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. α-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 (and n+4), and β-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 α helix to β strand. Intramolecular hydrogen bonds between fragments 2-4 and 2-5 control the geometrical preference of (Gly)5 for the β-strand structure. The pitch of one turn of the α helix of (Gly)10 elongated and thus weakened during dynamics due to a shifting of the intramolecular hydrogen bonds, and enabled the β-strand structure to form. Changes in interaction energies due to the intramolecular hydrogen bonds controlled the tendency toward α-helix or β-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.

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