Conformational interconversions in peptide beta-turns: Analysis of turns in proteins and computational estimates of barriers

The two most important beta-turn features in peptides and proteins are the type I and type II turns, which differ mainly in the orientation of the cen tral peptide unit. Facile conformational interconversion is possible, in pr inciple, by a flip of the central peptide unit. Homologous crystal structur es afford an opportunity to structurally characterize both possible conform ational states, thus allowing identification of sites that are potentially stereochemically mobile. A representative data set of 250 high-resolution ( less than or equal to 2.0 Angstrom), non-homologous protein crystal structu res and corresponding variant and homologous entries, obtained from the Bro okhaven Protein Data Bank, was examined to identify turns that are assigned different conformational types (type I/type II) in related structures. A t otal of 55 examples of beta-turns were identified as possible candidates fo r a stereochemically mobile site. Of the 55 examples, 45 could be classifie d as a potential site for interconversion between type I and type II beta-t urns, while ten correspond to flips from type I' to type II' structures. As a further check, the temperature factors of the central peptide unit carbo nyl oxygen atom of the 55 examples were examined. The analysis reveals that the turn assignments ape indeed reliable. Examination of the secondary str uctures at the flanking positions of the flippable beta-turns reveals that seven examples occur in the loop region of beta-hairpins, indicating that t he formation of ordered secondary structures on either side of the beta-tur n does not preclude local conformational variations. In these beta-turns, P ro (11 examples), Lys (nine examples) and Ser (seven examples) were most of ten found at the i + 1 position. Glycine was found to occur overwhelmingly at position i + 2 (28 examples), while Ser (seven examples) and Asn (six ex amples) were amongst the most frequent residues. Activation energy barriers for the interconversion between type I and type II beta-turns were compute d using the peptide models Ac-Pro-Aib-NHMe and Ac-Pro-Gly-NHMe within the f ramework of the AM1 semi-empirical molecular orbital procedure. In order to have a uniform basis for comparison and to eliminate the distracting influ ence of the deviation of backbone dihedral angles from that expected for id eal beta-turns, the dihedral angles phi(i+1) and psi(i+2) were fixed at the ideal values (phi(i+1) = -60 degrees and psi(i+2) = 0 degrees). The other two angles (psi(i+1) and phi(i+2)) were varied systematically to go from ty pe II to type I beta-turn structures. The computational results suggest tha t there exists one stereospecific, concerted flip of the central peptide un it involving correlated single bond rotation that can occur with an activat ion barrier of the order of 3 kcal/mol. The results presented here suggest that conformational variations in beta-turns are observed in protein crysta l structures and such changes may be an important dynamic feature in soluti on. (C) 1998 Academic Press.