title: Valence selectivity of the gramicidin channel: a molecular dynamics free energy perturbation study.
abstract: The valence selectivity of the gramicidin channel is examined using computer simulations based on atomic models. The channel interior is modeled using a gramicidin-like periodic poly (L,D)-alanine beta-helix. Free energy perturbation calculations are performed to obtain the relative affinity of K+ and Cl- for the channel. It is observed that the interior of the gramicidin channel provides an energetically favorable interaction site for a cation but not for an anion. Relative to solvation in bulk water, the carbonyl CO oxygens can provide a favorable interaction to stabilize K+, whereas the amide NH hydrogens are much less effective in stabilizing Cl-. The results of the calculations demonstrate that, as a consequence of the structural asymmetry of the backbone charge distribution, a K+ cation can partition spontaneously from bulk water to the interior of the gramicidin channel, whereas a Cl- anion cannot.
authors.affiliation: Départements de physique et de chimie, Université de Montréal, Québec, Canada. rouxb@PLGCN.umontreal.ca
authors.forename: B
authors.initials: B
authors.lastname: Roux
mesh_terms: D002151:Calorimetry; D002712:Chlorides; D003198:Computer Simulation; D006096:Gramicidin; D007473:Ion Channels; D008954:Models, Biological; D010455:Peptides / Q000737:chemistry*; D011188:Potassium; D017433:Protein Structure, Secondary; D012984:Software; D013816:Thermodynamics
chemical_list: D002712:Chlorides; D007473:Ion Channels; D010455:Peptides; D006096:Gramicidin; C019529:polyalanine; D011188:Potassium