Peptides of aminoxy acids: A molecular dynamics simulation study of conformational equilibria under various conditions

Molecular dynamics simulations have been performed to study the conformatio nal behavior of peptide analogues formed by alpha-aminoxy acids. The influe nce 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-me chanical calculations, indicate the presence of strong intramolecular hydro gen bonds between adjacent residues. In the simulations in chloroform the e ight-membered-ring strucures formed by these hydrogen bonds were frequently observed, leading to st very stable 1,8(8)-helix both for a tri- and a tet ramer, in good agreement with experimental results, In water those secondar y structure elements were broken up, and completely different parts of conf ormational space were sampled. The conformational distributions in chlorofo rm and water show only a small overlap. This illustrates the importance of treating solvent degrees of freedom explicitly especially in biomolecular s imulations.