Length preferences and periodicity in β-strands. Antiparallel edge β-sheets are more likely to finish in non-hydrogen bonded rings

Abstract

We analysed the length distributions of different types of β-strand in a high resolution, non-homologous set of 500 protein structures, finding differences in their mean lengths. Antiparallel edge strands in strand-turn-strand motifs show a preference for an even number of residues. This propensity is enhanced if the length is corrected for β-bulges, which insert an extra residue into the strand. Residues in antiparallel edge β-strands alternate between being in hydrogen bonded and non-hydrogen bonded rings. Antiparallel edges with an even number of residues are more likely to have their final β residue in a non-hydrogen bonded ring. This suggests that non-hydrogen bonded rings are intrinsically more stable than hydrogen bonded rings, perhaps because its side chain packing is closer. Therefore, we suggest that a simple way to increase β-hairpin stability, or the stability of an antiparallel edge strand, is to have a non-hydrogen bonded ring at the end of the strand.