Molecular dynamics simulations for a series of cis- and trans- N-acethyl-N'-methylamide of Xaa-Pro

Abstract

It has been commonly accepted that the occurrence of cis amide bonds in proteins is quite rare due to the unfavorable contacts between adjacent amino acid residues in cis isomeric form, but the occurrence of cis imide bonds in proteins is relatively high because the trans isomeric form is unstable by steric clash between $\delta$-carbon of proline and $\beta$-carbon of the residue preceding proline. To examine the relationship between this occurrence of cis imide bonds and the residue preceding proline, we perform molecular dynamics simulations for a series of trans-and cis-N-acethyl-N``-methylamides of Xaa-Pro dipeptides. We investigate the conformational energies and structures of trans-and cis-blocked dipeptides for each amino acid, in both vacuum and solutions state. It is found that the occurrence of cis imide bonds is strongly affected by the residue preceding proline and the dihedral angles ($\varphi$, $\Psi$) of backbone in Ac-Xaa-Pro-NHMe are influenced by the configuration of imide bond. We also findthat the equilibrium properties of Xaa-Pro in solution state are more similar to X-ray crystallographic data analysis than those in vacuum.