RNDr. Karel Berka, Ph.D.

Education

2010

Ph.D. Modelling of chemical properties of nano- and biomaterials, Charles University in Prague with collaboration of Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic. Thesis: "Side-chain Side-chain Interactions in Proteins."

2008

RNDr. in Physical Chemistry, Charles University in Prague

2001 – 2006

Mgr. (M.Sc. equivalent) in Physical chemistry, Department of Physical and Macromolecular Chemistry, Faculty of Science, Charles University in Prague Thesis: "Modelling of ligand-binding site structure of the human MT2 melatonin receptor"

Employment

2010 – today

Junior researcher, Regional Centre of Advanced Technologies and Materials, Faculty of Science, Palacky University, Olomouc

2010 – today

PostDoc Fellow, Department of Physical Chemistry, Faculty of Science, Palacky University, Olomouc

2007 – 2010

Ph.D. student, Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Prague

2003 – 2006

Technician, Institute of Physiology, Academy of Sciences of the Czech Republic, Prague

2002 – 2003

Technician, Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Prague

Visits

2008 (Nov), 2012 (Sep)

European Bioinformatics Institute (EBI-EMBL), Hinxton, UK, group of prof. J. Thornton

2010 (Sep), 2012 (Feb)

Université de Limoges, Faculté de Pharmacie, Limoges, France, group of Patrick Trouillas

2010 (Aug – Oct)

POSTECH, Pohang, South Korea, group of prof. Kwang S. Kim

2005 (Nov.)

Laboratoire de biologie et de pharmacologie appliquee (LBPA) at ENS Cachan, Paris, France, group of prof. A. Lewit-Bentley

Research specialization

Protein stabilization and function, molecular dynamics of biomolecules and their complexes, membrane protein simulations, docking, small molecule penetration through membranes, cytochrome P450 enzymes, structural bioinformatics.

Grants, projects, awards

• 2012-2014 - GACR P303/12/P019 - Mechanism of ligand access/egress to/from active site of microsomal drug-metabolising cytochromes P450 (PI, post-doc, 1 mil. CZK)
• 2010, 2011, 2012 - Dean award, Faculty of Science, Palacky University, Olomouc
• 2007 - Second best poster award, Prostab, Exeter, UK

Cooperation

Prof. Pavel Anzenbacher, Institute of Pharmacology, Faculty of Medicine and Dentistry, Palacky University, Olomouc - cytochrome P450 enzymes

RNDr. Jiri Vondrasek – Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Prague. - interaction in proteins and bioinformatics (ELIXIR)

Teaching activities

• Charles University in Prague, Faculty of Science - 160 h / 3 years
  • General and Physical Chemistry (5 h/week - two months as lecturer)
  • General chemistry (3 h/week, teaching assistant)
  • Biophysical chemistry (2 h/week, teaching assistant)
• Palacký University in Olomouc, Faculty of Science - 290 h / 3 years
  • Chapters from Physical Chemistry (KFC/KFCH, 2 h/week, lecturer, guarantor, 2010-)
  • Bioinformatics and Computational Biology (KFC/BIN, 2 h/week, lecturer, guarantor, 2010-)
  • Structural bioinformatics (KFC/STBI, 2 h/week, lecturer, guarantor, 2011-)
  • in silico Drug design (KFC/DD, 2 h/week, lecturer, quarantor, 2012-)
  • Physical Chemistry 2 (KFC/FC2, 2 h/week, teaching assistant, 2010-)
  • Physical Chemistry 1 (KFC/FC1, 2 h/week, teaching assistant, 2011-)
  • Scientific Communication (KFC/COM and KEF/BVEK, 1h/week, teaching assistant, 2011-)
• High school students
  • Cofounder and author of Korespondenční Seminář Inspirovaný Chemickou Tematikou (KSICHT) - free-time teaching activities of high-school students in chemistry since 2001.
  • Chemistry olympiad (ChO) category B (2008) and category A (2012).
  • Member of organizing committee of national round of ChO in Olomouc (2012).
  • Supervisor of high-school students in theoretical chemistry projects within project Badatel (since 2010).
  • Lecturer in project Přírodovědec (2011-2012).

Lecture notes (in czech language)

• KFC/KFCH - Kapitoly z fyzikalni chemie
• KFC/BIN - Bioinformatika a výpočetní biologie
• KFC/STBI - Strukturní bioinformatika
• KFC/DD - Racionální návrh léčiv - in silico drug design

Supervised students

• Viktor Vozár (2010-2011) - Bc. Informatics (consultant)
• Markéta Paloncýová (2010-2012) - Mgr. Physical Chemistry, (2012-) - Ph.D. Physical Chemistry (consultant)
• Václav Bazgier (2011-) - Ph.D. Physical Chemistry (consultant)
• Veronika Navrátilová (2011-) - Mgr. Material Chemistry
• Tomás Medek (2011-) - Bc. Biochemistry (discontinued)
• Miroslav Brumovský (2012-) - Mgr. Biomolekulární chemie (Masaryk Univesity)

