β-Hairpins in proteins revisited: Lessons for de novo design

Abstract

β-Hairpins with short connecting loops (1-5 residues) have been identified from a data set of 250 non-homologous, high resolution (≤ 2.0 Å) protein crystal structures. The conformational preferences of the loop segments have been analyzed with the specific aim of identifying frequently occurring motifs. Type I' and II' β-turns were found to have a high propensity for occurrence in two residue loops. For three and four residue loops, the major conformational motif in the linking segments is α(R)-α(R)-α(L) (type I β-turn followed by a residue in a left-handed helical conformation) and α(R)-α(R)-α(R)-α(L) (a π-turn motif), respectively. The present larger data set confirms the high occurrences of these moths which have been identified in earlier analyses. In addition to type I' and type II' β-turns, several examples of type I β-turn nucleated two residue loop hairpins, in spite of having an opposing sense of twist to that of type I' β-turn, have also been observed. Examination of these frequently occurring motifs (flanked by extended conformation [β]) in the data set reveals that the motifs β-α(R)-α(R)-α(L)-β and β-type I'-β have equal propensity and type II' indeed having highest propensity to nucleate β-hairpins. The larger number of examples in this study allows the estimation of the specific amino acid preferences for loop positions in two, three and four residue loops. Small polar residues Asn, Asp, Ser, Thr, Gly and Pro in general have a high propensity for the loop positions but they reveal specific positional preferences in these frequently occurring motifs. There are no strong compositional preferences in the strand segments. Amino acid pair correlations across strands also do not show any significant pattern, with the exception of Cys-Cys pairs. Several Cys-Cys pairs have been identified at the non-hydrogen bonded positions of β-hairpins; as many as six are disulfide bonded pairs. An examination of longer loop length hairpins reveals that the distortions of hairpins nucleated by tight turns (two residues) are much less frequently observed. The results presented in this study provide inputs for the de novo design of consensus loop segments in synthetic hairpins.