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Bioinformatics Advance Access originally published online on April 8, 2004
Bioinformatics 2004 20(14):2197-2204; doi:10.1093/bioinformatics/bth218
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Bioinformatics 20(14) © Oxford University Press 2004; all rights reserved.

An examination of the conservation of surface patch polarity for proteins

H. P. Shanahan * and J. M. Thornton

European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD,UK

Received on February 17, 2004; accepted on March 24, 2004
Advance Access Publication April 8, 2004

Motivation: The solubility of a protein is crucial for its function and is therefore an evolutionary constraint. As the solubility of a protein is related to the distribution of polar and hydrophobic residues on its solvent accessible surface, such a constraint should provide a valuable insight into the evolution of protein surfaces. We examine how the surfaces of proteins have evolved by considering how the average hydrophobicities of patches of surface residues vary across homologous proteins. We derive distributions for the average hydrophobicity/philicity of surface patches at a residue-based level—which we refer to as the residue hydrophobic density. This is computed for a set of 28 monomeric proteins and their homologues. The resulting distributions are compared with a set of randomized sequences, with the same residue content.

Results: We find that the patches, involving typically more than 10 residues, maintain a more hydrophilic surface than one would expect from a random substitution model, indicating a cooperative behaviour for these surfaces residues in terms of this single variable.

Supplementary information: Additional plots for all of the proteins examined in this paper can be found at: http://www.ebi.ac.uk/~shanahan/PCon/index.html

Contact: shanahan{at}ebi.ac.uk

* To whom correspondence should be addressed.


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