and G Bodenhausen and D Kurzbach}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85053232886&doi=10.1002%2fchem.201802885&partnerID=40&md5=65d2aa185f12361021010b6644e8938c}, doi = {10.1002/chem.201802885}, year = {2018}, date = {2018-01-01}, journal = {Chemistry - A European Journal}, volume = {24}, number = {51}, pages = {13418--13423}, abstract = {Hyperpolarized 2D exchange spectroscopy (HYPEX) to obtain high-resolution nuclear magnetic resonance (NMR) spectra of folded proteins under near-physiological conditions is reported. The technique is based on hyperpolarized water, which is prepared by dissolution dynamic nuclear polarization and mixed in situ in an NMR spectrometer with a protein in a physiological saline buffer at body temperature. Rapid exchange of labile protons with the hyperpolarized solvent, combined with cross-relaxation effects (NOEs), leads to boosted signal intensities for many amide 1H\textendash15N correlations in the protein ubiquitin. As the introduction of hyperpolarization to the target protein is mediated via the solvent, the method is applicable to a broad spectrum of target molecules. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim}, keywords = {}, pubstate = {published}, tppubtype = {article} } Hyperpolarized 2D exchange spectroscopy (HYPEX) to obtain high-resolution nuclear magnetic resonance (NMR) spectra of folded proteins under near-physiological conditions is reported. The technique is based on hyperpolarized water, which is prepared by dissolution dynamic nuclear polarization and mixed in situ in an NMR spectrometer with a protein in a physiological saline buffer at body temperature. Rapid exchange of labile protons with the hyperpolarized solvent, combined with cross-relaxation effects (NOEs), leads to boosted signal intensities for many amide 1H–15N correlations in the protein ubiquitin. As the introduction of hyperpolarization to the target protein is mediated via the solvent, the method is applicable to a broad spectrum of target molecules. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim |
2017 |
Full Correlations across Broad NMR Spectra by Two-Field Total Correlation Spectroscopy Article de journal P Kadeřávek; L Strouk; S F Cousin; C Charlier; G Bodenhausen; T Marquardsen; J -M Tyburn; P -A Bovier; F Engelke; W Maas; F Ferrage ChemPhysChem, 18 (19), p. 2772–2776, 2017. @article{Kaderavek:2017, title = {Full Correlations across Broad NMR Spectra by Two-Field Total Correlation Spectroscopy}, author = {P Kade\v{r}\'{a}vek and L Strouk and S F Cousin and C Charlier and G Bodenhausen and T Marquardsen and J -M Tyburn and P -A Bovier and F Engelke and W Maas and F Ferrage}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85030717312&doi=10.1002%2fcphc.201700369&partnerID=40&md5=d073ea9e024a1ce650d0c4b2cf57df88}, doi = {10.1002/cphc.201700369}, year = {2017}, date = {2017-01-01}, journal = {ChemPhysChem}, volume = {18}, number = {19}, pages = {2772--2776}, abstract = {Total correlation spectroscopy (TOCSY) is a key experiment to assign nuclear magnetic resonance (NMR) spectra of complex molecules. Carbon-13 TOCSY experiments are essential to assign signals of protein side chains. However, the performance of carbon-13 TOCSY deteriorates at high magnetic fields since the necessarily limited radiofrequency irradiation fails to cover the broad range of carbon-13 frequencies. Here, we introduce a new concept to overcome the limitations of TOCSY by using two-field NMR spectroscopy. In two-field TOCSY experiments, chemical shifts are labelled at high field but isotropic mixing is performed at a much lower magnetic field, where the frequency range of the spectrum is drastically reduced. We obtain complete correlations between all carbon-13 nuclei belonging to amino acids across the entire spectrum: aromatic, aliphatic and carboxylic. Two-field TOCSY should be a robust and general approach for the assignment of uniformly carbon-13 labelled molecules in high-field and ultra-high field NMR spectrometers beyond 1000 MHz. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim}, keywords = {}, pubstate = {published}, tppubtype = {article} } Total correlation spectroscopy (TOCSY) is a key experiment to assign nuclear magnetic resonance (NMR) spectra of complex molecules. Carbon-13 TOCSY experiments are essential to assign signals of protein side chains. However, the performance of carbon-13 TOCSY deteriorates at high magnetic fields since the necessarily limited radiofrequency irradiation fails to cover the broad range of carbon-13 frequencies. Here, we introduce a new concept to overcome the limitations of TOCSY by using two-field NMR spectroscopy. In two-field TOCSY experiments, chemical shifts are labelled at high field but isotropic mixing is performed at a much lower magnetic field, where the frequency range of the spectrum is drastically reduced. We obtain complete correlations between all carbon-13 nuclei belonging to amino acids across the entire spectrum: aromatic, aliphatic and carboxylic. Two-field TOCSY should be a robust and general approach for the assignment of uniformly carbon-13 labelled molecules in high-field and ultra-high field NMR spectrometers beyond 1000 MHz. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim |
