Assessment of the optimization of affinity and specificity at protein-DNA interfaces

TitleAssessment of the optimization of affinity and specificity at protein-DNA interfaces
Publication TypeJournal Article
Year of Publication2009
AuthorsAshworth, J., & Baker D.
JournalNucleic acids research
Date Published2009 Jun
KeywordsAmino Acids, Computational Biology, Crystallography, X-Ray, Deoxyribonuclease I, Deoxyribonucleases, Type II Site-Specific, DNA, DNA Restriction Enzymes, DNA-Binding Proteins, Endonucleases, Models, Molecular, Primary Publication, Transcription Factors

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.

Alternate JournalNucleic Acids Res.
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