Theoretical study of intramolecular interaction energies during dynamics simulations of oligopeptides by the fragment molecular orbital-Hamiltonian algorithm method

We analyzed the interaction energies between residues (fragments) in an oligopeptide occurring during dynamic simulations by using the fragment molecular orbital-Hamiltonian algorithm (FMO-HA) method, an ab initio MO-molecular dynamics technique. The FMO method enables not only calculation of large molecules based on ab initio MO but also easy evaluation of interfragment interaction energies. The glycine pentamer [(Gly)(5)] and decamer [(Gly)(10)] were divided into five and ten fragments, respectively. alpha-helix structures of (Gly)(5) and (Gly)(10) were stabilized by attractive interaction energies owing to intramolecular hydrogen bonds between fragments n and n+3 sand n+4d, and beta-strand structures were characterized by repulsive interaction energies between fragments n and n+2. We analyzed interfragment interaction energies during dynamics simulations as the peptides' geometries changed from alpha helix to beta strand. Intramolecular hydrogen bonds between fragments 2-4 and 2-5 control the geometrical preference of (Gly)(5) for the beta-strand structure. The pitch of one turn of the alpha helix of (Gly)(10) elongated and thus weakened during dynamics due to a shifting of the intramolecular hydrogen bonds, and enabled the beta-strand structure to form. Changes in interaction energies due to the intramolecular hydrogen bonds controlled the tendency toward alpha-helix or beta-strand structure of (Gly)(5) and (Gly)(10). Evaluation of interfragment interaction energies during dynamics simulations thus enabled detailed analysis of the process of the geometrical changes occurring in oligopeptides. (C) 2005 American Institute of Physics.