Ultra-wide range field-dependent measurements of the relaxivity of Gd1-x Eux VO4 nanoparticle contrast agents using a mechanical sample-shuttling relaxometer Article de journal C -Y Chou; M Abdesselem; C Bouzigues; M Chu; A Guiga; T -H Huang; F Ferrage; T Gacoin; A Alexandrou; D Sakellariou Scientific Reports, 7 , 2017. @article{Chou:2017, title = {Ultra-wide range field-dependent measurements of the relaxivity of Gd1-x Eux VO4 nanoparticle contrast agents using a mechanical sample-shuttling relaxometer}, author = {C -Y Chou and M Abdesselem and C Bouzigues and M Chu and A Guiga and T -H Huang and F Ferrage and T Gacoin and A Alexandrou and D Sakellariou}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85015977501&doi=10.1038%2fsrep44770&partnerID=40&md5=b8e41b32dbcc097b80e689bd90ba5617}, doi = {10.1038/srep44770}, year = {2017}, date = {2017-01-01}, journal = {Scientific Reports}, volume = {7}, abstract = {The current trend for Magnetic Resonance Imaging points towards higher magnetic fields. Even though sensitivity and resolution are increased in stronger fields, T1 contrast is often reduced, and this represents a challenge for contrast agent design. Field-dependent measurements of relaxivity are thus important to characterize contrast agents. At present, the field-dependent curves of relaxivity are usually carried out in the field range of 0 T to 2 T, using fast field cycling relaxometers. Here, we employ a high-speed sample shuttling device to switch the magnetic fields experienced by the nuclei between virtually zero field, and the center of any commercial spectrometer. We apply this approach on rare-earth (mixed Gadolinium-Europium) vanadate nanoparticles, and obtain the dispersion curves from very low magnetic field up to 11.7 T. In contrast to the relaxivity profiles of Gd chelates, commonly used for clinical applications, which display a plateau and then a decrease for increasing magnetic fields, these nanoparticles provide maximum contrast enhancement for magnetic fields around 1-1.5 T. These field-dependent curves are fitted using the so-called Magnetic Particle (MP) model and the extracted parameters discussed as a function of particle size and composition. We finally comment on the new possibilities offered by this approach. © 2017 The Author(s).}, keywords = {}, pubstate = {published}, tppubtype = {article} } The current trend for Magnetic Resonance Imaging points towards higher magnetic fields. Even though sensitivity and resolution are increased in stronger fields, T1 contrast is often reduced, and this represents a challenge for contrast agent design. Field-dependent measurements of relaxivity are thus important to characterize contrast agents. At present, the field-dependent curves of relaxivity are usually carried out in the field range of 0 T to 2 T, using fast field cycling relaxometers. Here, we employ a high-speed sample shuttling device to switch the magnetic fields experienced by the nuclei between virtually zero field, and the center of any commercial spectrometer. We apply this approach on rare-earth (mixed Gadolinium-Europium) vanadate nanoparticles, and obtain the dispersion curves from very low magnetic field up to 11.7 T. In contrast to the relaxivity profiles of Gd chelates, commonly used for clinical applications, which display a plateau and then a decrease for increasing magnetic fields, these nanoparticles provide maximum contrast enhancement for magnetic fields around 1-1.5 T. These field-dependent curves are fitted using the so-called Magnetic Particle (MP) model and the extracted parameters discussed as a function of particle size and composition. We finally comment on the new possibilities offered by this approach. © 2017 The Author(s). |
Structure and Dynamics of an Intrinsically Disordered Protein Region That Partially Folds upon Binding by Chemical-Exchange NMR Article de journal C Charlier; G Bouvignies; P Pelupessy; A Walrant; R Marquant; M Kozlov; P De Ioannes; N Bolik-Coulon; S Sagan; P Cortes; A K Aggarwal; L Carlier; F Ferrage Journal of the American Chemical Society, 139 (35), p. 12219–12227, 2017. @article{Charlier:2017, title = {Structure and Dynamics of an Intrinsically Disordered Protein Region That Partially Folds upon Binding by Chemical-Exchange NMR}, author = {C Charlier and G Bouvignies and P Pelupessy and A Walrant and R Marquant and M Kozlov and P De Ioannes and N Bolik-Coulon and S Sagan and P Cortes and A K Aggarwal and L Carlier and F Ferrage}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85028941202&doi=10.1021%2fjacs.7b05823&partnerID=40&md5=ce8846a9b03d31576ec301899a2c40f1}, doi = {10.1021/jacs.7b05823}, year = {2017}, date = {2017-01-01}, journal = {Journal of the American Chemical Society}, volume = {139}, number = {35}, pages = {12219--12227}, abstract = {Many intrinsically disordered proteins (IDPs) and protein regions (IDRs) engage in transient, yet specific, interactions with a variety of protein partners. Often, if not always, interactions with a protein partner lead to partial folding of the IDR. Characterizing the conformational space of such complexes is challenging: in solution-state NMR, signals of the IDR in the interacting region become broad, weak, and often invisible, while X-ray crystallography only provides information on fully ordered regions. There is thus a need for a simple method to characterize both fully and partially ordered regions in the bound state of IDPs. Here, we introduce an approach based on monitoring chemical exchange by NMR to investigate the state of an IDR that folds upon binding through the observation of the free state of the protein. Structural constraints for the bound state are obtained from chemical shifts, and site-specific dynamics of the bound state are characterized by relaxation rates. The conformation of the interacting part of the IDR was determined and subsequently docked onto the structure of the folded partner. We apply the method to investigate the interaction between the disordered C-terminal region of Artemis and the DNA binding domain of Ligase IV. We show that we can accurately reproduce the structure of the core of the complex determined by X-ray crystallography and identify a broader interface. The method is widely applicable to the biophysical investigation of complexes of disordered proteins and folded proteins. © 2017 American Chemical Society.