Conformational Analysis for Oligopeptides using Hamiltonian Algorithm coupled with ab initio Molecular Orbital Calculation -Hydrogen-bond controlled conformational analysis-

Abstract

Hydrogen bond and hydrophobic interaction are important to determine three-dimensional structure of protein. We analyzed conformational change of oligopeptides caused by intra-molecular hydrogen-bond formation and/or deformation using ab initio MO-MD method based on the Hamiltonian Algorithm at the HF/3-21G level. All initial conformations were assumed as alpha-helix structures. A glycine pentamer has two intra-molecular hydrogen bonds an initial alpha-helix conformation. One of these hydrogen bonds was formed between 1- and 4-residues, the other was between 2- and 5-residues. Both hydrogen bonds were deformed at around 3000 steps in an energy trajectory and new three intra-molecular hydrogen bonds were formed simultaneously. In the case of alanine pentamer, two hydrogen bonds between similar residues as a glycine pentamer exist at an initial conformation. These hydrogen bonds were deformed at earlier (about 1500) steps than the glycine pentamer. After 4000 steps, new hydrogen bond between 1- and 5-residues was furthermore formed. We also carried out the analysis for typical acidic oligopeptides such as asparatic and glutamic acids pentamers. Our proposed ab initio MO-MD method is efficient to theoretically analyze dynamical process of hydrogen-bond formation/deformation in oligopeptides.