Mechanism of the Unfolding of Transmembrane α-Helical Segment (1−36)-Bacteriorhodopsin Studied by Molecular Dynamics Simulations

Abstract

The unfolding of the first transmembrane segment 1−36 bacteriorhodopsin (BR) was studied using 1.25 ns molecular dynamics (MD) simulation with an explicit representation of chloroform/methanol 1:1 mixture and a series of long (from 10 to 60 ns) Langevin dynamics (LD) simulations. Comparison of MD and LD simulations shows that the random and frictional forces of Langevin equation provides a good model for the weakly polar chloroform/methanol mixture. The dielectric permeability εo = 1−2 (ε = εor) was found to be suitable for the modeling of the shielding effect of a weakly polar solvent in the LD simulations. The enhancement of short-range electrostatic interactions stabilizes the α-helix in LD simulations. The α-helix unfolding proceeds through the formation of local regions, stabilized by π-helical hydrogen bonds (π-bulges), in the central part of (1−36)-BR. Being formed, the π-bulges can propagate to metastable structures with partially solvated backbone intermediates on the way to an α-helix−random coil transition. Two regions of the π-bulges formation within (1−36)-BR are attached to the Leu-Gly-Thr sequence.