A new method for finding the minimum free energy pathway of ions and small molecule transportation through protein based on 3D-RISM theory and the string method

摘要

A new method for finding the minimum free energy pathway (MFEP) of ions andsmall molecule transportation through a protein based on the three-dimensionalreference interaction site model (3D-RISM) theory combined with the stringmethod has been proposed. The 3D-RISM theory produces the distributionfunction, or the potential of mean force (PMF), for transporting substancesaround and inside proteins. By applying the string method to the PMF surface,one can readily determine the MFEP of the transporting substances inside aprotein. The method has been applied to consider the Na+ conduction pathway ofchannelrhodopsin as an example.