Molecular Dynamics Simulation for Membrane Fusion.

Abstract

The soluble N-ethylmaleimide sensitive factor attachment protein receptor (SNARE) protein complex drives membrane fusion, and this process is further aided by accessory proteins, including complexin and α-synuclein. To understand the molecular mechanism underlying membrane fusion, we introduce an all-atom molecular dynamics (MD) simulation method. This method is used to understand and predict the conformations of protein and lipids, membrane geometry, and their interaction at femtosecond precision, by describing complex chemical systems with atomic models. Simulation results reveal information on distinct membrane fusion stages, including docking, hemifusion, and kiss-and-run fusion. Here, we introduce the simulation workflow, consisting of pre-MD construction, pre-MD setup in GROMACS, MD in GROMACS, and analysis.