The Laboratoire International Associé between the Centre National de la Recherche Scientifique and the University of Illinois at Urbana-Champaign was launched at the end of 2012. Its primary objective is to develop methods for high-performance molecular simulation with the aim of understanding the function of complex biological assemblies, transcending the frontiers of traditional disciplines by uniting mathematicians, physicists, theoretical chemists and biologists on both sides of the Atlantic. In France, the major contributors are located at the Université de Lorraine, the École des Ponts ParisTech, the Institut de Biologie Structurale and the Laboratoire de Biologie Physico-Chimique. In the United States, the contributors belong to the NIH Resource for Macromolecular Modeling and Bioinformatics. In Nancy, the partner is a theoretical chemistry and biophysics group incepted in 2003. Its expertise lies in describing the structure and the dynamic properties of the biological membrane and elucidating the mechanisms of the cell machinery. To attain this goal, its members leverage numerical simulations over size and timescales commensurate with the biological process at hand. Over the years, the team has gleaned milestone results in such diverse research areas as membrane transport, interaction with the biological membrane, membrane protein structure and function, as well as self-organized molecular systems. They also develop original approaches in the field of free-energy calculations to tackle rare events in biology.
Highlight

CryoEM and MD infer water-mediated proton transport and autoinhibition mechanisms of VO complex. Rotary motor V-ATPases drive trans-membrane proton transport through a VO proton channel subcomplex. Despite recent high-resolution structures of several rotary ATPases, the dynamic mechanism of proton pumping remains elusive. Here, we have determined a 2.7 Å cryoEM structure of yeast VO proton channel in nanodisc that reveals the location of ordered water molecules along the proton path, as well as details of specific protein-lipid interactions and the architecture of the membrane scaffold protein. We also uncover a state of VO that shows the ten membrane-embedded c-ring proteins rotated by ~14º. Molecular dynamics simulations demonstrate that the two rotary states are in thermal equilibrium, and depict how the protonation state of essential glutamic acid residues in the proton path couples water mediated proton transfer with c-ring rotation. Our cryoEM models and simulations rationalize a mechanism for inhibition of passive proton transport as observed for free VO that is generated as a result of V-ATPase regulation by reversible disassembly in vivo. Science Advances, 2020.
Recent publications
Standard Binding Free Energy and Membrane Desorption Mechanism for a Phospholipase C
Emmanuel E. Moutoussamy; Hanif M. Khan; Mary F. Roberts; Anne Gershenson; Christophe Chipot; Nathalie Reuter;
Journal of Chemical Information and Modeling (2022)
MLCV: Bridging Machine-Learning-Based Dimensionality Reduction and Free-Energy Calculation
Haochuan Chen; Han Liu; Heying Feng; Haohao Fu; Wensheng Cai; Xueguang Shao; Christophe Chipot;
Journal of Chemical Information and Modeling (2022) 62 (1): 1-8
Conformational transitions and ligand-binding to a muscle-type nicotinic acetylcholine receptor
Eleftherios Zarkadas; Eva Pebay-Peyroula; Mackenzie John Thompson; Guy Schoehn; Tomasz Uchanski; Jan Steyaert; Christophe Chipot; Francois Dehez; John Edward Baenziger; Hugues Nury;
Neuron (2022) 7 (8): e42166-1370.e5