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 711CNRS UMR 5558Université 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
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Abstract |
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Keywords: antiparallel/ß-bulge/ß-sheet/ß-turn/secondary structure
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Introduction |
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ß-Sheets are complex structures, in which hydrogen bonding between adjacent strands can be parallel or antiparallel, and residues in edge strands can have their backbone NH and CO groups either hydrogen bonding within the sheet or oriented toward solvent. Figure 1 shows the following distinct structural locations for residues in ß-sheets, arranged in a hierarchy: mixed, antiparallel centre, parallel centre, hydrogen bonded antiparallel edge, non-hydrogen bonded antiparallel edge, hydrogen bonded parallel edge and non-hydrogen bonded parallel edge. We further distinguish between coherent and non-coherent ß-strands. Coherent strands are bonded to the same ß-strand throughout the strand edge. Non-coherent strands are bonded to more than one different strand. Non-coherent strands are often not possible to classify simply, as they may, for example, be edge on one end and centre at the other.
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Materials and methods |
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Results |
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We previously found that there is an approximately 3.6 residue periodicity in frequencies of -helix lengths, corresponding to 3.6 residues per turn found in the helix (Penel et al., 1999
). Favoured helix lengths have their N and C ends on the same face of the helix. In view of this, we investigated whether a similar periodicity was present in ß-strand lengths. As side chains in strands alternate between the two sides of the sheet, we investigated whether there is a 2-fold periodicity in strand length so that either an odd or an even number of residues per strand is favoured. Table I gives the fractions of strands with odd or even lengths for each strand type. A small variation is seen, though none vary by more than 8% from 50%.
More interesting results were found when examining a ß-hairpin subset of the antiparallel edge group, specifically antiparallel edges immediately following a reverse turn joining the edge strand to another strand (a strandturnstrand ß-hairpin motif, Figure 2a). These were found by searching for the secondary structure motif ETTEnX, where n is the length of the antiparallel edge, T is a turn residue, E is a ß-sheet residue and X is a non-sheet residue. Table II gives the results for this strand. A preference for an even number of residues in the strand is now apparent, with 215/342 = 63% of strands having an even length. This preference is only present for short lengths (less than six), however.
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Distortions from the regular patterns of hydrogen bonding in antiparallel edge strands, shown in Figures 2 and 3, are occasionally present. It is expected that strands that finish with a hydrogen bonded ring have an odd number of residues, while strands that finish with a non-hydrogen bonded ring should have an even number of residues. This is the case 79 and 84% of the time, respectively. When corrected for the number of ß-bulges, in ETTEnX motifs 93% of strands that finish with a hydrogen bonded ring have an odd number of residues (increased from 76%) and 94% of strands that finish with a non-hydrogen bonded ring have an even number of residues (increased from 80%, Table II). In XEnTTE motifs, 95% of strands that finish with a hydrogen bonded ring have an odd number of residues (increased from 79%) and 98% of strands that finish with a non-hydrogen bonded ring have an even number of residues (increased from 84%), after the ß-bulge correction (Table III). These data show that deviations from the expected antiparallel edge strand structure are found in 5% of cases. These may arise from distortions so that a hydrogen bond is missing, for example.
We analysed the complete set of antiparallel edge strands, not just those that are preceded or followed by a ß-turn. We found that 2045/4507 = 45% of antiparallel edges have hydrogen bonded rings at their C-terminal ends and 2169/4507 = 48% of antiparallel edges have hydrogen bonded rings at their N-terminal ends. Non-hydrogen bonded rings are therefore more abundant at the N and C ends in all edge ß-strands, further supporting our conclusion.
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Discussion |
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Wouters and Curmi (Wouters and Curmi, 1995) found differences in the amino acid preference for hydrogen bonded and non-hydrogen bonded sites in antiparallel ß-sheets. Hutchinson et al. (1998
) compared side chain pair frequencies and structures across the two types of ring and found some clear differences in preferred interactions. Smith and Regan measured some side chain interactions within a hydrogen bonded ring in protein G (Smith and Regan, 1995
). While these studies show that there are differences in preference between the two sites, they do not show whether one site is intrinsically more stable than another. This could be tested in principle in a ß-hairpin peptide. ß-Hairpin structures will finish in either hydrogen bonded or non-hydrogen bonded rings. We suggest that ß-hairpins with a non-hydrogen bonded ring at their ends are more likely to be stable. Hence, a systematic investigation of hairpin stability as a function of length would show a periodicity in stability. Such a study has not been performed to our knowledge; all the peptides made by Stanger et al. (2001
) in their work on the length dependence of ß-hairpin stability finished with a hydrogen bonded ring. A range of ß-sheet peptides have been shown to successfully fold (for recent reviews see Serrano, 2000
; Cheng et al., 2001
; Searle, 2001
; Venkatraman et al., 2001
). Our work suggests that a simple way to increase hairpin stability, or the stability of an antiparallel edge strand, is to have a non-hydrogen bonded ring at the end of the ß-strand. This can be achieved if the number of residues in the ß-hairpin with the two strands linked by a ß-turn and with no ß-bulges is 4N + 2, where N is an integer. An alternative explanation for the periodicity we observe is that the end residues in antiparallel edge strands are more stable with a peptide NH group facing solvent than with a peptide CO group facing solvent, though we know of no reason why this might be the case.
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Acknowledgements |
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References |
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Received June 19, 2003; revised October 25, 2003; accepted November 7, 2003