Computational Biophysics - Simon Bernèche
The Computational Biophysics group is interested in the structure-function relationship of membrane proteins. Using molecular mechanics simulations, the group aims at understanding the microscopic mechanisms underlying the functions of proteins involved in the membrane transport of various substrates. A central topic of study concerns the elucidation of gating mechanisms regulating the activity of potassium channels in excitable cells.
Membrane proteins are dynamical structures that change conformation in response to the environment, allowing for their contribution to different signalling processes. Ion channels are notably involved in the regulation of action potentials in excitable tissues, such as the heart and brain. Despite extensive electrophysiological and structural data, the atomistic mechanisms regulating the conductance of these protein channels remain unknown. By combining explicit molecular dynamics simulations and statistical physics principles, the group aims at elucidating the molecular basis of these mechanisms in the potassium channels and various transporters. A multi-scale stochastic simulation framework is also developed to reproduce measurable data and to ultimately bridge atomistic simulations of membrane systems with macroscopic simulations of excitable tissues.