A theoretical study of screw-sense reversal process of alpha-helix

Abstract

A helix structure is one of the important building components of proteins. In this study, we focus on the screw-sense reversal process between the right- and left-handed alpha-helices. We calculated the phi-psi map of alanine model molecule by optimizing all other geometrical parameters. Based on the phi-psi map, we found four TS structures, which might be related to reversal pathways. We performed direct ab initio MD simulations from each of those TS structures and found two appropriate routes. In addition, we calculated the energy of 10-mer alanine model to estimate the required number of amino acid residues for the reversal. We found that the reversal pathway of right-handed alpha helix to left-handed alpha helix might proceed via beta region and 2 amino acid residues are necessary for the reversal.