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 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.
journal_name
Biophys Jjournal_title
Biophysical journalauthors
Fuxreiter M,Mezei M,Simon I,Osman Rdoi
10.1529/biophysj.105.063263subject
Has Abstractpub_date
2005-08-01 00:00:00pages
903-11issue
2eissn
0006-3495issn
1542-0086pii
S0006-3495(05)72742-9journal_volume
89pub_type
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