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Many intrinsically disordered proteins (IDPs) and protein regions (IDRs) engage in transient, yet specific, interactions with a variety of protein partners. Often, if not always, interactions with a protein partner lead to partial folding of the IDR. Characterizing the conformational space of such complexes is challenging: in solution-state NMR, signals of the IDR in the interacting region become broad, weak, and often invisible, while X-ray crystallography only provides information on fully ordered regions. There is thus a need for a simple method to characterize both fully and partially ordered regions in the bound state of IDPs. Here, we introduce an approach based on monitoring chemical exchange by NMR to investigate the state of an IDR that folds upon binding through the observation of the free state of the protein. Structural constraints for the bound state are obtained from chemical shifts, and site-specific dynamics of the bound state are characterized by relaxation rates. The conformation of the interacting part of the IDR was determined and subsequently docked onto the structure of the folded partner. We apply the method to investigate the interaction between the disordered C-terminal region of Artemis and the DNA binding domain of Ligase IV. We show that we can accurately reproduce the structure of the core of the complex determined by X-ray crystallography and identify a broader interface. The method is widely applicable to the biophysical investigation of complexes of disordered proteins and folded proteins. © 2017 American Chemical Society. |
2016 |
Sample Shuttling Relaxometry of Contrast Agents: NMRD Profiles above 1 Ŧ with a Single Device Article de journal Y Gossuin; Z Serhan; L Sandiford; D Henrard; T Marquardsen; R T M de Rosales; D Sakellariou; F Ferrage Applied Magnetic Resonance, 47 (3), p. 237–246, 2016. @article{Gossuin:2016, title = {Sample Shuttling Relaxometry of Contrast Agents: NMRD Profiles above 1 {T} with a Single Device}, author = {Y Gossuin and Z Serhan and L Sandiford and D Henrard and T Marquardsen and R T M de Rosales and D Sakellariou and F Ferrage}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84956993966&doi=10.1007%2fs00723-015-0751-7&partnerID=40&md5=b321e483eb6d41b44065a0926ca8de06}, doi = {10.1007/s00723-015-0751-7}, year = {2016}, date = {2016-01-01}, journal = {Applied Magnetic Resonance}, volume = {47}, number = {3}, pages = {237--246}, abstract = {Nuclear magnetic relaxation dispersion (NMRD) profiles are essential tools to evaluate the efficiency and investigate the properties of magnetic compounds used as contrast agents for magnetic resonance imaging (MRI), namely gadolinium chelates and superparamagnetic iron oxide particles. These curves represent the evolution of proton relaxation rates with the magnetic field. NMRD profiles are unparalleled to probe extensively the spectral density function involved in the relaxation of water in the presence of the paramagnetic ion or the magnetic nanoparticles. This makes such profiles an excellent test of the adequacy of a theoretical relaxation model and allow for a predictive approach to the development and optimization of contrast agents. From a practical point of view they also allow to evaluate the efficiency of a contrast agent in a certain range of magnetic fields. Nowadays, these curves are recorded with commercial fast field cycling devices, often limited to a maximum Larmor frequency of 40 MHz (0.94 T). In this article, relaxation data were acquired on a wide range of magnetic fields, from 3.5 × 10−4 to 14 T, for a gadolinium-based contrast agent and for PEGylated iron oxide nanoparticles. We show that the low-field NMRD curves can be completed with high-field data obtained on a shuttle apparatus device using the superconductive magnet of a high-field spectrometer. This allows a better characterization of the contrast agents at relevant magnetic fields for clinical and preclinical MRI, but also refines the experimental data that could be used for the validation of relaxation models. © 2016, The Author(s).}, keywords = {}, pubstate = {published}, tppubtype = {article} } Nuclear magnetic relaxation dispersion (NMRD) profiles are essential tools to evaluate the efficiency and investigate the properties of magnetic compounds used as contrast agents for magnetic resonance imaging (MRI), namely gadolinium chelates and superparamagnetic iron oxide particles. These curves represent the evolution of proton relaxation rates with the magnetic field. NMRD profiles are unparalleled to probe extensively the spectral density function involved in the relaxation of water in the presence of the paramagnetic ion or the magnetic nanoparticles. This makes such profiles an excellent test of the adequacy of a theoretical relaxation model and allow for a predictive approach to the development and optimization of contrast agents. From a practical point of view they also allow to evaluate the efficiency of a contrast agent in a certain range of magnetic fields. Nowadays, these curves are recorded with commercial fast field cycling devices, often limited to a maximum Larmor frequency of 40 MHz (0.94 T). In this article, relaxation data were acquired on a wide range of magnetic fields, from 3.5 × 10−4 to 14 T, for a gadolinium-based contrast agent and for PEGylated iron oxide nanoparticles. We show that the low-field NMRD curves can be completed with high-field data obtained on a shuttle apparatus device using the superconductive magnet of a high-field spectrometer. This allows a better characterization of the contrast agents at relevant magnetic fields for clinical and preclinical MRI, but also refines the experimental data that could be used for the validation of relaxation models. © 2016, The Author(s). |
