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Řeha lab


Scientist
  Dr. David Řeha, PhD.
Graduate Student
  MSc. Saurabh Pandey
Head
Mgr. David Řeha, PhD.
Phone: +420 389033801
Fax: +420 386361279
reha@nh.cas.cz
Address
Zámek 136, CZ-37333 Nové Hrady

Research

Modelling Interactions in Biomolecules Using Methods of Quantum and Molecular Mechanics

Researchers involved from the group: David Reha, Lydie Plackova,

Internal collaboration: Daniel Bonhenry, Saurabh Kumar Pandey, Rudiger H. Ettrich, Babak Minofar

External collaboration: Jakub Sebera (IOCB, Prague, CZ), Christopher Reynolds (University of Essex, UK) and Jannette Carey (Princeton University, NJ, USA)

Research aims

The lab has its focus on the modelling of biomolecular systems and the study of intermolecular interactions using computational methods including molecular dynamics (MD) simulations, quantum mechanics/molecular mechanics (QM/MM) calculations, and molecular docking. Current research projects are focused on studying the functional properties of DNA and a wide range of proteins including membrane proteins; the study of mechanisms of enzymatic reactions and modelling their transition states; the study of charge transfer in DNA, photosynthetic proteins, and redox proteins; and calculation of spectroscopic properties (IR, NMR, UV) of macromolecules. The additional aims are development of new methods and their implemention for computational studies of biomolecules, e.g., MM polarization for QM/MM calculations.

Short annotation

Computational methods are important tools in study of biomolecules including their interactions with other molecules (pharmaceutical drugs) and bimolecular processes. Within our project we focus on a very accurate description of the active site of the proteins and their interactions with ligands, substrates or protein co-factors. Such a level of accuracy can be only achieved by methods of quantum mechanics (QM). Since QM calculations are computationally very demanding and the description of the large biomolecules by purely QM methods is very limiting, hybrid QM/MM methods would be employed. We apply QM/MM methods for calculation of the binding energy of various ligands in proteins as well as classical MD simulations in order to study biologically relevant molecules.

Selected recent publications from our group

  • [1] David Reha, Balasubramanian Harish, Dhiraj Sinha, Zdenek Kukacka, James McSally, Olga Ettrichova, Petr Novak, Jannette Carey, Rüdiger Ettrich (2014) Molecular dynamics comparison of E. coli WrbA apoprotein and holoprotein. Journal of Molecular Modeling,20 (9): 2400.
  • [2] Oksana Degtjarik, Jiři Brynda, Olga Ettrichova, Michal Kuty, Dhiraj Sinha, Ivana Kuta Smatanova, Jannette Carey, Rüdiger Ettrich, David Řeha (2016) Quantum calculations indicate effective electron transfer between FMN and benzoquinone in a new crystal structure of E. coli WrbA Journal of Physical Chemistry B, 120 (22): 4867-4877.
  • [3] Jakub Sebera, Yoshikazu Hattori, Daichi Sato, David Reha, Radim Nencka, TakashiKohno, Chojiro Kojima, Yoshiyuki Tanaka andVladimir Sychrovsky. The mechanism of the glycosylase reaction with hOGG1 base-excision repair enzyme: concerted effect of Lys249 and Asp268 during excision of 8-oxoguanine Nucleic Acids Research, 2017, Vol. 45, No. 9 5231–5242