The role of flexibility and hydration on the sequence-specific DNA recognition by the Tn916 integrase protein: A molecular dynamics analysis
Title | The role of flexibility and hydration on the sequence-specific DNA recognition by the Tn916 integrase protein: A molecular dynamics analysis |
Publication Type | Journal Article |
Year of Publication | 2004 |
Authors | Gorfe A.A, Caflisch A., Jelesarov I. |
Journal | Journal of Molecular Recognition |
Volume | 17 |
Issue | 2 |
Pagination | 120-131 |
Date Published | 2004 Mar-Apr |
Type of Article | Research Article |
Keywords | DNA-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. |
DOI | 10.1002/jmr.658 |
pubindex | 0056 |
Alternate Journal | J. Mol. Recognit. |
PubMed ID | 15027032 |