Recovering Invisible Signals by Two-Field NMR Spectroscopy Article de journal S F Cousin; P Kadeřávek; B Haddou; C Charlier; T Marquardsen; J -M Tyburn; P -A Bovier; F Engelke; W Maas; G Bodenhausen; P Pelupessy; F Ferrage Angewandte Chemie - International Edition, 55 (34), p. 9886–9889, 2016. @article{Cousin:2016, title = {Recovering Invisible Signals by Two-Field NMR Spectroscopy}, author = {S F Cousin and P Kade\v{r}\'{a}vek and B Haddou and C Charlier and T Marquardsen and J -M Tyburn and P -A Bovier and F Engelke and W Maas and G Bodenhausen and P Pelupessy and F Ferrage}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84978505346&doi=10.1002%2fanie.201602978&partnerID=40&md5=4461b77dffa32e9cd4094582a4e8241a}, doi = {10.1002/anie.201602978}, year = {2016}, date = {2016-01-01}, journal = {Angewandte Chemie - International Edition}, volume = {55}, number = {34}, pages = {9886--9889}, abstract = {Nuclear magnetic resonance (NMR) studies have benefited tremendously from the steady increase in the strength of magnetic fields. Spectacular improvements in both sensitivity and resolution have enabled the investigation of molecular systems of rising complexity. At very high fields, this progress may be jeopardized by line broadening, which is due to chemical exchange or relaxation by chemical shift anisotropy. In this work, we introduce a two-field NMR spectrometer designed for both excitation and observation of nuclear spins in two distinct magnetic fields in a single experiment. NMR spectra of several small molecules as well as a protein were obtained, with two dimensions acquired at vastly different magnetic fields. Resonances of exchanging groups that are broadened beyond recognition at high field can be sharpened to narrow peaks in the low-field dimension. Two-field NMR spectroscopy enables the measurement of chemical shifts at optimal fields and the study of molecular systems that suffer from internal dynamics, and opens new avenues for NMR spectroscopy at very high magnetic fields. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim}, keywords = {}, pubstate = {published}, tppubtype = {article} } Nuclear magnetic resonance (NMR) studies have benefited tremendously from the steady increase in the strength of magnetic fields. Spectacular improvements in both sensitivity and resolution have enabled the investigation of molecular systems of rising complexity. At very high fields, this progress may be jeopardized by line broadening, which is due to chemical exchange or relaxation by chemical shift anisotropy. In this work, we introduce a two-field NMR spectrometer designed for both excitation and observation of nuclear spins in two distinct magnetic fields in a single experiment. NMR spectra of several small molecules as well as a protein were obtained, with two dimensions acquired at vastly different magnetic fields. Resonances of exchanging groups that are broadened beyond recognition at high field can be sharpened to narrow peaks in the low-field dimension. Two-field NMR spectroscopy enables the measurement of chemical shifts at optimal fields and the study of molecular systems that suffer from internal dynamics, and opens new avenues for NMR spectroscopy at very high magnetic fields. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim |
Protein dynamics from nuclear magnetic relaxation Article de journal C Charlier; S F Cousin; F Ferrage Chemical Society Reviews, 45 (9), p. 2410–2422, 2016. @article{Charlier:2016, title = {Protein dynamics from nuclear magnetic relaxation}, author = {C Charlier and S F Cousin and F Ferrage}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84968834767&doi=10.1039%2fc5cs00832h&partnerID=40&md5=d1695ff88ad83ccfad98b81c2681b00d}, doi = {10.1039/c5cs00832h}, year = {2016}, date = {2016-01-01}, journal = {Chemical Society Reviews}, volume = {45}, number = {9}, pages = {2410--2422}, abstract = {Nuclear magnetic resonance is a ubiquitous spectroscopic tool to explore molecules with atomic resolution. Nuclear magnetic relaxation is intimately connected to molecular motions. Many methods and models have been developed to measure and interpret the characteristic rates of nuclear magnetic relaxation in proteins. These approaches shed light on a rich and diverse range of motions covering timescales from picoseconds to seconds. Here, we introduce some of the basic concepts upon which these approaches are built and provide a series of illustrations. © 2016 The Royal Society of Chemistry.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Nuclear magnetic resonance is a ubiquitous spectroscopic tool to explore molecules with atomic resolution. Nuclear magnetic relaxation is intimately connected to molecular motions. Many methods and models have been developed to measure and interpret the characteristic rates of nuclear magnetic relaxation in proteins. These approaches shed light on a rich and diverse range of motions covering timescales from picoseconds to seconds. Here, we introduce some of the basic concepts upon which these approaches are built and provide a series of illustrations. © 2016 The Royal Society of Chemistry. |
