Michael Ramek, Ching-Hsing Yu, Joshua Sakon, and Lothar Schäfer,
Ab Initio Study of the Conformational Dependence of the Nonplanarity of the Peptide Group
J. Phys. Chem. A, 104, 9636-9645 (2000).


Publication abstract:

To study the nonplanarity of peptide bonds, the conformationally dependent variations of the N-C torsional angle, omega_2, of the central peptide group in N-formyl-L-alanyl-L-alanine amide (ALA-ALA) was investigated using a database of 11 664 RHF/4-21G ab initio gradient optimized structures. The data base 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 defined by 40° increments along the outer torsions phi_1 and psi_2 and by 30° 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 omega_2 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 long-range effects present in the latter but not in the former. This finding indicates the general difficulty of predicting the exact positions of the 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.

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Informations required by Austrian law (Offenlegung gem. §25 MedienG): Dr. Michael Ramek, Graz.