Journal of Physical Chemistry A, Vol.107, No.40, 8035-8046, 2003
Determination of the potentials of mean force for rotation about C-alpha-C-alpha virtual bonds in polypeptides from the ab initio energy surfaces of terminally blocked glycine, alanine, and proline
The diabatic energy surfaces of terminally-blocked amino-acid residues (modeling the bulk of backbone-local interaction patterns in proteins: trans-N-acetyl-glycyl-trans-N'-methylamide, trans-N-acetyl-glycyl-N,N'-dimethylamide, trans-N-acetyl-L-alanyl-trans-N'-methylamide, trans-N-acetyl-L-alanyl-N,N'-dimethylamide, trans-N-acetyl-L-prolyl-trans-N'-methylamide, and trans-N-acetyl-L-prolyl-N,N'-dimethylamide) were calculated at the Moller-Plesset (MP2) ab initio level of theory with the 6-31G(d,p) basis set. The dihedral angles for rotation of the peptide groups about the C-alpha-C-alpha virtual-bond axes (lambda((1)) and lambda((2))) were used as variables; for the proline-derived peptide, only lambda((2)) was variable, because of the presence of the pyrrolidine-ring constraint. The resulting energy maps were compared with those obtained with the ECEPP/3 force field. On the basis of the MP2/6-31G(d,p) energy surfaces of terminally blocked single residues, the torsional potentials of mean force for rotation about the C-alpha-C-alpha virtual-bond axes and the double-torsional potentials of mean force for rotations about two consecutive virtual bond axes of all pairs and triplets of the prototypes of L-trans-amino acid residues were determined by numerical integration, fitted to one- and two-dimensional Fourier series in the virtual-bond-dihedral angles gamma of the C-alpha trace of a polypeptide chain, and implemented in the united-residue force field.