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Bioinformatics Advance Access published online on April 6, 2006
Bioinformatics, 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
Received October 12, 2005
Revised March 8, 2006
Accepted March 25, 2006

Article

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

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

1 School of Animal & Microbial Sciences, University of Reading, Whiteknights, P.O. Box 228, Reading RG6 6AJ, UK; Present address: School of Biological and Chemical Sciences, Queen Mary, University of London, Mile End Road, London E1 4NS, 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.
Andrew C. R. Martin, E-mail: andrew{at}bioinf.org.uk; martin@biochem.ucl.ac.uk


  Abstract

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 assessment of 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/.

Associate Editor: Anna Tramontano

{ddagger} This work was initiated while working at: School of Animal & Microbial Sciences, University of Reading, Whiteknights, P.O. Box 228, Reading RG6 6AJ, U.K.


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