Molecular dynamics simulations of proteins in lipid bilayers

James Gumbart, Yi Wang, Aleksei Aksimentiev, Emad Tajkhorshid, and Klaus Schulten
Curr Opin Struct Biol 15(4) 423-31 (2005)
DOI:10.1016/  PMID:16043343  BibTex

With recent advances in X-ray crystallography of membrane proteins promising many new high-resolution structures, molecular dynamics simulations will become increasingly valuable for understanding membrane protein function, as they can reveal the dynamic behavior concealed in the static structures. Dramatic increases in computational power, in synergy with more efficient computational methodologies, now allow us to carry out molecular dynamics simulations of any structurally known membrane protein in its native environment, covering timescales of up to 0.1 micros. At the frontiers of membrane protein simulations are ion channels, aquaporins, passive and active transporters, and bioenergetic proteins.