Pseudotorsional OCCO backbone angle as a single descriptor of protein secondary structure

Abstract

Protein secondary structure is conventionally identified using characteristic ranges of two backbone torsional angles π and Ψ We suggest that the secondary structure can be adequately characterized by a single descriptor, the Oi‐1 Ci‐1CiOi (where i is the residue number) pseudotorsional backbone angle. A set of 102 structurally distinct protein chains from the Protein Data Bank was used to evaluate the adequacy of this descriptor. We find that a specific range of OCCO angles corresponds to each major secondary structure. The complete range of OCCO angles (‐180° to 179°) was broken into 18 consecutive subranges of 20° each, and each subrange was assigned a letter. Thus, the OCCO profiles for each protein in the database were “translated” into a sequence of letters. The Needleman‐Wunsch primary sequence alignment algorithm was then used for secondary/tertiary structure comparison and alignment. Preliminary results indicate that this new approach has a significant potential for rapid identification of fold families in the Protein Data Bank. Copyright © 1995 The Protein Society