Prof. Michal Otyepka, Ph.D.

Contact:

Email: michal.otyepka@upol.cz
Addrress: 17. listopadu 12, Olomouc, 771 46, Czech Republic
Phone: (+420) 58 563 4764 (4756)
Fax: (+420) 585 634 761






Professional

2004 Ph.D. Physical chemistry, Palacký University, Olomouc
2007 Doc. (Associate Prof.), Palacký University, Olomouc
2008 Researcher, Institute of Biophysics (group of prof. Šponer), Brno
2009 Head of the Department of Physical Chemistry, Palacký University, Olomouc
2010 Head of the Workpackage „Carbon nanostructures and biomolecules“ of the project RCPTM, Palacký University, Olomouc
2012 Prof., Palacký University, Olomouc

International experience

2000 (May) EMBL Heidelberg, Germany, group of prof. R. C. Wade
2005 (Nov.) SISSA/ISAS Trieste, Italy, group of prof. Paolo Carloni
2006 (Jun.) SISSA/ISAS Trieste, Italy, group of prof. Paolo Carloni
2011 (Nov.) Limoges University, France – ERASMUS, teaching in molecular modeling
2012 (Nov.) Limoges University, France – ERASMUS, teaching in molecular modeling

 

  • Editorial Board Member – Scientific Reports (Nature PG)

Research activities

Physical-chemical properties and reactivity of graphene derivatives and 2D materials, non-covalent interactions to 2D materials (2D chemistry).

Interactions of drugs, antioxidants, and cytochrome P450 with biomembranes. Coauthor of software projects for analysis of molecular channels MOLE and CAVER 1.0.

Molecular dynamics of biomolecules and complex molecular systems, force field development, QM/MM methods and their applications in biomolecular research.

Publication activities

Author or co-author of more than 200 papers in international journals, three book chapters and one book. More than 9000 citations; H-index 47.

Selected Grants

ERC – Consolidator, 2D-Chemistry, 2016-2021

GACR – Center of Excellence: Controlling Structure and Function of Biomolecules at the Molecular Scale: Theory Meets Experiment (co-PI), 2012-2018

GACR – Catalytic strategies of RNA and RNP enzymes studied by multi-scale computational approach (co-PI), 2012-2016

NIH – Unraveling folding and mechanism of a small model ribozyme (co-PI; PI prof. N. G. Walter, University of Michigan, USA), 2011-2015

GACR – Biochemistry on the Crossroad from in silico to in vitro (PI), 2009-2012 (12 mil. CZK)

GACR – Structural Determinants of Substrate Specificity of Human Cytochromes P450 (PI), 2009-2012 (3 mil. CZK)

LC512 – Research Center for Biomolecules and Complex Molecular Systems (co-PI), 2005-2011 (3 mil. CZK)

Supervised Ph.D. Students

  • Pavel Banáš (2005-2009)
  • Petr Sklenovský (2008-2011)
  • Petra Florová (2007-2011)
  • Tereza Hendrychová (2008-2012)
  • Vojtěch Mlýnský (2009-2014)
  • Markéta Paloncýová (2012-2017)
  • Veronika Navrátilová (2014-2018)
  • Barbora Prudilová (2015-)

Selected publications

Graphene and Graphene Derivatives

Zboril R, Karlický F, Bourlinos* AB, Steriotis TA, Stubos AK, Georgakilas V, Safarova K, Jancik D, Trapalis C, Otyepka* M: Graphene fluoride: a stable stoichiometric graphene derivative and its chemical conversion to graphene. Small, 6 (24), 2010

Georgakilas V, Otyepka M, Bourlinos AB, Chandra V, Kim N, Kemp KC, Hobza P, Zboril* R, Kim* KS; Functionalization of Graphene; Covalent and Non-Covalent Approaches, Derivatives and Applications. Chem. Rev., 112(11), 6156-6214, 2012

Lazar P, Karlicky F, Jurecka P, Kocman M, Otyepkova E, Safarova K, Otyepka M: Adsorption of Small Organic Molecules on Graphene. J. Am. Chem. Soc., 135(16), 6372–6377, 2013

