Self-assembly of transmembrane helices of bacteriorhodopsin by a replica-exchange Monte Carlo simulation

We examine by a molecular simulation whether or not the transmembrane helices of bacteriorhodopsin have the ability to self-assemble into the native configuration by themselves. Starting from random initial configurations of seven transmembrane helices, the same helix arrangement as the experimental one (PDB code: 1C3W) was obtained by a replica-exchange Monte Carlo simulation. This implies that helix–helix interactions are the main driving force for the native structure formation of bacteriorhodopsin.