Cis–trans isomerization and puckering of proline residue Original Research Article

We report here the results on N-acetyl-l-proline-N′-methylamide (Ac-Pro-NHMe) calculated at the HF/6-31+G(d) level with the conductor-like polarizable continuum model (CPCM) of self-consistent reaction field methods to investigate the changes of backbone and prolyl ring along the cis–trans isomerization of the prolyl peptide bond. From the potential energy surface, the barrier to ring flip from the down-puckered conformation to the up-puckered one is estimated to be 2.5 and 3.2 kcal/mol for trans and cis conformers of Ac-Pro-NHMe, respectively. In particular, the ring flip seems to be inaccessible in the intermediate regions between trans and cis conformations, because of higher barriers (∼13–19 kcal/mol) to rotation of the prolyl peptide bond. The torsion angles for backbone and prolyl ring vary largely around the transition states at ω′≈120° and −70° for the prolyl peptide bond. Three kinds of puckering amplitudes show the same trend of puckering along the cis–trans isomerization although their absolute values are different. In particular, trans and cis conformations have the almost same degree of puckering. The cis populations and barriers to rotation of the prolyl peptide bond for Ac-Pro-NHMe are increased with the increase of solvent polarity, which is mainly ascribed to the decreases of relative free energies for cis conformations and the increase of relative free energies for transition states.