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Dr. David Řeha, PhD
Position
Head of the laboratory
Zámek 136, CZ 373 33 Nové Hrady
Phone: +420 389 033 801
reha@nh.cas.cz
Current projects
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. Development of the new methods and their implementation for computational studies of biomolecules, e.g., MM polarization for QM/MM calculations.
Past Projects
- 2009-2011 Postdoc: Department of Biological Sciences, University of Essex, Colchester, United Kingdom
Project: Implementation of MM polarization in QM/MM calculations
PI: Prof. Christopher Reynolds - 2007-2009 Postdoc: School of Physics and Astronomy, University of Leeds, United Kingdom
Project: A Multi-Scale Model of Charge Transport through Melted, Stretched and in vacuo DNA Structures>
PI: Dr. Sarah Harris - 2005-2006 Postdoc: National Centre for Bimolecular Research, Faculty of Science, Masaryk University, Brno, Czech Republic.
Project: Ab initio calculations of the NMR parameters of the DNA.
PI: Prof. Vladimir Sklenar - 2000-2005 PhD Study: Faculty of Science, Charles University, Prague, Czech Republic Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic
Field of Study: Physical Chemistry
Topic of PhD Thesis: „Ab Initio Calculations and Molecular Dynamics Simulations of Biomolecules in the Gas Phase and in Aqueous Solution.“
Supervisor: Prof. Pavel Hobza - 1995-2000 MS Study: Faculty of Science, Charles University, Prague, Czech Republic
Field of Study: Physical Chemistry
Topic of Diploma Thesis: „Theoretical Study of Interaction between Intercalators and DNA“
Supervisor: Prof. Pavel Hobza
Publications
publicationslist.org/david.rehaInstitute publications in impacted journals
- Saurabh Kumar Pandey, Milan Melichercik, David Řeha, Rüdiger H. Ettrich,and Jannette Carey (2020) Conserved Dynamic Mechanism of Allosteric Response to L-arg in Divergent Bacterial Arginine Repressors. In: Molecules. Vol 25, pp. 1-24.
- Jakub Šebera, David Řeha, Jiří Fukal, Vladimír Sychrovský (2020) Interstrand Charge Transport within Metallo-DNA: the Effect Due to Hg(II)-and Ag(I)-Mediated Base Paris. In: The Journal of Physical Chemistry C. Vol 124, pp. 7477-7486.
- N. Kulik, M. Kutý, D. Řeha (2020) The study of conformational changes in photosystem II during a charge separation. In: Journal of Molecular Modeling. Vol Issue 26, pp. 1-13.
- Vitali Bialevich, Dhiraj Sinha, Katsiaryna Shamayeva, Alena Guzanova, David Řeha, Eva Csefalvay, Jannette Carey, Marie Weiserova, Rüdiger H Ettrich (2017) The helical domain of the EcoR124I motor subunit participates in ATPase activity and dsDNA translocation.. In: PeerJ. Vol 5, pp. 01-.
- Jakub Šebera, Yoshikazu Hattori, Daichi Sato, David Reha, Radim Nencka, Takashi Kohno, Chojiro Kojima, Yoshiyuki Tanaka, Vladimír Sychrovský (2017) The mechanism of the glycosylase reaction with hOGG1 base-excision repair enzyme: concerted effect of Lys249 and Asp268 during excision of 8-oxoguanine. In: Nucleic acids research. (9), pp. 5231-5242.
- Irena Kratochvílová, Martin Golan, Karel Pomeisl, Jan Richter, Silvia Sedláková, Jakub Šebera, Júlia Mičová, Martin Falk, Iva Falková, David Řeha, K Wade Elliott, Krisztina Varga, Shelby E Follett, Daniel Šimek (2017) Theoretical and experimental study of the antifreeze protein AFP752, trehalose and dimethyl sulfoxide cryoprotection mechanism: correlation with cryopreserved cell viability.. In: RSC advances. Vol 7, pp. 352-360.
- Irene Frischauf, Monika Litviňuková, Romana Schober, Vasilina Zayats, Barbora Svobodová, Daniel Bonhenry, Victoria Lunz, Sabrina Cappello, Laura Tociu, David Reha, Amrutha Stallinger, Anna Hochreiter, Teresa Pammer, Carmen Butorac, Martin Muik, Klaus Groschner, Ivan Bogeski, Rüdiger H Ettrich, Christoph Romanin, Rainer Schindl (2017) Transmembrane helix connectivity in Orai1 controls two gates for calcium-dependent transcription.. In: Science signaling. Vol 10, pp. 507-.
- Kopecky V. Jr; Ettrich R.; Pazderka T.; Hofbauerova K.; Reha D.; Baumruk V. (2016) Influence of ligand binding on structure and thermostability of human alpha1 -acid glycoprotein.. In: Journal of Molecular Recognition. Vol 29 (2), pp. 70-79.
- 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 Escherichia coli WrbA.. In: Journal of Physical Chemistry B. Vol 120, pp. 4867-4887.
- Ali Reza Harifi-Mood, Roohollah Ghobadi, Sara Matić, Babak Minofar, David Řeha (2016) Solvation analysis of some Solvatochromic probes in binary mixtures of reline, ethaline, and glyceline with DMSO. In: Journal of Molecular Liquids. Vol 222, pp. 845-853.
- Sinha D., Shamayeva K., Ramasubramani V., Reha D., Bialevich V., Khabiri M., Guzanova A., Milbar N., Weiserova M., Csefalvay E., Carey J., Ettrich R. (2014) Interdomain communication in the endonuclease/motor subunit of type I restriction-modification enzyme EcoR124I.. In: Journal of Molecular Modeling. Vol 20 (7), pp. 2334-.
- Iryna Kishko, Balasubramanian Harish, Vasilina Zayats, David Reha, Brian Tenner, Dhananjay Beri, Tobias Gustavsson, Rüdiger Ettrich, Jannette Carey (2012) Biphasic kinetic behavior of E. coli WrbA, an FMN-dependent NAD(P)H:quinone oxidoreductase.. In: PloS one. Vol 7, pp. e4390-.
