Proc Natl Acad Sci U S A. 1993 Sep 15;90(18):8402-6.

What determines the strength of noncovalent association of ligands to proteins in aqueous solution?

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Department of Pharmaceutical Chemistry, University of California, San Francisco 94143.

Abstract

Free energy perturbation methods using molecular dynamics have been used to calculate the absolute free energy of association of two ligand-protein complexes. The calculations reproduce the significantly more negative free energy of association of biotin to streptavidin, compared to N-L-acetyltryptophanamide/alpha-chymotrypsin. This difference in free energy of association is due to van der Waals/dispersion effects in the nearly ideally performed cavity that streptavidin presents to biotin, which involves four tryptophan residues.

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Absolute and relative binding free energy calculations of the interaction of biotin and its analogs with streptavidin using molecular dynamics/free energy perturbation approaches. [Proteins. 1993]
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