Nuclear overhauser spectroscopy of chiral CHD methylene groups Article de journal R Augustyniak; J Stanek; H Colaux; G Bodenhausen; W Koźmiński; T Herrmann; F Ferrage Journal of Biomolecular NMR, 64 (1), p. 27–37, 2016. @article{Augustyniak:2016, title = {Nuclear overhauser spectroscopy of chiral CHD methylene groups}, author = {R Augustyniak and J Stanek and H Colaux and G Bodenhausen and W Ko\'{z}mi\'{n}ski and T Herrmann and F Ferrage}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84957938000&doi=10.1007%2fs10858-015-0002-0&partnerID=40&md5=e030127e44f952f166811ff046087bff}, doi = {10.1007/s10858-015-0002-0}, year = {2016}, date = {2016-01-01}, journal = {Journal of Biomolecular NMR}, volume = {64}, number = {1}, pages = {27--37}, abstract = {Nuclear magnetic resonance spectroscopy (NMR) can provide a great deal of information about structure and dynamics of biomolecules. The quality of an NMR structure strongly depends on the number of experimental observables and on their accurate conversion into geometric restraints. When distance restraints are derived from nuclear Overhauser effect spectroscopy (NOESY), stereo-specific assignments of prochiral atoms can contribute significantly to the accuracy of NMR structures of proteins and nucleic acids. Here we introduce a series of NOESY-based pulse sequences that can assist in the assignment of chiral CHD methylene protons in random fractionally deuterated proteins. Partial deuteration suppresses spin-diffusion between the two protons of CH2 groups that normally impedes the distinction of cross-relaxation networks for these two protons in NOESY spectra. Three and four-dimensional spectra allow one to distinguish cross-relaxation pathways involving either of the two methylene protons so that one can obtain stereospecific assignments. In addition, the analysis provides a large number of stereospecific distance restraints. Non-uniform sampling was used to ensure optimal signal resolution in 4D spectra and reduce ambiguities of the assignments. Automatic assignment procedures were modified for efficient and accurate stereospecific assignments during automated structure calculations based on 3D spectra. The protocol was applied to calcium-loaded calbindin D9k. A large number of stereospecific assignments lead to a significant improvement of the accuracy of the structure. © 2015 Springer Science+Business Media Dordrecht.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Nuclear magnetic resonance spectroscopy (NMR) can provide a great deal of information about structure and dynamics of biomolecules. The quality of an NMR structure strongly depends on the number of experimental observables and on their accurate conversion into geometric restraints. When distance restraints are derived from nuclear Overhauser effect spectroscopy (NOESY), stereo-specific assignments of prochiral atoms can contribute significantly to the accuracy of NMR structures of proteins and nucleic acids. Here we introduce a series of NOESY-based pulse sequences that can assist in the assignment of chiral CHD methylene protons in random fractionally deuterated proteins. Partial deuteration suppresses spin-diffusion between the two protons of CH2 groups that normally impedes the distinction of cross-relaxation networks for these two protons in NOESY spectra. Three and four-dimensional spectra allow one to distinguish cross-relaxation pathways involving either of the two methylene protons so that one can obtain stereospecific assignments. In addition, the analysis provides a large number of stereospecific distance restraints. Non-uniform sampling was used to ensure optimal signal resolution in 4D spectra and reduce ambiguities of the assignments. Automatic assignment procedures were modified for efficient and accurate stereospecific assignments during automated structure calculations based on 3D spectra. The protocol was applied to calcium-loaded calbindin D9k. A large number of stereospecific assignments lead to a significant improvement of the accuracy of the structure. © 2015 Springer Science+Business Media Dordrecht. |
High-resolution two-field nuclear magnetic resonance spectroscopy Article de journal S F Cousin; C Charlier; P Kadeřávek; T Marquardsen; J -M Tyburn; P -A Bovier; S Ulzega; T Speck; D Wilhelm; F Engelke; W Maas; D Sakellariou; G Bodenhausen; P Pelupessy; F Ferrage Physical Chemistry Chemical Physics, 18 (48), p. 33187–33194, 2016. @article{Cousin:2016a, title = {High-resolution two-field nuclear magnetic resonance spectroscopy}, author = {S F Cousin and C Charlier and P Kade\v{r}\'{a}vek and T Marquardsen and J -M Tyburn and P -A Bovier and S Ulzega and T Speck and D Wilhelm and F Engelke and W Maas and D Sakellariou and G Bodenhausen and P Pelupessy and F Ferrage}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85011895555&doi=10.1039%2fc6cp05422f&partnerID=40&md5=a4f118c70abcc3192ed0f1d61e213b0d}, doi = {10.1039/c6cp05422f}, year = {2016}, date = {2016-01-01}, journal = {Physical Chemistry Chemical Physics}, volume = {18}, number = {48}, pages = {33187--33194}, abstract = {Nuclear magnetic resonance (NMR) is a ubiquitous branch of spectroscopy that can explore matter at the scale of an atom. Significant improvements in sensitivity and resolution have been driven by a steady increase of static magnetic field strengths. However, some properties of nuclei may be more favourable at low magnetic fields. For