Krepl Miroslav, RNDr., Ph.D.

Extension: +420 541-517- 109
Email: krepl@ibp.cz

Name: RNDr. Miroslav Krepl, Ph.D.

Education:

  • Bachelor’s degree studies – Faculty of Science, Masaryk University, Biochemistry, 2008 – 2011
  • Master’s degree studies – Faculty of Science, Masaryk University, Biomolecular chemistry, 2011 – 2013
  • D. degree studies – Faculty of Science, Masaryk University, Biomolecular chemistry, 2013 – 2017

Current employment:

  • Researcher, Department of structure and dynamics of nucleic acids, Institute of Biophysics, Academy of Sciences of the Czech Republic, Brno
  • Research lecturer, Faculty of Science, Regional Centre of Advanced Technologies and Materials, Palacky University, Olomouc

Research interests:

My research focuses on study of biologically relevant nucleic acids and proteins by the methods of molecular dynamics (MD) simulations. My primary focus is protein/RNA and protein/DNA complexes.1-17 I am especially interested in biomolecular systems where a significant role of structural dynamics is known or suspected. Although my research is through theoretical methods, I have extensive experience in collaborating with experimental research groups focused on X-ray crystallography, NMR spectroscopy, Cryo-EM, or other biochemical methods.1-4, 9-10, 12-13, 18 In addition to practical application of computational methods in biological and biochemical research, I also have experience in developing and benchmarking computational methods.5, 8, 19-21 Apart from protein/RNA and protein/DNA complexes, I have also studied neomycin-sensing riboswitch,18 human HP1 protein,22-23 folding pathways of guanine quadruplexes,24-26 HIV-1 kissing loop,27 and free energy calculations.28

 

In the near future, I intend to study protein/RNA and other complexes in which local interface dynamics is prominently involved and can influence affinity and specificity of such complexes.

 

References:

(1) Campagne, S.; Krepl, M.; Sponer, J.; Allain, F. H. T., Chapter Fourteen - Combining NMR Spectroscopy and Molecular Dynamic Simulations to Solve and Analyze the Structure of Protein–RNA Complexes. In Methods Enzymol., Wand, A. J., Ed. Academic Press: 2019; Vol. 614, pp 393-422.

(2) Ripin, N.; Boudet, J.; Duszczyk, M. M.; Hinniger, A.; Faller, M.; Krepl, M.; Gadi, A.; Schneider, R. J.; Šponer, J.; Meisner-Kober, N. C., et al., Proc. Natl. Acad. Sci. U.S.A. 2019, 116, 2935-2944.

(3) Górecka, K. M.; Krepl, M.; Szlachcic, A.; Poznański, J.; Šponer, J.; Nowotny, M., Nat. Commun. 2019, 10, e4102.

(4) Figiel, M.; Krepl, M.; Park, S.; Poznański, J.; Skowronek, K.; Gołąb, A.; Ha, T.; Šponer, J.; Nowotny, M., J. Biol. Chem. 2018, 293, 191-202.

(5) Šponer, J.; Bussi, G.; Krepl, M.; Banáš, P.; Bottaro, S.; Cunha, R. A.; Gil-Ley, A.; Pinamonti, G.; Poblete, S.; Jurečka, P., et al., Chem. Rev. 2018, 118, 4177–4338.

(6) Pokorná, P.; Kruse, H.; Krepl, M.; Šponer, J., J. Chem. Theory Comput. 2018, 14, 5419-5433.

(7) Bochicchio, A.; Krepl, M.; Yang, F.; Varani, G.; Sponer, J.; Carloni, P., Plos Comput. Biol. 2018, 14, e1006642.

(8) Šponer, J.; Krepl, M.; Banáš, P.; Kührová, P.; Zgarbová, M.; Jurečka, P.; Havrila, M.; Otyepka, M., Wiley Interdiscip. Rev.: RNA 2017, 8, e1405.

(9) Figiel, M.; Krepl, M.; Poznański, J.; Gołąb, A.; Šponer, J.; Nowotny, M., Nucleic Acids Res. 2017, 45, 3341-3352.

