Ab initio study of the conformational dependence of the nonplanarity of the peptide group

by Ramek, Michael; Yu, Ching-Hsing; Sakon, Josh; Schäfer, Lothar

To study the nonplanarity of peptide bonds, the conformationally dependent variations of the N-C torsional angle, omega (2) (Figure 1), of the central peptide group in N-formyl L-alanyl L-alanine amide (ALA-ALA) was investigated using a database of Il 664 RHF/4-21G ab initio gradient optimized structures. The database was generated by optimizing the geometries of ALA-ALA at grid points in its four-dimensional (phi (1),psi (1),phi (2),psi (2)) conformational space (Figure I) defined by 40 degrees increments along the outer torsions phi (1) and psi (2), and by 30 degrees increments along the inner torsions psi (1) and phi (2). Using cubic spline functions, the grid structures were then used to construct analytical representations of complete surfaces of omega (2) in (phi (1),psi (1),phi (2),psi (2))-space. Analyses of the conformational surfaces of oz reveal that the peptide N-C torsion is a smoothly varying function of associated phi and psi angles and that, for many conformational regions, deviations from planarity are the rule rather than the exception. Comparisons with protein crystallographic data show that, in contrast to peptide torsional angles calculated for an entire protein, the omega (2) angles of smaller model peptides, such as ALA-ALA, cannot be used to model peptide groups in proteins, because of lone-range effects present in the latter but not the former. This finding indicates the general difficulty of predicting the exact positions of backbone torsional angles in proteins from smaller model peptides. Furthermore, the results confirm the directional nature of polypeptide chains. That is, conformation transmission effects from neighboring groups differ, depending on whether they are transmitted from right to left or from left to right in the peptide chain.

Journal
Journal of Physical Chemistry A
Volume
104
Issue
42
Year
2000
Start Page
9636
ISBN/ISSN
1520-5215; 1089-5639
DOI
10.1021/jp002498x