title: Low free energy barrier for ion permeation through double-helical gramicidin.
abstract: The pentadecapeptide gramicidin forms a cation-specific ion channel in membrane environment. The two main conformations are the head-to-head helical dimer (HD) known as the channel conformation and the intertwined double helical form (DH) often refer to as nonchannel conformation. In this comparative study, the energetics of single potassium ion permeation by means of the potential of mean force (PMF) for both gramicidin conformations embedded in a DMPC bilayer has been addressed by molecular dynamics simulations. A significantly decreased free energy barrier by approximately 25 kJ/mol for potassium ion passage through DH as compared to HD is reported. Favorable electrostatic side chain-cation interactions in HD are overcompensated by phospholipid-cation interactions in DH. The latter are coupled to an increased accessibility of the channel entrance in DH due to distributed tryptophans along the channel axis. This result underscores the importance of the lipid environment of this channel not only for the equilibrium between the different conformations but also for their function as cation channels.
authors.affiliation: Theoretical and Computational Membrane Biology, Center for Bioinformatics, Saarland University, P.O. Box 15 11 50, 66041 Saarbrücken, Germany.
authors.forename: Shirley W I
authors.initials: SW
authors.lastname: Siu
authors.forename: Rainer A
authors.initials: RA
authors.lastname: Böckmann
mesh_terms: D001407:Bacillus / Q000378:metabolism; D002412:Cations; D019281:Dimerization; D004134:Dimyristoylphosphatidylcholine / Q000737:chemistry; D006096:Gramicidin / Q000737:chemistry*; D007477:Ions; D008051:Lipid Bilayers / Q000737:chemistry; D008055:Lipids / Q000737:chemistry; D008954:Models, Biological; D008962:Models, Theoretical; D008968:Molecular Conformation; D010743:Phospholipids / Q000737:chemistry; D012997:Solvents / Q000737:chemistry; D013499:Surface Properties; D013816:Thermodynamics
chemical_list: D002412:Cations; D007477:Ions; D008051:Lipid Bilayers; D008055:Lipids; D010743:Phospholipids; D012997:Solvents; D006096:Gramicidin; D004134:Dimyristoylphosphatidylcholine