PhD student, École Normale Supérieure
Laboratoire des Biomolécules, UMR7203
ENS – Département de chimie
24 rue Lhomond, 75005 Paris
Email: nicolas.bolik-coulon@ens.psl.eu
Office: ES111
Short bio
Nicolas Bolik-Coulon was an undergrad at the Chemistry department of the École Normale Supérieure, Paris, where he received training in organic, inorganic and physical chemistry and then specialized in biophysics. He joined the Laboratoire des Biomolecules in 2016 for his master thesis under the supervision of Prof. Fabien Ferrage on the characterization of the structural ensemble of a long Intrinsically Disordered Protein (IDP) using Nuclear Magnetic Resonance (NMR). As part of his program, he stayed another year in the lab developing computational tools to analyze high-resolution relaxometry data to characterize the dynamics of proteins over a wide range of timescales (pico- to nanosecond). In 2017-2018, he joined Prof. Wolfgrang Peti at the University of Arizona, Tucson, USA. He started his PhD under the supervision of Prof. Fabien Ferrage in 2018 on the development of tools to characterize the dynamics of protein by NMR.
Education and professional experience
- since 2018 PhD student under the supervision of Prof. Fabien Ferrage, Ecole Normale Supérieure, Paris
- 2019-2021 Co-chair of the Gordon Research Seminar on Computational Aspects of Biomolecular NMR
- 2017-2018 Research Technician in Prof. Wolfgang Peti lab, University of Arizona, USA
- 2016-2017 Internship student under the supervision of Prof. Fabien Ferrage, Ecole Normale Supérieure, Paris
- 2014-2016 Master of Science in Chemistry and Biophysics, with distinction
- 2011-2014 Bachelor of Science in Chemistry, with distinction
Research interests
- Protein dynamics
- Nuclear Magnetic Resonance
- Structural biology
Awards and distinctions
- 2018-2021 PhD fellowship from the École Normale Supérieure, Paris
- 2013-2017 4-year fellowship from the École Normale Supérieure, Paris
Teaching
- Teaching Assistant at the Chemistry Department of the École Normale Supérieure
Significant publications
- Time-Resolved Protein Side-Chain Motions Unraveled by High-resolution Relaxometry and Molecular Dynamics Simulations, S.F. Cousin, P. Kadeřávek, N. Bolik-Coulon, Y. Gu, C. Charlier, L. Carlier, L. Bruschweiler-Li, T. Marquardsen, J-M Tybrun, R. Bruschweiler, F. Ferrage, J. Am. Chem. Soc., 140, 13456 (2018)
Publications
2020 |
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 Kadeřávek 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 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{Jasenáková2020, title = {Boosting the resolution of low‐field 15N relaxation experiments on intrinsically disordered proteins with triple‐resonance NMR}, author = {Z Jasenáková 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 𝛿 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 𝛿 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{Kadeřávek2019, title = {Protein Dynamics from Accurate Low-Field Site-Specific Longitudinal and Transverse Nuclear Spin Relaxation}, author = {P Kadeřávek 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} } |
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 Kadeřávek 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 |
The structure of SDS22 provides insights into the mechanism of heterodimer formation with PP1 Article de journal M.S. Choy; N Bolik-Coulon; T.L. Archuleta; W. Peti; R. Page Acta Crystallographica Section F, F74 , p. 817, 2018. @article{Choy2018, title = {The structure of SDS22 provides insights into the mechanism of heterodimer formation with PP1}, author = {M.S. Choy and N Bolik-Coulon and T.L. Archuleta and W. Peti and R. Page}, url = {http://scripts.iucr.org/cgi-bin/paper?S2053230X18016503}, doi = {10.1107/S2053230X18016503}, year = {2018}, date = {2018-11-19}, journal = {Acta Crystallographica Section F}, volume = {F74}, pages = {817}, abstract = {Protein phosphatase 1 (PP1) dephosphorylates hundreds of key biological targets by associating with nearly 200 regulatory proteins to form highly specific holoenzymes. The vast majority of regulators are intrinsically disordered proteins (IDPs) and bind PP1 via short linear motifs within their intrinsically disordered regions. One of the most ancient PP1 regulators is SDS22, a protein that is conserved from yeast to mammals. Sequence analysis of SDS22 revealed that it is a leucine-rich repeat (LRR) protein, suggesting that SDS22, unlike nearly every other known PP1 regulator, is not an IDP but instead is fully structured. Here, the 2.9 A ̊ resolution crystal structure of human SDS22 in space group P212121 is reported. SDS22 adopts an LRR fold with the horseshoe-like curvature typical for this family of proteins. The structure results in surfaces with distinct chemical characteristics that are likely to be critical for PP1 binding.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Protein phosphatase 1 (PP1) dephosphorylates hundreds of key biological targets by associating with nearly 200 regulatory proteins to form highly specific holoenzymes. The vast majority of regulators are intrinsically disordered proteins (IDPs) and bind PP1 via short linear motifs within their intrinsically disordered regions. One of the most ancient PP1 regulators is SDS22, a protein that is conserved from yeast to mammals. Sequence analysis of SDS22 revealed that it is a leucine-rich repeat (LRR) protein, suggesting that SDS22, unlike nearly every other known PP1 regulator, is not an IDP but instead is fully structured. Here, the 2.9 A ̊ resolution crystal structure of human SDS22 in space group P212121 is reported. SDS22 adopts an LRR fold with the horseshoe-like curvature typical for this family of proteins. The structure results in surfaces with distinct chemical characteristics that are likely to be critical for PP1 binding. |
