Paper Citing NAMD - Abstract
Liu, Z.W.; Xu, Y.; Tang, P.
Steered molecular dynamics simulations of Na+ permeation across the gramicidin a channel
JOURNAL OF PHYSICAL CHEMISTRY B, 110:12789-12795, JUN 29 2006
The potential of mean forces (PMF) governing Na+ permeation through gramicidin A (gA) channels with explicit water and membrane was characterized using steered molecular dynamics (SMD) simulations. Constant-force SMD with a steering force parallel to the channel axis revealed at least seven energy wells in each monomer of the channel dimer. Except at the channel dimer interface, each energy well is associated with at least three and at most four backbone carbonyl oxygens and two water oxygens in a pseudo-hexahedral or pseudo-octahedral coordination with the Na+ ion. Repeated constant-velocity SMD by dragging a Na+ ion from each energy well in opposite directions parallel to the channel axis allowed the computation of the PMF across the gA channel, revealing a global minimum corresponding to Na+ binding sites near the entrance of gA at +/- 9.3 angstrom from the geometric center of the channel. The effect of volatile anesthetics on the PMF was also analyzed in the presence of halothane molecules. Although the accuracy of the current PMF calculation from SMD simulations is not yet sufficient to quantify the PMF difference with and without anesthetics, the comparison of the overall PMF profiles nevertheless confirms that the anesthetics cause insignificant changes to the structural makeup of the free energy wells along the channel and the overall permeation barrier. On average, the PMF appears less rugged in the outer part of the channel in the presence of anesthetics, consistent with our earlier finding that halothane interaction with anchoring residues makes the gA channel more dynamic. A causal relationship was observed between the reorientation of the coordinating backbone carbonyl oxygen and Na+ transit from one energy well to another, suggesting the possibility that even minute changes in the conformation of pore-lining residues due to dynamic motion could be sufficient to trigger the ion permeation. Because some of the carbonyl oxygens contribute to Na+ coordination in two adjacent energy wells, our SMD results reveal that the atomic picture of ion "hopping" through a gA channel actually involves a Na+ ion being carried in a relay by the coordinating oxygens from one energy well to the next. Steered molecular dynamics complements other computational approaches as an attractive means for the atomistic interpretation of experimental permeation studies.
