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

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. Copyright © 2004 John Wiley & Sons, Ltd.