Protein Engineering vol. 16 no. 12 pp. 957-961, 2003
© 2003 Oxford University Press
Length preferences and periodicity in ß-strands. Antiparallel edge ß-sheets are more likely to finish in non-hydrogen bonded rings
1Department of Biomolecular Sciences, UMIST, PO Box 88,Manchester M60 1QD and 3Merck, Sharp & Dohme Research Laboratories, Neuroscience Research Centre, Terlings Park, Eastwick Road, Harlow, Essex CM20 2QR, UK 2Present address: Laboratoire de Biometrie et Biologie Evolutive,Bât 711—CNRS UMR 5558—Université Lyon 1, 43 bd du 11 novembre 1918, 69622 Villeurbanne Cedex, France
4 To whom correspondence should be addressed. e-mail: andrew.doig{at}umist.ac.uk
We analysed the length distributions of different types of ß-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 ß-bulges, which insert an extra residue into the strand. Residues in antiparallel edge ß-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 ß 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 ß-hairpin stability, or the stability of an antiparallel edge strand, is to have a non-hydrogen bonded ring at the end of the strand.
Received June 19, 2003; revised October 25, 2003; accepted November 7, 2003