Olivier WALKER
Biophysics of complex systems, Group Leader
Theoretical & experimental approaches for molecular interactions, Axis coordinator
Assistant Professor, PhD
Contact
olivier.walker[@]isa-lyon.fr
Research
Structural and dynamical characterization of protein/protein and protein/ligand interactions in the liquid state by means of NMR methods. Methodological developments based on spin relaxation, paramagnetic probes, residual dipolar couplings and Small Angle Neutron Scattering. Free energy calculations based on the combination of metadynamics and NMR to understand interaction processes.
Biography
Olivier Walker is currently Assistant Professor (French Maître de Conférence) in the department of Chemistry and Biochemistry at the University of Lyon (France). He obtained his M.Sc. in physical chemistry in 1997 while he received his Ph.D. degree in physical chemistry from the University of Nancy (France) in 2001 where he developed new NMR methodologies to study the rotational diffusion of small molecules in the liquid state, under the supervision of Pr. Daniel Canet. He joined Pr. David Fushman’s lab in 2002 at the University of Maryland (USA) as a postdoctoral fellow to work on protein/protein interactions and more particularly proteins involved in the Proteasome-Ubiquitin system. He developed different approaches to characterize the structure and dynamics of multi-domain proteins. In 2004, he moved to the Institut des Sciences Analytiques where he focused his research on protein/protein (proteins involved in lysosomal degradation) and protein/ligand interactions (proteins of the Prx family) by nuclear magnetic resonance and computational methods based on GPU technology.
Keywords
NMR, protein, interactions, metadynamics, molecular dynamics, paramagnetism
Publications
2023
Journal articles
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- Yoan Monneau, Cyrielle Arrault, Coraline Duroux, Marie Martin, Fabien Chirot, et al.. Structural and dynamical insights into SilE silver binding from combined analytical probes. Physical Chemistry Chemical Physics, 2023, 25 (4), pp.3061-3071. ⟨10.1039/x0xx00000x⟩. ⟨hal-03960103⟩
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2021
Journal articles
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- Tingting Niu, Charlotte de Rosny, Séverine Chautard, Amaury Rey, Danish Patoli, et al.. NLRP3 phosphorylation in its LRR domain critically regulates inflammasome assembly. Nature Communications, 2021, 12 (1), pp.Article number: 5862. ⟨10.1038/s41467-021-26142-w⟩. ⟨hal-03401509⟩
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- Lucille Babel, Minh-Ha Nguyen, Cédric Mittelheisser, Marie Martin, Katharina Fromm, et al.. NMR reveals the interplay between SilE and SilB model peptides in the context of silver resistance. Chemical Communications, 2021, 57 (70), pp.8726-8729. ⟨10.1039/d1cc02597j⟩. ⟨hal-03967989⟩
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- Lucille Babel, Minh-Ha Nguyen, Cédric Mittelheisser, Marie Martin, Katharina Fromm, et al.. NMR reveals the interplay between SilE and SilB model peptides in the context of silver resistance. Chemical Communications, 2021, 57, pp.8726-8729. ⟨10.1039/d1cc02597j⟩. ⟨hal-03324047⟩
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2020
Journal articles
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- Moreno Marcellini, Minh-Ha Nguyen, Marie Martin, Maggy Hologne, Olivier Walker. Accurate Prediction of Protein NMR Spin Relaxation by Means of Polarizable Force Fields. Application to Strongly Anisotropic Rotational Diffusion. Journal of Physical Chemistry B, 2020, 124 (25), pp.5103-5112. ⟨10.1021/acs.jpcb.0c01922⟩. ⟨hal-03968000⟩
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- Moreno Marcellini, Minh-Ha Nguyen, Marie Martin, Maggy Hologne, Olivier Walker. Accurate Prediction of Protein NMR Spin Relaxation by Means of Polarizable Force Fields. Application to Strongly Anisotropic Rotational Diffusion. Journal of Physical Chemistry B, 2020, 124 (25), pp.5103-5112. ⟨10.1021/acs.jpcb.0c01922⟩. ⟨hal-03026991⟩
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2019
Journal articles
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- Minh-Ha Nguyen, Marie Martin, Henry Kim, Frank Gabel, Olivier Walker, et al.. Molecular recognition of ubiquitin and Lys63-linked diubiquitin by STAM2 UIM-SH3 dual domain: the effect of its linker length and flexibility. Scientific Reports, 2019, 9 (1), pp.14645. ⟨10.1038/s41598-019-51182-0⟩. ⟨hal-03968013⟩
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- Minh-Ha Nguyen, Marie Martin, Henry Kim, Frank Gabel, Olivier Walker, et al.. Molecular recognition of ubiquitin and Lys63-linked diubiquitin by STAM2 UIM-SH3 dual domain: the effect of its linker length and flexibility. Scientific Reports, 2019, 9 (1), ⟨10.1038/s41598-019-51182-0⟩. ⟨hal-02441244⟩
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- Louis-Marie Bloyet, Antoine Schramm, Carine Lazert, Bertrand Raynal, Maggy Hologne, et al.. Regulation of measles virus gene expression by P protein coiled-coil properties. Science Advances , 2019, 5 (5), pp.eaaw3702. ⟨10.1126/sciadv.aaw3702⟩. ⟨hal-02133726⟩
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2018
Journal articles
