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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.

SUBMITTER: Ashworth J 

PROVIDER: S-EPMC2691843 | biostudies-literature | 2009 Jun

REPOSITORIES: biostudies-literature

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

Ashworth Justin J   Baker David D  

Nucleic acids research 20090423 10


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 resi  ...[more]

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