Computational study of the dimethylphosphate hydrolysis as the reference system for the understanding of the restriction endonucleases mechanism


Z. Střelcová1,2, J. Štěpán 1,2, P. Kulhánek 1,2, P. Carloni3 and J. Koča 1,2


1 Central European Institute of Technology, Masaryk University, Kamenice 5, 625 00 Brno,   Czech Republic

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

3 German Research School for Simulation Sciences GmbH, 52425 Jülich, Germany


Understanding enzymatic mechanisms is essential knowledge for further medicine and biotechnology development. Our long-standing effort is aimed at the explanation of the reaction mechanism of endonucleases (enzymes cleaving DNA chain(s)) using computational approaches. According to the published experimental and theoretical results, the suggested mechanism is SN2 hydrolysis of the phosphate backbone. [1]

Presented work is focused on the study of simplified model of the enzymatic reaction. This model consists of dimethylphosphate and the nucleophile (water, hydroxyl ion) attacking the phosphodiester bond. The hydrolysis was simulated using Car Parrinello Molecular Dynamics (CPMD) [2] in vacuum and in water. The reaction free energy profiles were evaluated using metadynamics  [3] and obtained results were compared to the experimental data [4]. The model serves as a reference system for the upcoming simulation of the enzymatic reactions.

This work has been supported by the Ministry of Education of the Czech Republic (MSM0021622413 and LC06030 to J.K.), the Grant Agency of Czech Republic (GD301/09/H004 to Z.S. and J.S.), and the European Community's Seventh Framework Program (grant agreement n° 205872 to P.K.).The access to the Jülich Center Computer facilities and MetaCentrum supercomputing facilities provided under the research intent MSM6383917201 is highly appreciated.


 [1]     A. Pingoud, M. Fuxreiter, V. Pingoud, W. Wende, Cell. Mol. Life Sci. , 62, (2005), 685-707.


 [3]     A. Laio, M. Parrinello, P. Natl. Acad. Sci. USA , 99, (2002), 12562-12566.

 [4]     J.H. Kim, J. Chin, Journal of the American Chemical Society , 114, (1992), 9792-9795.