example, transverse relaxation due to chemical shift anisotropy increases sharply at higher magnetic fields leading to line-broadening and inefficient coherence transfers. Here, we present a two-field NMR spectrometer that permits the application of rf-pulses and acquisition of NMR signals in two magnetic centres. Our prototype operates at 14.1 T and 0.33 T. The main features of this system are demonstrated by novel NMR experiments, in particular a proof-of-concept correlation between zero-quantum coherences at low magnetic field and single quantum coherences at high magnetic field, so that high resolution can be achieved in both dimensions, despite a ca. 10 ppm inhomogeneity of the low-field centre. Two-field NMR spectroscopy offers the possibility to circumvent the limits of high magnetic fields, while benefiting from their exceptional sensitivity and resolution. This approach opens new avenues for NMR above 1 GHz. © the Owner Societies 2016.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Nuclear magnetic resonance (NMR) is a ubiquitous branch of spectroscopy that can explore matter at the scale of an atom. Significant improvements in sensitivity and resolution have been driven by a steady increase of static magnetic field strengths. However, some properties of nuclei may be more favourable at low magnetic fields. For example, transverse relaxation due to chemical shift anisotropy increases sharply at higher magnetic fields leading to line-broadening and inefficient coherence transfers. Here, we present a two-field NMR spectrometer that permits the application of rf-pulses and acquisition of NMR signals in two magnetic centres. Our prototype operates at 14.1 T and 0.33 T. The main features of this system are demonstrated by novel NMR experiments, in particular a proof-of-concept correlation between zero-quantum coherences at low magnetic field and single quantum coherences at high magnetic field, so that high resolution can be achieved in both dimensions, despite a ca. 10 ppm inhomogeneity of the low-field centre. Two-field NMR spectroscopy offers the possibility to circumvent the limits of high magnetic fields, while benefiting from their exceptional sensitivity and resolution. This approach opens new avenues for NMR above 1 GHz. © the Owner Societies 2016. |
2015 |
Simple method for the generation of multiple homogeneous field volumes inside the bore of superconducting magnets Article de journal C -Y Chou; F Ferrage; G Aubert; D Sakellariou Scientific Reports, 5 , 2015. @article{Chou:2015, title = {Simple method for the generation of multiple homogeneous field volumes inside the bore of superconducting magnets}, author = {C -Y Chou and F Ferrage and G Aubert and D Sakellariou}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84937458390&doi=10.1038%2fsrep12200&partnerID=40&md5=2a5c32c6d505a3820042f573884c23f9}, doi = {10.1038/srep12200}, year = {2015}, date = {2015-01-01}, journal = {Scientific Reports}, volume = {5}, abstract = {Standard Magnetic Resonance magnets produce a single homogeneous field volume, where the analysis is performed. Nonetheless, several modern applications could benefit from the generation of multiple homogeneous field volumes along the axis and inside the bore of the magnet. In this communication, we propose a straightforward method using a combination of ring structures of permanent magnets in order to cancel the gradient of the stray field in a series of distinct volumes. These concepts were demonstrated numerically on an experimentally measured magnetic field profile. We discuss advantages and limitations of our method and present the key steps required for an experimental validation.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Standard Magnetic Resonance magnets produce a single homogeneous field volume, where the analysis is performed. Nonetheless, several modern applications could benefit from the generation of multiple homogeneous field volumes along the axis and inside the bore of the magnet. In this communication, we propose a straightforward method using a combination of ring structures of permanent magnets in order to cancel the gradient of the stray field in a series of distinct volumes. These concepts were demonstrated numerically on an experimentally measured magnetic field profile. We discuss advantages and limitations of our method and present the key steps required for an experimental validation. |
Identification of hydrophobic interfaces in protein-ligand complexes by selective saturation transfer NMR spectroscopy Article de journal F Ferrage; K Dutta; D Cowburn Molecules, 20 (12), p. 21992–21999, 2015. @article{Ferrage:2015, title = {Identification of hydrophobic interfaces in protein-ligand complexes by selective saturation transfer NMR spectroscopy}, author = {F Ferrage and K Dutta and D Cowburn}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84954357489&doi=10.3390%2fmolecules201219824&partnerID=40&md5=a6e6ae48b26f8cf4911c7e6b66825451}, doi = {10.3390/molecules201219824}, year = {2015}, date = {2015-01-01}, journal = {Molecules}, volume = {20}, number = {12}, pages = {21992--21999}, abstract = {The proper characterization of protein-ligand interfaces is essential for structural biology, with implications ranging from the fundamental understanding of biological processes to pharmacology. Nuclear magnetic resonance is a powerful technique for such studies. We propose a novel approach to the direct determination of the likely pose of a peptide ligand onto a protein partner, by using frequency-selective cross-saturation with a low stringency isotopic labeling methods. Our method illustrates a complex of the Src homology 3 domain of C-terminal Src kinase with a peptide from the proline-enriched tyrosine phosphatase. © 2015 by The Authors.