title: Molecular dynamics simulations of gramicidin A in a lipid bilayer: from structure-function relations to force fields.
abstract: Molecular dynamics simulations of membrane proteins have become a popular tool for studying their dynamic features, which are not easily accessible by experiments. Whether the force fields developed for globular proteins are adequate this purpose is an important question that is often glossed over. Here we determine the permeation properties of potassium ions in the gramicidin A channel in a lipid bilayer from free energy simulations, and compare the results to experimental data. In particular, we check the dependence of the free energy barriers ions face at the channel center on the membrane size. The results indicate that there is a serious problem with the current rigid force fields independent of the membrane size, and new, possibly polarizable, force fields need to be developed to resolve this problem.
authors.affiliation: School of Physics, University of Sydney, NSW, Australia.
authors.forename: Turgut
authors.initials: T
authors.lastname: Baştuğ
authors.forename: Swarna M
authors.initials: SM
authors.lastname: Patra
authors.forename: Serdar
authors.initials: S
authors.lastname: Kuyucak
mesh_terms: D002412:Cations; D003198:Computer Simulation; D004553:Electric Conductivity; D004735:Energy Transfer; D006096:Gramicidin / Q000737:chemistry*; D007473:Ion Channels / Q000737:chemistry*; D008051:Lipid Bilayers / Q000737:chemistry*; D008560:Membrane Fluidity; D008564:Membrane Potentials; D008968:Molecular Conformation; D011188:Potassium / Q000737:chemistry; D013816:Thermodynamics; D014867:Water / Q000737:chemistry
chemical_list: D002412:Cations; D007473:Ion Channels; D008051:Lipid Bilayers; D014867:Water; D006096:Gramicidin; D011188:Potassium