THE GEOMETRICAL ANALYSIS OF PEPTIDE BACKBONE STRUCTURE AND ITS LOCAL DEFORMATIONS

A proposal to use a unified description of protein structures is prese nted, assuming that all peptide chain conformations (including beta-st ructure) may be considered as helix-derived. In this understanding the beta-conformation of the peptide chain may be obtained by extending o r unwinding the helical form. A unified description could be based on a commonly defined internal axis (Z-axis) determined by the averaged d irection of the CO bonds in a pentapeptide analytical unit. Five param eters were proposed to describe the peptide conformation: i) radius of curvature (R), calculated from the position of five consecutive pepti de bond planes; ii) horizontal angular displacement (H) of the neighbo ring (i+1-th) versus the central amino acid residue (i-th) in the pent apeptide fragment; iii) vertical angular displacement (V-i) of the pep tide bond plane of the i-th residue versus the Z-axis; iv) vertical an gular displacement (V-i+1) of the i+1-th peptide plane measured versus the Z-axis; and v) vertical rise (VR) defined for the i+2-th residue versus the i-th residue. This geometrical analysis was used to study t he mechanism of a possible transition from alpha(R) to beta and to alp ha(L) transition, based on data taken from the known Phi, Psi distribu tion in proteins. This analysis was also designed and preliminarily us ed to reveal local peptide backbone distortions and their distribution s in proteins for structure-function relation studies.