Karlicky F, Datta K K R, Otyepka M*, Zboril R*: Halogenated Graphenes: Rapidly Growing Family of Graphene Derivatives. ACS Nano, 7(8), 6434-6464, 2013

Karlicky F* and Otyepka M*: Band Gap and Optical Spectra of Chlorographene, Fluorographene and Graphane from G0W0, GW0 and GW Calculations on Top of PBE and HSE06 Orbitals. (with Cover Art) J. Chem. Theory Comput., 9 (9),4155-4164 , 2013

Urbanová V, Holá K, Bourlinos AB, Čépe K, Ambrosi A, Loo AH, Pumera M, Karlický F, Otyepka M, Zbořil R: Thiofluorographene-Hydrophilic Graphene Derivative with Semiconducting and Genosensing Properties. Adv. Mater., 27(14), 2305-2310, 2015.

Dubecký M, Otyepková E, Lazar P, Karlický F, Petr M, Čépe K, Banáš P, Zbořil R, Otyepka M: Reactivity of Fluorographene: A Facile Way toward Graphene Derivatives. J. Phys. Chem. Letters, 6(8), 1430-1434, 2015.

Tuček J, Holá K, Bourlinos AB, Blonski P, Bakandritsos A, Ugolotti J, Dubecký M, Karlický F, Ranc V, Cepe K, Otyepka M, Zbořil R: Room temperature organic magnets derived from sp3 functionalized graphene. Nat. Commun., 8, 14525 , 2017.

Bakandritsos A, Pykal M, Blonski P, Jakubec P, Chronopoulos DD, Poláková K, Georgakilas V, Cepe K, Tomanec O, Ranc V, Bourlinos AB, Zbořil R, Otyepka M: Cyanographene and Graphene Acid – Emerging Derivatives Enabling High-Yield and Selective Functionalization of Graphene. ACS Nano, 11(3), 2982–2991, 2017.

Blonski P, Tuček J, Sofer Z, Mazánek V, Petr M, Pumera M, Otyepka M, Zbořil R: Doping with Graphitic Nitrogen Triggers Ferromagnetism in Graphene. J. Am. Chem. Soc., 139(8), 3171–3180, 2017.

Tuček J, Blonski P, Malina O, Pumera M, Chua CK, Otyepka M, Zbořil R: Morphology‐Dependent Magnetism in Nanographene: Beyond Nanoribbons. Adv. Funct. Mater., 28(22), 1800592, 2018.

Matochová D, Medved M, Aristides B, Steklý T, Zbořil R, Otyepka M: 2D Chemistry – Chemical Control of Graphene Derivatization. J. Phys. Chem. Lett., 9(13), 3580–3585, 2018.

Medved M, Zoppellaro G, Ugolotti J, Matochová D, Lazar P, Pospíšil T, Bakandritsos A, Tuček J, Zbořil R, Otyepka M: Reactivity of fluorographene is triggered by point defects: beyond the perfect 2D world. Nanoscale, 10, 4696-4707, 2018.

Bakandritsos A, Chronopoulos DD, Jakubec P, Pykal M, Čépe K, Steriotis T, Kalytchuk S, Petr M, Zbořil R, Otyepka M: High‐Performance Supercapacitors Based on a Zwitterionic Network of Covalently Functionalized Graphene with Iron Tetraaminophthalocyanine. Adv. Funct. Mater., 28(29), 1801111, 2018.

 

Molecular dynamics of RNA

Ditzler M, Otyepka M, Sponer* J, Walter* N; Molecular Dynamics and Quantum Mechanics of RNA: Conformational and Chemical Change We Can Believe In. Acc. Chem. Res., 43(1), 40-47, 2010

Banas P, Hollas D, Zgarbova M, Jurecka P, Orozco M, Cheatham T, Sponer* J, Otyepka* M: Performance of Molecular Mechanics Force Fields for RNA Simulations. Stability of UUCG and GNRA hairpins. J. Chem. Theor. Comput, 6 (12), 3836-3849, 2010.

