The structures of membrane proteins are necessary to examine the functions and the mechanisms. The determination of membrane proteins takes a long time yet despite the development of experimental techniques. Thus, we have developed simulation methods for predicting alpha-helical membrane proteins. For the purpose, replica-exchange methods (REM) and a particular implicit membrane model are used. Distortions and kinked helix structures in transmembrane helices are frequently observed as a characteristic appearance of experimental membrane protein structures. Concerted rotation of torsion angles and dihedral angle of main chains in Monte Carlo move sets are implemented for including the distortions. Our implicit membrane model is to mimic the sampled configuration during native folding of membrane proteins after inserted membrane environment. We applied this method to bacteriorhodopsin, which has seven distorted transmembrane helices. From the random ideal helix configuration, we obtained local-minimum free energy states by REM simulations and principal component analysis. The RMSD value of whole backbone atoms from the PDB structure is 2.5 angstroms. The RMSD values in each helix structure about distortions are also less than about 1.5 angstroms.View Large Image | View Hi-Res Image | Download PowerPoint Slide