Genetics, Vol. 149, 445-458, May 1998, Copyright © 1998

Assessing the Impact of Secondary Structure and Solvent Accessibility on Protein Evolution

Nick Goldmana, Jeffrey L. Thorneb, and David T. Jonesc
a Department of Genetics, University of Cambridge, Cambridge CB2 3EH, United Kingdom,
b Program in Statistical Genetics, Department of Statistics, North Carolina State University, Raleigh, North Carolina 27695-8203
c Department of Biological Sciences, University of Warwick, Coventry CV4 7AL, United Kingdom

Corresponding author: Nick Goldman, Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK, n.goldman{at}gen.cam.ac.uk (E-mail).

Communicating editor: G. B. GOLDING

Empirically derived models of amino acid replacement are employed to study the association between various physical features of proteins and evolution. The strengths of these associations are statistically evaluated by applying the models of protein evolution to 11 diverse sets of protein sequences. Parametric bootstrap tests indicate that the solvent accessibility status of a site has a particularly strong association with the process of amino acid replacement that it experiences. Significant association between secondary structure environment and the amino acid replacement process is also observed. Careful description of the length distribution of secondary structure elements and of the organization of secondary structure and solvent accessibility along a protein did not always significantly improve the fit of the evolutionary models to the data sets that were analyzed. As indicated by the strength of the association of both solvent accessibility and secondary structure with amino acid replacement, the process of protein evolution—both above and below the species level—will not be well understood until the physical constraints that affect protein evolution are identified and characterized.




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