Poly(pro)II helices in globular proteins: identification and circular dichroic analysis.

A method to identify poly(L-proline)-type (PII) conformation in crystal structures of globular proteins is presented. Short segments of PII 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, PII, 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 PII fraction from the fraction of residues not assigned to alpha-helix or beta-sheet or -turns resulted in a distinctive PII CD spectrum and an unusual CD spectrum corresponding to the residual unassigned structures. The quality of prediction of PII fraction from CD spectra of proteins was comparable to that of beta-sheet and -turns.