Biophysical Journal 46: 805-819 (1984)
© 1984 the Biophysical Society

This Article Full Text (PDF) Alert me when this article is cited Alert me if a correction is posted Services Similar articles in this journal Similar articles in PubMed Alert me to new issues of the journal Download to citation manager Citing Articles Citing Articles via HighWire Citing Articles via Google Scholar Google Scholar Articles by Lee, W K Articles by Jordan, P C Search for Related Content PubMed PubMed Citation Articles by Lee, W K Articles by Jordan, P C

Molecular dynamics simulation of cation motion in water-filled gramicidinlike pores.

ABSTRACT

A model calculation is carried out to study the potential energy profile of a sodium ion with several water molecules inside a simplified model of the gramicidin ion channel. The sodium ion is treated as a Lennard-Jones sphere with a point charge at its center. The Barnes polarizable water model is used to mimic the water molecules. A polarizable and deformable gramicidinlike channel is constructed based on the model obtained by Koeppe and Kimura. Potential minima and saddle points are located and the static energy barriers are computed. The potential minima at the two mouths of the channel exhibit an aqueous solvation structure very different from that at any of the interior minima. These sites are approximately 23.6 and 24.4 A apart for binding of a sodium ion and a cesium ion, respectively. Ionic motion from these exterior sites to the first interior minimum requires substantial rearrangement of the waters of solvation; this rearrangement may be the hydration/dehydration step in ionic permeation through the channel. Based on these results, a mechanism by which the sodium ion moves from the exterior binding site to the interior of the channel is proposed. Our model channel accommodates about eight water molecules and the transport of the ion and water within the channel is found to be single file. Results of less extensive calculations for Cs+ and Li+ ions in a channel with or without water are also reported.

This article has been cited by other articles:

				V. L. Dorman and P. C. Jordan Ionic Permeation Free Energy in Gramicidin: A Semimicroscopic Perspective Biophys. J., June 1, 2004; 86(6): 3529 - 3541. [Abstract] [Full Text] [PDF]

				S. Garofoli and P. C. Jordan Modeling Permeation Energetics in the KcsA Potassium Channel Biophys. J., May 1, 2003; 84(5): 2814 - 2830. [Abstract] [Full Text] [PDF]