Interfacial water as a "hydration fingerprint" in the noncognate complex of BamHI.

ABSTRACT: The molecular code of specific DNA recognition by proteins as a paradigm in molecular biology remains an unsolved puzzle primarily because of the subtle interplay between direct protein-DNA interaction and the indirect contribution from water and ions. Transformation of the nonspecific, low affinity complex to a specific, high affinity complex is accompanied by the release of interfacial water molecules. To provide insight into the conversion from the loose to the tight form, we characterized the structure and energetics of water at the protein-DNA interface of the BamHI complex with a noncognate sequence and in the specific complex. The fully hydrated models were produced with Grand Canonical Monte Carlo simulations. Proximity analysis shows that water distributions exhibit sequence depen

SUBMITTER: Fuxreiter M 

PROVIDER: S-EPMC1366640 | biostudies-literature | 2005 Aug

REPOSITORIES: biostudies-literature