Galindo-Murillo R, Robertson JC, Zgarbová M, Šponer J, Otyepka M, Jurečka P, Cheatham TE: Assessing the current state of AMBER force field modifications for DNA. J. Chem. Theory Comput., 12(8), 4114–4127, 2016.

Šponer J, Krepl M, Banáš P, Kührová P, Zgarbová M, Jurečka P, Havrila M, Otyepka M: How to understand atomistic molecular dynamics simulations of RNA and protein– RNA complexes? WIREs RNA, 8(3), e1405, 2017.

Šponer J, Bussi G, Stadlbauer P, Kührová P, Banáš P, Islam B, Haider S, Neidle S, Otyepka M: Folding of guanine quadruplex molecules–funnel-like mechanism or kinetic partitioning? An overview from MD simulation studies. Biochim. Biophys. Acta, Gen. Subj., 1861(5), 1246–1263, 2017.

Šponer J, Bussi G, Krepl M, Banáš P, Bottaro S, Cunha RA, Ley AG, Pinamonti G, Poblete S, Jurečka P, Walter NG, Otyepka M: RNA Structural Dynamics As Captured by Molecular Simulations: A Comprehensive Overview. Chem. Rev., 118(8), 4177–4338, 2018.

 

Simulations of Proteins and Drug-Membrane Interaction

Berka K, Hendrychova T, Anzenbacher P, Otyepka* M; Membrane Position of Ibuprofen Agrees with Suggested Access Path Entrance to Cytochrome P450 2C9 Active Site. J. Phys. Chem. A, 115(41), 11248-11255, 2011

Paloncyova M, Berka K, Otyepka* M: Molecular Insight to Affinities of Drugs and Their Metabolites to Lipid Bilayers. J. Phys. Chem. B, 117(8), 2403-2410, 2013

Di Meo F, Fabre G, Berka K, Ossman T, Chantemargue B, Paloncýová M, Marquet P, Otyepka M, Trouillas P: In Silico Pharmacology: Drug Membrane Partitioning and Crossing. Pharmacol. Res., 111, 471–486, 2016.

Chantemargue B, Di Meo F, Berka K, Nicolas P, Arnion H, Essig M, Marquet P, Otyepka M, Trouillas P: Structural patterns of the human ABCC4/MRP4 exporter in lipid bilayers rationalize clinically observed polymorphisms. Pharmacol. Res., 133, 318-327, 2018.

Šrejber M, Navrátilová V, Paloncýová M, Bazgier V, Berka K, Anzenbacher P, Otyepka M: Membrane-attached mammalian cytochromes P450: An overview of the membrane’s effects on structure, drug binding, and interactions with redox partners. J Inorg Biochem, 183, 117-136, 2018.

Molecular Channels, Tunnels and Pores (MOLE, MOLEonline, ChannelsDB)

Link to MOLEonline 2.0

Sehnal D, Svobodova Varekova R, Berka K, Pravda L, Navratilova V, Banas P, Ionescu CM, Otyepka* M, Koca* J: MOLE 2.0: Advanced Approach for Analysis of Biomacromolecular Channels. J. Cheminform., 5, 39, 2013

Berka K, Hanak O, Sehnal D, Banas P, Navratilova V, Jaiswal D, Ionescu CM, Svobodova Varekova R, Koca* J, Otyepka* M; MOLEonline 2.0: Interactive Web-based Analysis of Biomacromolecular Channels. Nuc. Acids Res., 40(W1), W222-W227, 2012.

Pravda L, Sehnal D, Svobodová Vařeková R, Navrátilová V, Toušek D, Berka K, Otyepka M, Koča J: ChannelsDB: database of biomacromolecular tunnels and pores. Nucleic Acids Res, 46(D1), D399–D405, 2018.

Pravda L, Sehnal D, Toušek D, Navrátilová V, Bazgier V, Berka K, Svobodová Vařeková R, Koča J, Otyepka M: MOLEonline: a web-based tool for analyzing channels, tunnels and pores (2018 update). Nucleic Acids Res, 46(W1), W368–W373, 2018.