Length preferences and periodicity in beta-strands. Antiparallel edge beta-sheets are more likely to finish in non-hydrogen bonded rings.
We analysed the length distributions of different types of beta-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 beta-bulges, which insert an extra residue into the strand. Residues in antiparallel edge beta-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 beta 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 beta-hairpin stability, or the stability of an antiparallel edge strand, is to have a non-hydrogen bonded ring at the end of the strand.
Penel
Simon
S
Department of Biomolecular Sciences, UMIST, PO Box 88, Manchester M60 1QD, UK.
Morrison
R Gwilym
RG
Dobson
Paul D
PD
Mortishire-Smith
Russell J
RJ
Doig
Andrew J
AJ
D019295:Computational Biology; D003627:Data Interpretation, Statistical; D017433:Protein Structure, Secondary; D020539:Sequence Analysis, Protein