title: Assessment of the optimization of affinity and specificity at protein-DNA interfaces.
abstract: 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.
authors.affiliation: Department of Biochemistry, University of Washington, Seattle, WA 98195, USA. ashwortj@u.washington.edu
authors.forename: Justin
authors.initials: J
authors.lastname: Ashworth
authors.forename: David
authors.initials: D
authors.lastname: Baker
mesh_terms: D000596:Amino Acids / Q000737:chemistry; D019295:Computational Biology / Q000379:methods*; D018360:Crystallography, X-Ray; D004247:DNA / Q000737:chemistry; D004262:DNA Restriction Enzymes / Q000737:chemistry; D004268:DNA-Binding Proteins / Q000737:chemistry*; D003850:Deoxyribonuclease I / Q000737:chemistry; D015252:Deoxyribonucleases, Type II Site-Specific / Q000737:chemistry; D004720:Endonucleases / Q000737:chemistry; D008958:Models, Molecular; D014157:Transcription Factors / Q000737:chemistry
chemical_list: D000596:Amino Acids; D004268:DNA-Binding Proteins; D014157:Transcription Factors; D004247:DNA; D004720:Endonucleases; D004262:DNA Restriction Enzymes; D003850:Deoxyribonuclease I; D015252:Deoxyribonucleases, Type II Site-Specific; C027440:GATATC-specific type II deoxyribonucleases