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

TL;DR

This paper introduces a novel computational approach combining 3D-RISM theory and the string method to efficiently identify the minimum free energy pathways for ions and small molecules moving through proteins.

Contribution

The paper presents a new method that integrates 3D-RISM and the string method to determine MFEPs in protein transport processes, enhancing existing computational techniques.

Findings

Successfully applied to Na+ conduction in channelrhodopsin

Accurately identifies free energy pathways within proteins

Demonstrates efficiency of combined 3D-RISM and string method

Abstract

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