Computational prediction of native protein ligand-binding and enzyme active site sequences.

ABSTRACT: Recent studies reveal that the core sequences of many proteins were nearly optimized for stability by natural evolution. Surface residues, by contrast, are not so optimized, presumably because protein function is mediated through surface interactions with other molecules. Here, we sought to determine the extent to which the sequences of protein ligand-binding and enzyme active sites could be predicted by optimization of scoring functions based on protein ligand-binding affinity rather than structural stability. Optimization of binding affinity under constraints on the folding free energy correctly predicted 83% of amino acid residues (94% similar) in the binding sites of two model receptor-ligand complexes, streptavidin-biotin and glucose-binding protein. To explore the applicability of th

SUBMITTER: Chakrabarti R 

PROVIDER: S-EPMC1177389 | biostudies-literature | 2005 Jul

REPOSITORIES: biostudies-literature