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


Z. Střelcová1, P. Kulhánek1 and J. Koča1


1National Centre for Biomolecular Research, Masaryk University

 Kotlářská 2, CZ-61137 Brno, Czech Republic



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 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 close to the G base. Wrongly paired base is removed and after that, the missing parts of DNA can be re-synthesized by the DNA polymerase and the correct base pairing is reestablished [1].

Main goal of our project is the understanding of the reaction mechanism of MutH enzyme. We will 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 complex [2]. The calcium ions present in crystal structures inhibit the cleavage reaction therefore these structures are assumed as pre-reaction complexes.

The cleavage mechanism is studied on semiempirical level (Amber 10 [3], PDDG/PM3 [4]) considering two possible nucleophiles (H2O and OH-). We are comparing two different models of the protein/DNA complexes with both inhibitors (Ca2+ ions) and activators (Mg2+ ions) of the cleavage reaction. Since the used level of theory gives only rough results, the major outcome of this study will be structure of the post-reaction complex, which has not been solved yet.


The presented work is supported by following grants: The Ministry of Education of the Czech Republic (contracts LC06030, MSM0021622413), Czech Science Foundation (301/09/H004), and the European Community's Seventh Framework Programme under grant agreement n° 205872. The access to the MetaCentrum supercomputing facilities provided under the research intent MSM6383917201 is highly appreciated.




 [1] K.G. Au, K. Welsh, P. Modrich, J. Biol. Chem., 267, (1992), 12142-12148.

 [2] J. Lee, J. Chang, N. Joseph, R. Ghirlando, D. Rao, W. Yang, Mol. Cell., 20, (2005), 155-166.

 [3] D.A. Case, T. Darden, T. Cheatham, C. Simmerling, J. Wang, R. Duke, R. Luo, M. Crowley, Ross C. Walker, W. Zhang, K.M. Merz, B. Wang, S. Hayik, A. Roitberg, G. Seabra, I. Kolossváry, K. Wong, F. Paesani, J. Vanicek, X. Wu, S. Brozell, T. Steinbrecher, H. Gohlke, L. Yang, C. Tan, J. Mongan, V. Hornak, G. Cui, D. Mathews, M. Seetin, C. Sagui, V. Babin, P.A. Kollman, Amber 10, University of California, San Francisco (2008).

 [4] M.P. Repasky, J. Chandrasekhar, W.L. Jorgensen, J. Comput. Chem., 23, (2002), 1601-1622.