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 'α₀' is found to be relatively stable, the sum parameters have been found to be more useful in the analysis of β-turns. The 'α₀' at the second and third residue sites and 'α₁' 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 'σ₁' 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 σ₁, α₁ 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 α₀vsβ₀, α₀vsα₁ and σ₁vsα₁ bring out the conformational features related to secondary structures of proteins.