POLY(PRO)II HELICES IN GLOBULAR-PROTEINS - IDENTIFICATION AND CIRCULAR DICHROIC ANALYSIS

A method to identify poly(L-proline)-type (P-II) conformation in crystal structures of globular proteins is presented. Short segments of P-II structure were identified in globular protein structures, and these form a significant fraction of the residues which are not assigned to alpha-helix, beta-sheet, and beta-turns. The fractions of alpha-helix, beta-sheet, beta-turns, P-II, and unordered, identified in conjunction with the Kabsch and Sander method [(1983) Biopolymers 22, 2577], were incorporated in the analysis of circular dichroism (CD) spectra of proteins. The separation of P-II fraction from the fraction of residues not assigned to alpha-helix or beta-sheet or -turns resulted in a distinctive P-II CD spectrum and an unusual CD spectrum corresponding to the residual unassigned structures. The quality of prediction of P-II fraction from CD spectra of proteins was comparable to that of beta-sheet and -turns.