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Originally published as Biophys J. BioFAST on May 13, 2005.
doi:10.1529/biophysj.105.063263
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Biophysical Journal 89:903-911 (2005)
© 2005 The Biophysical Society

Interfacial Water as a "Hydration Fingerprint" in the Noncognate Complex of BamHI

Monika Fuxreiter *, Mihaly Mezei {dagger}, István Simon * and Roman Osman {dagger}

* Institute of Enzymology, Hungarian Academy of Sciences, H-1518 Budapest, Hungary; and {dagger} Department of Physiology and Biophysics, Mount Sinai School of Medicine, New York University, New York, New York 10029

Correspondence: Address reprint requests to Monika Fuxreiter, E-mail: monika{at}enzim.hu.

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 dependent variations in both complexes and, in particular, in the noncognate complex they discriminate between the correct and the star site. Variations in water distributions control the number of water molecules released from a given sequence upon transformation from the loose to the tight complex as well as the local entropy contribution to the binding free energy. We propose that interfacial waters can serve as a "hydration fingerprint" of a given DNA sequence.






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Copyright © 2005 by the Biophysical Society.