Protein Conformational Analysis by Multicanonical Molecular Dynamics Simulation

Abstract

Energy landscapes of three peptides were studied with multicanonical molecular dynamics. The landscapes were different depending on the amino-acid sequence of the peptides. The landscapes, which consisted of conformational clusters, showed the existence of free-energy barriers among the clusters, and provided pathways of conformational changes. Folding mechanism of proteins was discussed from the current results. Some problems, which should be overcome to treat a protein system, are pointed out.