Predictions of peptide and protein backbone structural parameters from first principles .4. Systematic comparisons of calculated N-C(alpha)-C' angles with peptide crystal structures
by Jiang, X. Q.; Cao, M.; Newton, S. Q.; Schafer, L.
For some fifty oligopeptides for which high resolution crystal structures have been deposited in the Cambridge Crystallographic Data File, the crystallographic N-C(alpha)-C' angles, (cryst)alpha(i), were compared with values calculated on the basis of first principles. Crystal structures of cyclic and non-cyclic peptides were included in this comparison, with sizes ranging from six to sixteen residues, if they were refined to an R-factor of at least 0.08 or better. The calculated values were obtained using an algorithm which employs spline-function representations of ab initio dipeptide conformational geometry maps to predict backbone bond lengths and angles in oligopeptides and proteins as functions of the phi[N-C(alpha)]/psi[C(alpha)-C'] torsions. Tc perform this comparison for the ith residues of the peptides included in the analysis, the observed parameters, (cryst)alpha(i), (cryst)phi(i) and (cryst)psi(i), Were retrieved from the crystal structures and compared with values calculated, (calc)alpha(i), at the crystallographic phi(i)/psi(i)-torsions. The average root mean square (rms) deviation between the two sets of angles for the peptides included in the test is 2.26 degrees, while angle variations are similar to 8 degrees, ranging from 107 degrees to 115 degrees. When the (cryst)alpha(i) and (calc)alpha(i) are ordered by regions in phi/psi space defined by a 30 degrees grid and region-average values calculated, the average rms deviation between the two sets in the most populated regions is 1.52 degrees. As in the previous protein studies, helix compression is found in the oligopeptides. The analysis reveals that the phi/psi-torsional dependence of N-C(alpha)-C' in oligopeptides is similar to that previously found for proteins. We expect the computational procedure to be useful for establishing flexible geometry functions for use in empirical peptide and protein modeling and protein crystallography.
- Journal
- Electronic Journal of Theoretical Chemistry
- Volume
- 1
- Year
- 1996
- Start Page
- 11-17
- URL
- https://dx.doi.org/10.1002/ejtc.4
- ISBN/ISSN
- 1082-4928
- DOI
- 10.1002/ejtc.4