Guillaume BOUVIGNIES

@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}
}

@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}
}

@article{Yuwen:2018a,
title = {Exploring methods to expedite the recording of CEST datasets using selective pulse excitation},
author = {T Yuwen and G Bouvignies and L E Kay},
url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85046777410&doi=10.1016%2fj.jmr.2018.04.013&partnerID=40&md5=48a37dc0b711e94e1e0f83e223623b17},
doi = {10.1016/j.jmr.2018.04.013},
year = {2018},
date = {2018-01-01},
journal = {Journal of Magnetic Resonance},
volume = {292},
pages = {1--7},
abstract = {Chemical Exchange Saturation Transfer (CEST) has emerged as a powerful tool for studies of biomolecular conformational exchange involving the interconversion between a major, visible conformer and one or more minor, invisible states. Applications typically entail recording a large number of 2D datasets, each of which differs in the position of a weak radio frequency field, so as to generate a CEST profile for each nucleus from which the chemical shifts of spins in the invisible state(s) are obtained. Here we compare a number of band-selective CEST schemes for speeding up the process using either DANTE or cosine-modulated excitation approaches. We show that while both are essentially identical for applications such as 15N CEST, in cases where the probed spins are dipolar or scalar coupled to other like spins there can be advantages for the cosine-excitation scheme. © 2018 Elsevier Inc.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}

@article{Yuwen:2018b,
title = {Dramatic Decrease in CEST Measurement Times Using Multi-Site Excitation},
author = {T Yuwen and L E Kay and G Bouvignies},
url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85046716242&doi=10.1002%2fcphc.201800249&partnerID=40&md5=96d6aeb08f487d281571fadb84e95055},
doi = {10.1002/cphc.201800249},
year = {2018},
date = {2018-01-01},
journal = {ChemPhysChem},
volume = {19},
number = {14},
pages = {1707--1710},
abstract = {Chemical exchange saturation transfer (CEST) has recently evolved into a powerful approach for studying sparsely populated, “invisible” protein states in slow exchange with a major, visible conformer. Central to the technique is the use of a weak, highly selective radio-frequency field that is applied at different frequency offsets in successive experiments, “searching” for minor state resonances. The recording of CEST profiles with enough points to ensure coverage of the entire spectrum at sufficient resolution can be time-consuming, especially for applications that require high static magnetic fields or when small chemical shift differences between exchanging states must be quantified. Here, we show \textendash with applications involving 15N CEST \textendash that the process can be significantly accelerated by using a multi-frequency irradiation scheme, leading in some applications to an order of magnitude savings in measurement time. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim},
keywords = {},
pubstate = {published},
tppubtype = {article}
}

@article{Delaforge:2018,
title = {Deciphering the Dynamic Interaction Profile of an Intrinsically Disordered Protein by NMR Exchange Spectroscopy},
author = {E Delaforge and J Kragelj and L Tengo and A Palencia and S Milles and G Bouvignies and N Salvi and M Blackledge and M R Jensen},
url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85041194645&doi=10.1021%2fjacs.7b12407&partnerID=40&md5=7a13917d1fd4bd0a9adf7a30ff193101},
doi = {10.1021/jacs.7b12407},
year = {2018},
date = {2018-01-01},
journal = {Journal of the American Chemical Society},
volume = {140},
number = {3},
pages = {1148--1158},
abstract = {Intrinsically disordered proteins (IDPs) display a large number of interaction modes including folding-upon-binding, binding without major structural transitions, or binding through highly dynamic, so-called fuzzy, complexes. The vast majority of experimental information about IDP binding modes have been inferred from crystal structures of proteins in complex with short peptides of IDPs. However, crystal structures provide a mainly static view of the complexes and do not give information about the conformational dynamics experienced by the IDP in the bound state. Knowledge of the dynamics of IDP complexes is of fundamental importance to understand how IDPs engage in highly specific interactions without concomitantly high binding affinity. Here, we combine rotating-frame R1?, Carr-Purcell-Meiboom Gill relaxation dispersion as well as chemical exchange saturation transfer to decipher the dynamic interaction profile of an IDP in complex with its partner. We apply the approach to the dynamic signaling complex formed between the mitogen-activated protein kinase (MAPK) p38α and the intrinsically disordered regulatory domain of the MAPK kinase MKK4. Our study demonstrates that MKK4 employs a subtle combination of interaction modes in order to bind to p38α, leading to a complex displaying significantly different dynamics across the bound regions. © 2017 American Chemical Society.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}

@article{Sekhar:2018,
title = {Conserved conformational selection mechanism of Hsp70 chaperone-substrate interactions},
author = {A Sekhar and A Velyvis and G Zoltsman and R Rosenzweig and G Bouvignies and L E Kay},
url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-85043488787&doi=10.7554%2feLife.32764&partnerID=40&md5=d3081dfdf16cadcee7ad704e25984def},
doi = {10.7554/eLife.32764},
year = {2018},
date = {2018-01-01},
journal = {eLife},
volume = {7},
abstract = {Molecular recognition is integral to biological function and frequently involves preferred binding of a molecule to one of several exchanging ligand conformations in solution. In such a process the bound structure can be selected from the ensemble of interconverting ligands a priori (conformational selection, CS) or may form once the ligand is bound (induced fit, IF). Here we focus on the ubiquitous and conserved Hsp70 chaperone which oversees the integrity of the cellular proteome through its ATP-dependent interaction with client proteins. We directly quantify the flux along CS and IF pathways using solution NMR spectroscopy that exploits a methyl TROSY effect and selective isotope-labeling methodologies. Our measurements establish that both bacterial and human Hsp70 chaperones interact with clients by selecting the unfolded state from a pre-existing array of interconverting structures, suggesting a conserved mode of client recognition among Hsp70s and highlighting the importance of molecular dynamics in this recognition event. © Sekhar et al.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}

@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}
}

@article{Sekhar:2016,
title = {Hsp70 biases the folding pathways of client proteins},
author = {A Sekhar and R Rosenzweig and G Bouvignies and L E Kay},
url = {https://www.scopus.com/inward/record.uri?eid=2-s2.0-84969972739&doi=10.1073%2fpnas.1601846113&partnerID=40&md5=29683d385ffff9deb58f7988ba40b5af},
doi = {10.1073/pnas.1601846113},
year = {2016},
date = {2016-01-01},
journal = {Proceedings of the National Academy of Sciences of the United States of America},
volume = {113},
number = {20},
pages = {E2794--2801},
abstract = {The 70-kDa heat shock protein (Hsp70) family of chaperones bind cognate substrates to perform a variety of different processes that are integral to cellular homeostasis. Although detailed structural information is available on the chaperone, the structural features of folding competent substrates in the bound form have not been well characterized. Here we use paramagnetic relaxation enhancement (PRE) NMR spectroscopy to probe the existence of long-range interactions in one such folding competent substrate, human telomere repeat binding factor (hTRF1), which is bound to DnaK in a globally unfolded conformation. We show that DnaK binding modifies the energy landscape of the substrate by removing long-range interactions that are otherwise present in the unbound, unfolded conformation of hTRF1. Because the unfolded state of hTRF1 is only marginally populated and transiently formed, it is inaccessible to standard NMR approaches. We therefore developed a 1H-based CEST experiment that allows measurement of PREs in sparse states, reporting on transiently sampled conformations. Our results suggest that DnaK binding can significantly bias the folding pathway of client substrates such that secondary structure forms first, followed by the development of longer-range contacts between more distal parts of the protein.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}