Molecular dynamics

Molecular dynamics (MD) simulation enables us to observe atomic-level or more coarse-grained views of molecular motions in silico. MD is widely used to investigate biomembrane phase transition, small molecule permeation across biomembrane, ion channels, and cell fusion. This chapter provides an overview of MD studies on membrane shaping induced by the Bin/Amphiphysin/Rvs (BAR) domain superfamily, a well-known protein family involved in the deformation of biomembranes. As deformation is a relatively large-scale phenomenon, a wide variety of models have been used. For example, MD with all-atom models provides atomistic mechanisms of the BAR domain binding to the membrane and membrane bending, whereas the use of coarse-grained models simulates the formation of BAR domain assemblies and large deformations of the membrane. This chapter summarizes the possible membrane deformation mechanisms (helix insertion and scaffolding), the roles of the flexibility of BAR domains, and BAR domain assemblies that induce different shapes of membranes.