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

Abstract

The paired torsional angle representation φ i, ψ i in protein conformational analysis is only one type of correlation with a focus on a given C α 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 φ i, ψ i−1 and other parameters derived therefrom. General sum ( α n = φ i + ψ i−n) and the difference ( β n = φ i − ψ 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 ‘ α 0’ is found to be relatively stable, the sum parameters have been found to be more useful in the analysis of β-turns. The ‘ α 0’ at the second and third residue sites and ‘ α 1’ at the middle peptide plane of the four residue corner is found to offer a numerical triplet code for resolving various β-turn types. Besides these, an additional parameter introduced under the DRMP model is a virtual torsion angle ‘ σ 1’ involving C i−1 β ⋯ C′ i−1 − N i ⋯ C i β , which is expected to reflect the effect of interaction of the side chain atoms. The σ 1, α 1 pair is found to play a role parallel to φ, ψ at a given residue site. Various combinations of the sum and difference parameters, as two dimensional plots, like the α 0 vs β 0, α 0 vs α 1 and σ 1 vs α 1 bring out the conformational features related to secondary structures of proteins.