Molecular Dynamics Simulation of the Hin-Recombinase—DNA Complex

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Abstract
Molecular dynamics simulation was performed for 1 ns for a peptide:DNA complex formed by Hin recombinase 52mer peptide and a 13 base-pair synthetic hixL half-site. The Ewald summation method was employed to treat the electrostatic interaction without the cutoff. Comparison with the results of the conventional cutoff method revealed that proper treatment of the electrostatic interaction was required to produce a stable trajectory. The trajectory thus obtained was used to analyze the interaction between the peptide and the DNA. Both N- and C-terminal regions reside within two regions of the minor groove. The N-terminus-DNA interaction was fairly stable in the current simulation, but the C-terminus-DNA interaction was only marginally stable. These simulation results were consistent with reported experimental data that the N-terminal residues were required for the DNA recognition, while the C-terminal ones were supportive but not necessary.