Peptides of Aminoxy Acids : A Molecular Dynamics Simulation Study of Conformational Equilibria under Various Conditions

Abstract

Molecular dynamics simulations have been performed to study the conformational behavior of peptide analogues formed by α-aminoxy acids. The influence of temperature, type of solvent, and chain length has been investigated. The NMR and CD spectra of these peptides, as well as ab initio quantum-mechanical calculations, indicate the presence of strong intramolecular hydrogen bonds between adjacent residues. In the simulations in chloroform the eight-membered-ring strucures formed by these hydrogen bonds were frequently observed, leading to a very stable 1.88-helix both for a tri- and a tetramer, in good agreement with experimental results. In water those secondary structure elements were broken up, and completely different parts of conformational space were sampled. The conformational distributions in chloroform and water show only a small overlap. This illustrates the importance of treating solvent degrees of freedom explicitly especially in biomolecular simulations.