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Bioinformatics Advance Access originally published online on April 6, 2006
Bioinformatics 2006 22(12):1464-1470; doi:10.1093/bioinformatics/btl120
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© The Author 2006. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

Analysing the ability to retain sidechain hydrogen-bonds in mutant proteins

Alison L. Cuff 1,{dagger}, Robert W. Janes 2 and Andrew C.R. Martin 3,*

1 School of Animal and Microbial Sciences, University of Reading Whiteknights, PO Box 228, Reading RG6 6AJ, UK
2 School of Biological and Chemical Sciences, Queen Mary, University of London Mile End Road, London E1 4NS, UK
3 Department of Biochemistry and Molecular Biology, University College London Gower Street, London WC1E 6BT, UK

*To whom correspondence should be addressed.

Motivation: Hydrogen bonds are one of the most important inter-atomic interactions in biology. Previous experimental, theoretical and bioinformatics analyses have shown that the hydrogen bonding potential of amino acids is generally satisfied and that buried unsatisfied hydrogen-bond-capable residues are destabilizing. When studying mutant proteins, or introducing mutations to residues involved in hydrogen bonding, one needs to know whether a hydrogen bond can be maintained. Our aim, therefore, was to develop a rapid method to evaluate whether a sidechain can form a hydrogen-bond.

Results: A novel knowledge-based approach was developed in which the conformations accessible to the residues involved are taken into account. Residues involved in hydrogen bonds in a set of high resolution crystal structures were analyzed and this analysis is then applied to a given protein. The program was applied to assess mutations in the tumour-suppressor protein, p53. This raised the number of distinct mutations identified as disrupting sidechain–sidechain hydrogen bonding from 181 in our previous analysis to 202 in this analysis.

Availability: http://www.bioinf.org.uk/hbonds/

Contact: andrew{at}bioinf.org.uk

Received on October 12, 2005; revised on March 8, 2006; accepted on March 25, 2006

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