(10) Krepl, M.; Blatter, M.; Cléry, A.; Damberger, F. F.; Allain, F. H. T.; Sponer, J., Nucleic Acids Res. 2017, 45, 8046-8063.

(11) Pokorna, P.; Krepl, M.; Kruse, H.; Sponer, J., J. Chem. Theory Comput. 2017, 13, 5658–5670.

(12) Konté, N. D. d.; Krepl, M.; Damberger, F. F.; Ripin, N.; Duss, O.; Sponer, J.; Allain, F. H.-T., Nat. Commun. 2017, 8, e654.

(13) Krepl, M.; Cléry, A.; Blatter, M.; Allain, F. H. T.; Sponer, J., Nucleic Acids Res. 2016, 44, 6452-6470.

(14) Estarellas, C.; Otyepka, M.; Koca, J.; Banas, P.; Krepl, M.; Sponer, J., Biochim. Biophys. Acta, Gen. Subj. 2015, 1850, 1072-1090.

(15) Krepl, M.; Havrila, M.; Stadlbauer, P.; Banas, P.; Otyepka, M.; Pasulka, J.; Stefl, R.; Sponer, J., J. Chem. Theory Comput. 2015, 11, 1220-1243.

(16) Šponer, J.; Banáš, P.; Jurečka, P.; Zgarbová, M.; Kührová, P.; Havrila, M.; Krepl, M.; Stadlbauer, P.; Otyepka, M., J. Phys. Chem. Lett. 2014, 5, 1771-1782.

(17) Krepl, M.; Reblova, K.; Koca, J.; Sponer, J., J. Phys. Chem. B 2013, 117, 5540-5555.

(18) Krepl, M.; Vögele, J.; Kruse, H.; Duchardt-Ferner, E.; Wöhnert, J.; Sponer, J., Nucleic Acids Res. 2018, 46, 6528–6543.

(19) Kuhrova, P.; Mlynsky, V.; Zgarbova, M.; Krepl, M.; Bussi, G.; Best, R. B.; Otyepka, M.; Sponer, J.; Banas, P., J. Chem. Theory Comput. 2019, 15, 3288-3305.

(20) Mladek, A.; Krepl, M.; Svozil, D.; Cech, P.; Otyepka, M.; Banas, P.; Zgarbova, M.; Jurecka, P.; Sponer, J., Phys. Chem. Chem. Phys. 2013, 15, 7295-7310.

(21) Krepl, M.; Zgarbová, M.; Stadlbauer, P.; Otyepka, M.; Banáš, P.; Koča, J.; Cheatham, T. E.; Jurečka, P.; Šponer, J., J. Chem. Theory Comput. 2012, 8, 2506-2520.

(22) Legartová, S.; Lochmanová, G.; Zdráhal, Z.; Kozubek, S.; Šponer, J.; Krepl, M.; Pokorná, P.; Bártová, E., Cells 2019, 8, 1097.

(23) Pokorná, P.; Krepl, M.; Bártová, E.; Šponer, J., J. Chem. Theory Comput. 2019, 15, 5659-5673.

(24) Islam, B.; Stadlbauer, P.; Krepl, M.; Havrila, M.; Haider, S.; Sponer, J., J. Chem. Theory Comput. 2018, 14, 5011-5026.

(25) Islam, B.; Stadlbauer, P.; Krepl, M.; Koca, J.; Neidle, S.; Haider, S.; Sponer, J., Nucleic Acids Res. 2015, 43, 8673-8693.

(26) Stadlbauer, P.; Krepl, M.; Cheatham, T. E., III; Koca, J.; Sponer, J., Nucleic Acids Res. 2013, 41, 7128-7143.

(27) Havrila, M.; Zgarbová, M.; Jurečka, P.; Banáš, P.; Krepl, M.; Otyepka, M.; Šponer, J., J. Phys. Chem. B 2015, 119, 15176-15190.

(28) Krepl, M.; Otyepka, M.; Banas, P.; Sponer, J., J. Phys. Chem. B 2013, 117, 1872-1879.