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- Po-Chia Chen, Maggy Hologne, Olivier Walker, Janosch Hennig. Ab Initio Prediction of NMR Spin Relaxation Parameters from Molecular Dynamics Simulations. Journal of Chemical Theory and Computation, 2018, 14 (2), pp.1009 - 1019. ⟨10.1021/acs.jctc.7b00750⟩. ⟨hal-01767727⟩
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- Valentin Chabert, Maggy Hologne, Olivier Sénèque, Olivier Walker, Katharina Fromm. Alpha-helical folding of SilE models upon Ag(His)(Met) motif formation. Chemical Communications, 2018, 54 (74), pp.10419 - 10422. ⟨10.1039/c8cc03784a⟩. ⟨hal-01900232⟩
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2017
Journal articles
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- Mark Nakasone, Timothy A. Lewis, Olivier Walker, Anita Thakur, Wissam Mansour, et al.. Structural Basis for the Inhibitory Effects of Ubistatins in the Ubiquitin-Proteasome Pathway. Structure, 2017, 25 (12), pp.1839 - 1855.e11. ⟨10.1016/j.str.2017.10.007⟩. ⟨hal-01679528⟩
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- V. Chabert, Maggy Hologne, O. Sénéque, A. Crochet, Olivier Walker, et al.. Model peptide studies of Ag + binding sites from the silver resistance protein SilE. Chemical Communications, 2017, 53 (45), pp.6105 - 6108. ⟨10.1039/c7cc02630g⟩. ⟨hal-01546472⟩
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- Po-Chia Chen, Maggy Hologne, Olivier Walker. Computing the rotational diffusion of biomolecules via molecular dynamics simulation and quaternion orientations . Journal of Physical Chemistry B, 2017, 121 (8), pp.1812-1823. ⟨10.1021/acs.jpcb.6b11703⟩. ⟨hal-01520066⟩
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2016
Journal articles
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- Maggy Hologne, Xavier Cantrelle, Gwladys Riviere, Florence Guillière, Xavier Trivelli, et al.. NMR Reveals the Interplay among the AMSH SH3 Binding Motif, STAM2, and Lys63-Linked Diubiquitin.. Journal of Molecular Biology, 2016, 428 (22), pp.4544-4558. ⟨10.1016/j.jmb.2016.10.002⟩. ⟨hal-01546483⟩
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- Mélanie Rigard, Jeanette E. Bröms, Amandine Mosnier, Maggy Hologne, Amandine Martin, et al.. Francisella tularensis IglG Belongs to a Novel Family of PAAR-Like T6SS Proteins and Harbors a Unique N-terminal Extension Required for Virulence. PLoS Pathogens, 2016, 12 (9), pp.article number: e1005821. ⟨10.1371/journal.ppat.1005821⟩. ⟨hal-01546486⟩
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- Carlos A Castaneda, Emma K Dixon, Olivier Walker, Apurva Chaturvedi, Mark A Nakasone, et al.. Linkage via K27 bestows ubiquitin chains with unique properties among polyubiquitins. Structure, 2016, 24 (3), pp.423-436. ⟨10.1016/j.str.2016.01.007⟩. ⟨hal-01359763⟩
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2015
Journal articles
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- Urszula Nowicka, Daoning Zhang, Olivier Walker, Daria Krutauz, Carlos A Castaneda, et al.. DNA-damage-inducible 1 protein (Ddi1) contains an uncharacteristic ubiquitin-like domain that binds ubiquitin. Structure, 2015, 23 (3), pp.542-557. ⟨10.1016/j.str.2015.01.010⟩. ⟨hal-01187309⟩
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- Laura Troussicot, Florence Guillière, Vittorio Limongelli, Olivier Walker, Jean-Marc Lancelin. Funnel-metadynamics and solution NMR to estimate protein-ligand affinities. Journal of the American Chemical Society, 2015, 137 (3), pp.1273-1281. ⟨10.1021/ja511336z⟩. ⟨hal-01187402⟩
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2014
Journal articles
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- Zoi Erpapazoglou, Olivier Walker, Rosine Haguenauer-Tsapis. Versatile Roles of K63-Linked Ubiquitin Chains in Trafficking. STEM CELLS, 2014, 3 (4), pp.1027-1088. ⟨10.3390/cells3041027⟩. ⟨hal-01128389⟩
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2013
Journal articles
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- Clémentine Aguirre, Tim Ten Brink, Olivier Walker, Florence Guillière, D. Davesne, et al.. BcL-xL Conformational Changes upon Fragment Binding Revealed by NMR. PLoS ONE, 2013, 8, pp.e64400. ⟨10.1371/journal.pone.0064400⟩. ⟨in2p3-00839023⟩
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2012
Journal articles
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- Anja Lange, Mouhamad-Baligh Ismail, Gwladys Rivière, Maggy Hologne, Denis Lacabanne, et al.. Competitive binding of UBPY and ubiquitin to the STAM2 SH3 domain revealed by NMR. FEBS Letters, 2012, 586 (19), pp.3379-3384. ⟨10.1016/j.febslet.2012.07.047⟩. ⟨hal-00819142⟩
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- Anja Lange, Carlos Castaneda, Daniela Hoeller, Jean-Marc Lancelin, David Fushman, et al.. Evidence for cooperative and domain-specific binding of the signal transducing adaptor molecule 2 (STAM2) to lys(63)-linked diubiquitin. Journal of Biological Chemistry, 2012, 287 (22), pp.18687-18699. ⟨10.1074/jbc.M111.324954⟩. ⟨hal-00873866⟩
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2011
Journal articles
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- Anja Lange, Daniela Hoeller, Hans Wienk, Olivier Marcillat, Jean-Marc Lancelin, et al.. NMR Reveals a Different Mode of Binding of the Stam2 VHS Domain to Ubiquitin and Diubiquitin. Biochemistry, 2011, 50 (1), pp.48-62. ⟨10.1021/bi101594a⟩. ⟨hal-00873854⟩
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