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.

Molecular dynamics simulation studies of the transport and adsorption of a charged macromolecule onto a charged adsorbent solid surface immersed in an electrolytic solution

“…They are both modeled as charged spherical particles [40,41]. It is worth emphasizing that only a very small number of formate ions (less than 20) are simulated in this study, making the approximation of spherical formate ions more reasonable.…”

“…The LJ potential parameters for the like ion pairs are σ Na + = 1.897 Å, ε Na + = 0.112 kcal/mol, σ HCOO − = 6.04 Å, and ε HCOO − = 0.75 kcal/mol, and these values were determined from the expressions in Refs. [40] and [41]. The LJ potential parameters for the unlike ion pairs are σ Na + -HCOO − = 4.6 Å and ε Na + -HCOO − = 0.10 kcal/mol, which are adopted from Ref.…”

“…The LJ potential parameters for the unlike ion pairs are σ Na + -HCOO − = 4.6 Å and ε Na + -HCOO − = 0.10 kcal/mol, which are adopted from Ref. [41]. The LJ potential parameters between ions and water are σ O-Na…”

Structure and function of channels and channelogs as studied by computational chemistry

“…These range from continuum electrostatic treatments [53] to microscopic calculations involving energy minimization [32,74,85], Monte Carlo [57], and molecular dynamics simulations [62,65]. However, although these studies provide much valuable information, they are disappointing in the differing, and generally unrealistically large, values they predict for the energy difference between the outside and the central region of the channel.…”

Ion Transport through Gramicidin A. Water Structure and Functionality

“…In the investigations by M ackay et al [13], Lee and Jo rd a n [14] an d E tchebest and Pullm an [15] less th a n 24 w ater m olecules were considered. T herefore the w ater m olecules occupy essentially the channel in terio r an d only som e o f them are found outside in the entrance region o f the ch an nel.…”