Study of HincII endonuclease by molecular dynamics methods
Centre for Biomolecular Research, Faculty of Science,
HincII is one of restriction endonucleases which are present in bacterial cells. They work in defense against alien DNAs (e.g. phages). HincII is homotetramer consisting of two functional dimers which recognize sequence GTPyPuAC. Bound oligonucleotide is double-bent and its specific bending is partially caused by intercalating glutamine 138 on each monomer. HincII enzyme needs ions for its function, Mg2+ or Mn2+ ions work like natural cofactors and Ca2+ inhibits the cleavage reaction.
The goals of this study are as follows: a) what
is the influence of intercalated glutamine 138, b) what is the role of ions in the
active site, c) describe dynamics of HincII complexes. To address these
questions, molecular dynamic simulations were performed on pre-reaction
complexes of restriction endonuclease HincII. The crystal structures data from
work  and , deposited in PDB database, were used.
The simulated systems consist of wildtype protein or Q138F mutated protein and of substrate 5’-GTCGAC-3’ or 5’-GTTAAC-3’. From crystals containing Ca2+ ions were prepared two variations of each: original with Ca2+ ions and changed with Mg2+ ions. Force field parm99sb  with parmbsc0  was used for all of the simulations.
The analyses show the protein is a rigid part and the DNA is flexible part of the complex. The ions’ analyses demonstrate the ions with 2+ formal charge stay almost in their places but some Na+ ions changed their positions. The influence of intercalation of amino acids 138 is studied by anisotropic thermal diffusion method (ATD) . ATD method should reveal how the thermal energy is distributed in the system, in this case, which part of system is affected by the intercalated amino acid. The molecular dynamics simulation of DNA molecule is rather problematic because DNA is sensible for imbalances in parameters. Even though the corrected force field was used, it is observed the DNA is forced to the canonical form but still better than containing artefacts. In spite of existing problems of simulations, usable results were obtained.
This work has been supported by
Ministry of Education of the
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