π‐Turns in proteins and peptides: Classification, conformation, occurrence, hydration and sequence

Abstract

Abstract The i + 5 → i hydrogen bonded turn conformation (7r‐turn) with the fifth residue adopting α L conformation is frequently found at the C‐terminus of helices in proteins and hence is speculated to be a “helix termination signal.” An analysis of the occurrence of i + 5 → i hydrogen bonded turn conformation at any general position in proteins (not specifically at the helix C‐terminus), using coordinates of 228 protein crystal structures determined by X‐ray crystallography to better than 2.5 Å resolution is reported in this paper. Of 486 detected π‐turn conformations, 367 have the ( i + 4)th residue in α L conformation, generally occurring at the C‐terminus of α‐helices, consistent with previous observations. However, a significant number (111) of π‐turn conformations occur with ( i + 4)th residue in α R conformation also, generally occurring in α‐helices as distortions either at the terminii or at the middle, a novel finding. These two sets of 7r‐turn conformations are referred to by the names π αL and π αR ‐turns, respectively, depending upon whether the ( i + 4)th residue adopts α L or α R conformations. Four π‐turns, named π' αL ‐turns, were noticed to be mirror images of π αL ‐turns, and four more π‐turns, which have the ( i + 4)th residue in β conformation and denoted as π β ‐turns, occur as a part of hairpin bend connecting twisted β‐strands. Consecutive π‐turns occur, but only with π αR ‐turns. The preference for amino acid residues is different in π αL and π αR ‐turns. However, both show a preference for Pro after the C‐termini. Hydrophilic residues are preferred at positions i + 1, i + 2, and i + 3 of π αL ‐turns, whereas positions i and i + 5 prefer hydrophobic residues. Residue i + 4 in π αL ‐turns is mainly Gly and less often Asn. Although π αR ‐turns generally occur as distortions in helices, their amino acid preference is different from that of helices. Poor helix formers, such as His, Tyr, and Asn, also were found to be preferred for π αR ‐turns, whereas good helix former Ala is not preferred. π‐Turns in peptides provide a picture of the π‐turn at atomic resolution. Only nine peptide‐based π‐turns are reported so far, and all of them belong to π αL ‐turn type with an achiral residue in position i + 4. The results are of importance for structure prediction, modeling, and de novo design of proteins.