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Bioinformatics. 2006 Jun 15;22(12):1464-70. Epub 2006 Apr 6.

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

Author information

1
School of Animal and Microbial Sciences, University of Reading Whiteknights, PO Box 228, Reading RG6 6AJ, 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 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.

PMID:
16601005
DOI:
10.1093/bioinformatics/btl120
[Indexed for MEDLINE]

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