Reaction Mechanism of MutH Enzyme – Quantum Mechanics/Molecular Mechanics Study

J. Štěpán, Z. Střelcová, P. Kulhánek and J. Koča

CEITEC – Central European Institute of Technology, Masaryk University, Kamenice 5, CZ-625-00 Brno, Czech Republic

and

²National Centre for Biomolecular Research, Masaryk University, Kotlářská 2, CZ-61137 Brno, Czech Republic

xstepan3@chemi.muni.cz

Enzymes are catalysts of many crucial reactions in living organisms. Therefore, the knowledge of their reaction mechanisms can be helpful in many fields such as biology, medicine or pharmacy. In our study, we are focused on MutH enzyme, which is an integral part of Methyl-directed Mismatch Repair process, together with MutL and MutS enzymes. A mismatch introduced during DNA replication is recognized by MutS enzyme, information about the mismatch is transferred through MutL to MutH enzyme. MutH specifically recognizes the GATC sequence on daughter DNA strand and cleaves this strand next to the G base. After wrong paired base is removed, the missing part of DNA is to be re-synthesized by the DNA polymerase and the correct base pairing is reestablished¹.

Main goal of our project is the understanding of the reaction mechanism of MutH enzyme. We present the Quantum Mechanics / Molecular Mechanics (QM/MM) study of the MutH enzyme reactivity based on models prepared from the available crystal structures of protein / DNA complex².

The cleavage mechanism is studied on ab initio level using CPMD³ implementation of Density Functional Theory and on semi-empirical level using PM3 Hamiltonian⁴ in Amber package⁵. We are considering two possible nucleophiles. We are also comparing two different models of the protein / DNA complexes with both Ca²⁺ ions (inhibitor) and Mg²⁺ ions co-factor) of the cleavage reaction. We evaluate the free energy profiles of various processes in the active site including cleavage itself.

Acknowledgements

This work was realized in CEITEC - Central European Institute of Technology with research infrastructure supported by the project CZ.1.05/1.1.00/02.0068 financed from European Regional Development Fund. The access to the MetaCentrum computing facilities provided under the program "Projects of Large Infrastructure for Research, Development, and Innovations" LM2010005 funded by the Ministry of Education, Youth, and Sports of the Czech Republic is acknowledged. The work has been supported by the Grant Agency of Czech Republic (GD301/09/H0040).

References

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(3) CPMD; http://www.cpmd.org.; Copyright IBM Corp 1990-2008, Copyright MPI für Festkörperforshung Stuttgart 1997-2001.

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