}, keywords = {}, pubstate = {published}, tppubtype = {article} } The proper characterization of protein-ligand interfaces is essential for structural biology, with implications ranging from the fundamental understanding of biological processes to pharmacology. Nuclear magnetic resonance is a powerful technique for such studies. We propose a novel approach to the direct determination of the likely pose of a peptide ligand onto a protein partner, by using frequency-selective cross-saturation with a low stringency isotopic labeling methods. Our method illustrates a complex of the Src homology 3 domain of C-terminal Src kinase with a peptide from the proline-enriched tyrosine phosphatase. © 2015 by The Authors. |
Cross-correlated relaxation measurements under adiabatic sweeps: Determination of local order in proteins Article de journal P Kadeřávek; S Grutsch; N Salvi; M Tollinger; L Žídek; G Bodenhausen; F Ferrage Journal of Biomolecular NMR, 63 (4), p. 353–365, 2015. @article{Kaderavek:2015, title = {Cross-correlated relaxation measurements under adiabatic sweeps: Determination of local order in proteins}, author = {P Kade\v{r}\'{a}vek and S Grutsch and N Salvi and M Tollinger and L \v{Z}\'{i}dek and G Bodenhausen and F Ferrage}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84957936663&doi=10.1007%2fs10858-015-9994-8&partnerID=40&md5=f9d604e7442d0e345608c3837e35b0d5}, doi = {10.1007/s10858-015-9994-8}, year = {2015}, date = {2015-01-01}, journal = {Journal of Biomolecular NMR}, volume = {63}, number = {4}, pages = {353--365}, abstract = {Adiabatically swept pulses were originally designed for the purpose of broadband spin inversion. Later, unexpected advantages of their utilization were also found in other applications, such as refocusing to excite spin echoes, studies of chemical exchange or fragment-based drug design. Here, we present new experiments to characterize fast (ps-ns) protein dynamics, which benefit from little-known properties of adiabatic pulses. We developed a strategy for measuring cross-correlated cross-relaxation (CCCR) rates during adiabatic pulses. This experiment provides a linear combination of longitudinal and transverse CCCR rates, which is offset-independent across a typical amide 15N spectrum. The pulse sequence can be recast to provide accurate transverse CCCR rates weighted by the populations of exchanging states. Sensitivity can be improved in systems in slow exchange. Finally, the experiments can be easily modified to yield residue-specific correlation times. The average correlation time of motions can be determined with a single experiment while at least two different experiments had to be recorded until now. © 2015 The Author(s).}, keywords = {}, pubstate = {published}, tppubtype = {article} } Adiabatically swept pulses were originally designed for the purpose of broadband spin inversion. Later, unexpected advantages of their utilization were also found in other applications, such as refocusing to excite spin echoes, studies of chemical exchange or fragment-based drug design. Here, we present new experiments to characterize fast (ps-ns) protein dynamics, which benefit from little-known properties of adiabatic pulses. We developed a strategy for measuring cross-correlated cross-relaxation (CCCR) rates during adiabatic pulses. This experiment provides a linear combination of longitudinal and transverse CCCR rates, which is offset-independent across a typical amide 15N spectrum. The pulse sequence can be recast to provide accurate transverse CCCR rates weighted by the populations of exchanging states. Sensitivity can be improved in systems in slow exchange. Finally, the experiments can be easily modified to yield residue-specific correlation times. The average correlation time of motions can be determined with a single experiment while at least two different experiments had to be recorded until now. © 2015 The Author(s). |
Distribution of Pico- and Nanosecond Motions in Disordered Proteins from Nuclear Spin Relaxation Article de journal S N Khan; C Charlier; R Augustyniak; N Salvi; V Déjean; G Bodenhausen; O Lequin; P Pelupessy; F Ferrage Biophysical Journal, 109 (5), p. 988–999, 2015. @article{Khan:2015, title = {Distribution of Pico- and Nanosecond Motions in Disordered Proteins from Nuclear Spin Relaxation}, author = {S N Khan and C Charlier and R Augustyniak and N Salvi and V D\'{e}jean and G Bodenhausen and O Lequin and P Pelupessy and F Ferrage}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84940502229&doi=10.1016%2fj.bpj.2015.06.069&partnerID=40&md5=a733f31f586712b6335e41bab2799af1}, doi = {10.1016/j.bpj.2015.06.069}, year = {2015}, date = {2015-01-01}, journal = {Biophysical Journal}, volume = {109}, number = {5}, pages = {988--999}, abstract = {Intrinsically disordered proteins and intrinsically disordered regions (IDRs) are ubiquitous in the eukaryotic proteome. The description and understanding of their conformational properties require the development of new experimental, computational, and theoretical approaches. Here, we use nuclear spin relaxation to investigate the distribution of timescales of motions in an IDR from picoseconds to nanoseconds. Nitrogen-15 relaxation rates have been measured at five magnetic fields, ranging from 9.4 to 23.5 T (400-1000 MHz for protons). This exceptional wealth of data allowed us to map the spectral density function for the motions of backbone NH pairs in