Fast stability evaluation of protein quaternary structure by using coarse-grained potentials

Abstract

A lot of proteins retained activity in vivo forms quaternary structures. In the protein-protein docking to predict the quaternary structure, fast-evaluation of the protein-protein interactions is important. In our previous works on the development of a fast search method for protein-peptide ligand complex structures (peptide-ligand docking), we applied two statistical coarse-grained potentials, Krishnamoorthy’s original and our improvement, as the score evaluation function for quaternary structures of a protein. In this work, to review whether these potentials can be employed as the stability evaluation of protein quaternary structures, many polymorphic structures of the phosphofructokinase tetramer are generated and compared by using AMBER force field and their statistical coarse-grained potentials.