title: Test of molecular dynamics force fields in gramicidin A.
abstract: The force fields commonly used in molecular dynamics simulations of proteins are optimized under bulk conditions. Whether the same force fields can be used in simulations of membrane proteins is not well established, although they are increasingly being used for such purposes. Here we consider ion permeation in the gramicidin A channel as a test of the AMBER force field in a membrane environment. The potentials of mean force for potassium ions are calculated along the channel axis and compared with the one deduced from the experimental conductance data. The calculated result indicates a rather large central barrier similar to those obtained from other force fields, which are incompatible with the conductance data. We suggest that lack of polarizability is the most likely cause of this problem, and, therefore, urge development of polarizable force fields for simulations of membrane proteins.
authors.affiliation: School of Physics, University of Sydney, NSW 2006, Australia. turgut@physics.usyd.edu.au
authors.forename: Turgut
authors.initials: T
authors.lastname: Bastug
authors.forename: Serdar
authors.initials: S
authors.lastname: Kuyucak
mesh_terms: D000465:Algorithms; D000900:Anti-Bacterial Agents / Q000737:chemistry / Q000494:pharmacology; D001703:Biophysics / Q000379:methods*; D002462:Cell Membrane / Q000378:metabolism; D003198:Computer Simulation; D019281:Dimerization; D006096:Gramicidin / Q000737:chemistry / Q000494:pharmacology*; D007473:Ion Channels / Q000737:chemistry; D007477:Ions / Q000737:chemistry; D008051:Lipid Bilayers / Q000737:chemistry; D008958:Models, Molecular; D015233:Models, Statistical; D008968:Molecular Conformation; D010455:Peptides / Q000737:chemistry; D011188:Potassium / Q000737:chemistry; D011487:Protein Conformation; D012984:Software; D055672:Static Electricity; D013696:Temperature
chemical_list: D000900:Anti-Bacterial Agents; D007473:Ion Channels; D007477:Ions; D008051:Lipid Bilayers; D010455:Peptides; D006096:Gramicidin; D011188:Potassium