The role of flexibility and hydration on the sequence-specific DNA recognition by the Tn916 integrase protein: A molecular dynamics analysis

TitleThe role of flexibility and hydration on the sequence-specific DNA recognition by the Tn916 integrase protein: A molecular dynamics analysis
Publication TypeJournal Article
Year of Publication2004
AuthorsGorfe A.A, Caflisch A., Jelesarov I.
JournalJournal of Molecular Recognition
Volume17
Issue2
Pagination120-131
Date Published2004 Mar-Apr
Type of ArticleResearch Article
ISSN0952-3499
KeywordsDNA-Binding Proteins, Integrases, Molecular Conformation, Nuclear Magnetic Resonance, Biomolecular, Pliability, Protein Conformation, Protein Folding, Thermodynamics, Water
Abstract

The N-terminal domain of the Tn916 integrase protein (INT-DBD) is responsible for DNA binding in the process of strand cleavage and joining reactions required for transposition of the Tn916 conjugative transposon. Site-specific association is facilitated by numerous protein-DNA contacts from the face of a three-stranded β-sheet inserted into the major groove. The protein undergoes a subtle conformational transition and is slightly unfolded in the protein-DNA complex. The conformation of many charged residues is poorly defined by NMR data but mutational studies have indicated that removal of polar side chains decreases binding affinity, while non-polar contacts are malleable. Based on analysis of the binding enthalpy and binding heat capacity, we have reasoned that dehydration of the protein-DNA interface is incomplete. This study presents results from a molecular dynamics investigation of the INT-DBD-DNA complex aimed at a more detailed understanding of the role of conformational dynamics and hydration in site-specific binding. Comparison of simulations (total of 13 ns) of the free protein and of the bound protein conformation (in isolation or DNA-bound) reveals intrinsic flexibility in certain parts of the molecule. Conformational adaptation linked to partial unfolding appears to be induced by protein-DNA contacts. The protein-DNA hydrogen-bonding network is highly dynamic. The simulation identifies protein-DNA interactions that are poorly resolved or only surmised from the NMR ensemble. Single water molecules and water clusters dynamically optimize the complementarity of polar interactions at the "wet" protein-DNA interface. The simulation results are useful to establish a qualitative link between experimental data on individual residue's contribution to binding affinity and thermodynamic properties of INT-DBD alone and in complex with DNA.

DOI10.1002/jmr.658
pubindex

0056

Alternate JournalJ. Mol. Recognit.
PubMed ID15027032
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