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 Kadeřávek 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 Brüschweiler 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. |
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 Kadeřávek 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—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.}, 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. |
2017 |
Caspase-6 Undergoes a Distinct Helix-Strand Interconversion upon Substrate Binding Article de journal K.B. Dagbay; N Bolik-Coulon; S.N. Savinov; J.A. Hardy Journal of Biological Chemistry, 292 (12), p. 4885, 2017. @article{Dagbay2017, title = {Caspase-6 Undergoes a Distinct Helix-Strand Interconversion upon Substrate Binding}, author = {K.B. Dagbay and N Bolik-Coulon and S.N. Savinov and J.A. Hardy}, url = {http://www.jbc.org/content/292/12/4885.long}, doi = {10.1074/jbc.M116.773499}, year = {2017}, date = {2017-03-24}, journal = {Journal of Biological Chemistry}, volume = {292}, number = {12}, pages = {4885}, abstract = {Caspases are cysteine aspartate proteases that are major players in key cellular processes, including apoptosis and inflammation. Specifically, caspase-6 has also been implicated in playing a unique and critical role in neurodegeneration; however, structural similarities between caspase-6 and other caspase active sites have hampered precise targeting of caspase-6. All caspases can exist in a canonical conformation, in which the substrate binds atop a b-strand platform in the 130’s region. This caspase-6 region can also adopt a helical conformation that has not been seen in any other caspases. Understanding the dynamics and interconversion between the helical and strand conformations in caspase-6 is critical to fully assess its unique function and regulation. Here, hydrogen/deuterium exchange mass spectrometry indicated that caspase-6 is inherently and dramatically more conformationally dynamic than closely related caspase-7. In contrast to caspase-7, which rests constitutively in the strand conformation before and after substrate binding, the hydrogen/ deuterium exchange data in the L2' and 130’s regions suggested that before substrate binding, caspase-6 exists in a dynamic equilibrium between the helix and strand conformations. Caspase-6 transitions exclusively to the canonical strand con- formation only upon substrate binding. Glu-135, which showed noticeably different calculated pKa values in the helix and strand conformations, appears to play a key role in the interconversion between the helix and strand conformations. Because caspase-6 has roles in several neurodegenerative diseases, exploiting the unique structural features and conformational changes identified here may provide new avenues for regulating specific caspase-6 functions for therapeutic purposes.}, keywords = {}, pubstate = {published}, tppubtype = {article} } Caspases are cysteine aspartate proteases that are major players in key cellular processes, including apoptosis and inflammation. Specifically, caspase-6 has also been implicated in playing a unique and critical role in neurodegeneration; however, structural similarities between caspase-6 and other caspase active sites have hampered precise targeting of caspase-6. All caspases can exist in a canonical conformation, in which the substrate binds atop a b-strand platform in the 130’s region. This caspase-6 region can also adopt a helical conformation that has not been seen in any other caspases. Understanding the dynamics and interconversion between the helical and strand conformations in caspase-6 is critical to fully assess its unique function and regulation. Here, hydrogen/deuterium exchange mass spectrometry indicated that caspase-6 is inherently and dramatically more conformationally dynamic than closely related caspase-7. In contrast to caspase-7, which rests constitutively in the strand conformation before and after substrate binding, the hydrogen/ deuterium exchange data in the L2' and 130’s regions suggested that before substrate binding, caspase-6 exists in a dynamic equilibrium between the helix and strand conformations. Caspase-6 transitions exclusively to the canonical strand con- formation only upon substrate binding. Glu-135, which showed noticeably different calculated pKa values in the helix and strand conformations, appears to play a key role in the interconversion between the helix and strand conformations. Because caspase-6 has roles in several neurodegenerative diseases, exploiting the unique structural features and conformational changes identified here may provide new avenues for regulating specific caspase-6 functions for therapeutic purposes. |
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. |