Mechanism of the unfolding of transmembrane α-helical segment (1-36)-bacteriorhodopsin studied by molecular dynamics simulations

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 epsilon(o) = 1-2 (epsilon = epsilon(o)r) 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 alpha-helix in LD simulations. The alpha-helix unfolding proceeds through the formation of local regions, stabilized by pi-helical hydrogen bonds (pi-bulges), in the central part of (1-36)-BR. Being formed, the pi-bulges can propagate to metastable structures with partially solvated backbone intermediates on the way to an alpha-helix-random coil transition. Two regions of the pi-bulges formation within (1-36)-BR are attached to the Leu-Gly-Thr sequence.