Diresidue-monopeptide (DRMP) model for analysis of peptide and protein conformation

The paired torsional angle representation phi i, psi i in protein conformational analysis is only one type of correlation with a focus on a given C alpha residue and gives the relative orientation of a pair of peptide planes sandwiching a given residue (referred as mono-residue dipeptide model, MRDP). A shift of emphasis from a residue site to a given peptide plane (termed as diresidue monopeptide model, DRMP) leads to examination of pairs such as phi i, psi i-1 and other parameters derived therefrom. General sum (alpha n = phi i + psi i-n) and the difference (beta n = phi i - psi i-n) parameters are introduced, of which, n = 0 and n = 1 relate to MRDP models and DRMP models respectively. Apart from the helical regions, where 'alpha 0' is found to be relatively stable, the sum parameters have been found to be more useful in the analysis of beta-turns. The 'alpha 0' at the second and third residue sites and 'alpha 1' at the middle peptide plane of the four residue corner is found to offer a numerical triplet code for resolving various beta-turn types. Besides these, an additional parameter introduced under the DRMP model is a virtual torsion angle 'sigma 1' involving C beta i-1 ... C'i-1 - Ni ... C beta i, which is expected to reflect the effect of interaction of the side chain atoms. The sigma 1, alpha 1 pair is found to play a role parallel to phi, psi at a given residue site.(ABSTRACT TRUNCATED AT 250 WORDS)