The open state gating mechanism of gramicidin a requires relative opposed monomer rotation and simultaneous lateral displacement.

The gating mechanism of the open state of the gramicidin A (gA) channel is studied by using a new Monte Carlo Normal Mode Following (MC-NMF) technique, one applicable even without a target structure. The results demonstrate that the lowest-frequency normal mode (NM) at approximately 6.5 cm(-1) is the crucial mode that initiates dissociation.

Permeation and gating in proteins: kinetic Monte Carlo reaction path following.

We present a new Monte Carlo technique, kinetic Monte Carlo reaction path following (kMCRPF), for the computer simulation of permeation and large-scale gating transitions in protein channels. It combines ideas from Metropolis Monte Carlo (MMC) and kinetic Monte Carlo (kMC) algorithms, and is particularly suitable when a reaction coordinate is well defined. Evolution of transition proceeds on the reaction coordinate by small jumps (kMC technique) toward the nearest lowest-energy uphill or downhill states, with the jumps thermally activated (constrained MMC).

Crowding-induced organization in cells: spontaneous alignment and sorting of filaments with physiological control points.

Under sufficiently crowded conditions, elongated particles spontaneously align along a common axis and separate from particles with dissimilar packing parameters. Clarifying the relevance of these entropy-driven phenomena to intact cells has required the development of theoretical approaches that tractably take into account daunting physiological complexities including the extreme crowding of the cytosol, the complex mixture of macromolecules present, the process of filament self-assembly, and the characteristic widths, flexibilities and charges of filaments formed by different proteins. This review summarizes the approaches taken, including their validation by observations of simpler systems, and the insights that have been gained into the means by which cells can modulate and capitalize upon spontaneous ordering.