the partially disordered transcription factor Engrailed at 11 different frequencies. We introduce an approach called interpretation of motions by a projection onto an array of correlation times (IMPACT), which focuses on an array of six correlation times with intervals that are equidistant on a logarithmic scale between 21 ps and 21 ns. The distribution of motions in Engrailed varies smoothly along the protein sequence and is multimodal for most residues, with a prevalence of motions around 1 ns in the IDR. We show that IMPACT often provides better quantitative agreement with experimental data than conventional model-free or extended model-free analyses with two or three correlation times. We introduce a graphical representation that offers a convenient platform for a qualitative discussion of dynamics. Even when relaxation data are only acquired at three magnetic fields that are readily accessible, the IMPACT analysis gives a satisfactory characterization of spectral density functions, thus opening the way to a broad use of this approach. © 2015 The Authors.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Intrinsically disordered proteins and intrinsically disordered regions (IDRs) are ubiquitous in the eukaryotic proteome. The description and understanding of their conformational properties require the development of new experimental, computational, and theoretical approaches. Here, we use nuclear spin relaxation to investigate the distribution of timescales of motions in an IDR from picoseconds to nanoseconds. Nitrogen-15 relaxation rates have been measured at five magnetic fields, ranging from 9.4 to 23.5 T (400-1000 MHz for protons). This exceptional wealth of data allowed us to map the spectral density function for the motions of backbone NH pairs in the partially disordered transcription factor Engrailed at 11 different frequencies. We introduce an approach called interpretation of motions by a projection onto an array of correlation times (IMPACT), which focuses on an array of six correlation times with intervals that are equidistant on a logarithmic scale between 21 ps and 21 ns. The distribution of motions in Engrailed varies smoothly along the protein sequence and is multimodal for most residues, with a prevalence of motions around 1 ns in the IDR. We show that IMPACT often provides better quantitative agreement with experimental data than conventional model-free or extended model-free analyses with two or three correlation times. We introduce a graphical representation that offers a convenient platform for a qualitative discussion of dynamics. Even when relaxation data are only acquired at three magnetic fields that are readily accessible, the IMPACT analysis gives a satisfactory characterization of spectral density functions, thus opening the way to a broad use of this approach. © 2015 The Authors. |
2013 |
Side chain dynamics of carboxyl and carbonyl groups in the catalytic function of escherichia coli ribonuclease Ħ Article de journal K A Stafford; F Ferrage; J -H Cho; A G Palmer Journal of the American Chemical Society, 135 (48), p. 18024–18027, 2013. @article{Stafford:2013, title = {Side chain dynamics of carboxyl and carbonyl groups in the catalytic function of escherichia coli ribonuclease {H}}, author = {K A Stafford and F Ferrage and J -H Cho and A G Palmer}, url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84889763704&doi=10.1021%2fja409479y&partnerID=40&md5=1eb8f79b0bb1106d099ad41b74b8c967}, doi = {10.1021/ja409479y}, year = {2013}, date = {2013-01-01}, journal = {Journal of the American Chemical Society}, volume = {135}, number = {48}, pages = {18024--18027}, abstract = {Many proteins use Asx and Glx (x = n, p, or u) side chains as key functional groups in enzymatic catalysis and molecular recognition. In this study, NMR spin relaxation experiments and molecular dynamics simulations are used to measure the dynamics of the side chain amide and carboxyl groups, 13Cγ/δ, in Escherichia coli ribonuclease HI (RNase H). Model-free analysis shows that the catalytic residues in RNase H are preorganized on ps-ns time scales via a network of electrostatic interactions. However, chemical exchange line broadening shows that these residues display significant conformational dynamics on μs-ms time scales upon binding of Mg2+ ions. Two groups of catalytic residues exhibit differential line broadening, implicating distinct reorganizational processes upon binding of metal ions. These results support the "mobile metal ion" hypothesis, which was inferred from structural studies of RNase H. © 2013 American Chemical Society.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Many proteins use Asx and Glx (x = n, p, or u) side chains as key functional groups in enzymatic catalysis and molecular recognition. In this study, NMR spin relaxation experiments and molecular dynamics simulations are used to measure the dynamics of the side chain amide and carboxyl groups, 13Cγ/δ, in Escherichia coli ribonuclease HI (RNase H). Model-free analysis shows that the catalytic residues in RNase H are preorganized on ps-ns time scales via a network of electrostatic interactions. However, chemical exchange line broadening shows that these residues display significant conformational dynamics on μs-ms time scales upon binding of Mg2+ ions. Two groups of catalytic residues exhibit differential line broadening, implicating distinct reorganizational processes upon binding of metal ions. These results support the "mobile metal ion" hypothesis, which was inferred from structural studies of RNase H. © 2013 American Chemical Society. |