Nucleic Acids Research Advance Access published online on April 23, 2009
Nucleic Acids Research, doi:10.1093/nar/gkp242
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Methods Online |
Assessment of the optimization of affinity and specificity at protein–DNA interfaces
Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
*To whom correspondence should be addressed. Tel: +206 543 7228; Fax: +206 685 1792; Email: ashwortj{at}u.washington.edu Correspondence may also be addressed to David Baker. Tel: +206 328 1018; Fax: +206 685 1792; Email: dabaker{at}u.washington.edu
Received February 1, 2009. Revised March 19, 2009. Accepted April 1, 2009.
The biological functions of DNA-binding proteins often require that they interact with their targets with high affinity and/or high specificity. Here, we describe a computational method that estimates the extent of optimization for affinity and specificity of amino acids at a protein–DNA interface based on the crystal structure of the complex, by modeling the changes in binding-free energy associated with all individual amino acid and base substitutions at the interface. The extent to which residues are predicted to be optimal for specificity versus affinity varies within a given protein–DNA interface and between different complexes, and in many cases recapitulates previous experimental observations. The approach provides a complement to traditional methods of mutational analysis, and should be useful for rapidly formulating hypotheses about the roles of amino acid residues in protein–DNA interfaces.