Publications

Profile on Google Scholar | Researcher's ID | Profile on LinkedIn | Profile on Academia.edu | Profile on CiteULike | Profile on Mendeley

2013 (3)

1. Havlikova* M, Huliciak M, Bazgier V, Berka K, Kubala M: Fluorone dyes have binding sites on both cytoplasmic and extracellular domains of Na,K-ATPase. Biochim. Biophys. Acta - Biomembranes, 1828(2), 568-576, 2013 (Elsevier)
2. 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 (Am. Chem. Soc.)
3. Podloucka P, Berka K, Fabre G, Paloncyova M, Duroux JL, Otyepka M, Trouillas P: Lipid Bilayer Membrane Affinity Rationalizes Inhibition of Lipid Peroxidation by a Natural Lignan Antioxidant. J. Phys. Chem. B, 117 (17), 5043–5049, 2013 (Am. Chem. Soc.,MZ12-2)

2012 (7)

1. Berka K, Anzenbacherova E, Hendrychova T, Lange R, Masek V, Anzenbacher P, Otyepka M: Binding of Quinidine Radically Increases the Stability and Decreases the Flexibility of the Cytochrome P450 2D6 Active Site. J. Inorg. Biochem., 110, 46-50, 2012 (ScienceDirect)
2. 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 (Oxford Journals,MZ9-2)
3. Hendrychova T, Berka K; Navratilova V; Anzenbacher P, Otyepka M. Dynamics and Hydration of the Active Sites of Mammalian Cytochromes P540 Probed by Molecular Dynamics Simulations. Curr. Drug. Metab., 13(2), 177-189, 2012 (CDM)
4. Kosinova P, Berka K, Wykes M, Otyepka M, Trouillas P. Positioning of Antioxidant Quercetin and Its Metabolites in Lipid Bilayer Membranes: Implication for Their Lipid-Peroxidation Inhibition. J. Phys. Chem. B, 116 (4), 1309-1318, 2012 (Am. Chem. Soc.)
5. Otyepka M, Berka K, Anzenbacher P. Is There a Relationship Between the Substrate Preferences and Structural Flexibility of Cytochromes P450? Curr. Drug. Metab., 13(2), 130-142, 2012 (CDM)
6. Paloncyova M, Berka* K, Otyepka* M: Convergence of Free Energy Profile of Coumarin in Lipid Bilayer. (with Cover Art) J. Chem. Theory Comput., 8(4), 1200-1211, 2012 (Am. Chem. Soc.)
7. Rezanka M, Rezanka P, Míka L, Perlíková P, Berka K: Correspondence Seminar Inspired by Chemistry Topics (KSICHT). Chem. Listy, 106(4), 319-322, 2012 (Chem. Listy)

2011 (3)

1. 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 (Am. Chem. Soc.)
2. Berka K, Otyepka M: Insenstivity to close contacts and inability to predict protein foldability. J. Biomol. Struct. Dynam., 28(4), 633-634, 2011
3. Oncak M, Berka K, Slavicek* P: Novel Covalent Bond in Proteins: Calculations on Model Systems Question the Bond Stability. Chem. Phys. Chem., 12 (17), 3449-3457, 2011 (Wiley)

2010 (2)

1. Berka K, Laskowski RA, Hobza P, Vondrasek* J: Energy Matrix of Structurally Important Side-Chain/Side-Chain Interactions in Proteins. J. Chem. Theory Comput., 6(7), 2191-2203, 2010 (Am. Chem. Soc.)
2. Kolar M, Berka K, Jurecka P, Hobza* P; On the Reliability of the AMBER Force Field and its Empirical Dispersion Contribution for the Description of Noncovalent Complexes. ChemPhysChem, 11(11), 2399-2408, 2010 (Wiley)

2009 (2)

1. Berka K, Laskowski RA, Riley KE, Hobza P, Vondrasek* J: Representative Amino Acid Side Chain Interactions in Proteins. A Comparison of Highly Accurate Correlated ab Initio Quantum Chemical and Empirical Potential Procedures. J. Chem. Theory Comput., 5(4), 982-992, 2009 (Am. Chem. Soc.)
2. Berka K, Hobza P, Vondrasek J: Analysis of Energy Stabilization inside the Hydrophobic Core of Rubredoxin. ChemPhysChem, 10 (3), 543 - 548, 2009 (Wiley)

2008 - 2004 (5)

1. Biedermannova L, Riley KE, Berka K, Hobza P, Vondrasek J: Another role of proline: stabilization interactions in proteins and protein complexes concerning proline and tryptophane. Phys. Chem. Chem. Phys., 10, 6350 - 6359, 2008 (RSC Publishing)
2. Rezac J, Jurecka P, Riley KE, Cerný J, Valdes H, Pluhacková K, Berka K, Rezac T, Pitonak M, Vondrasek J, Hobza P: Quantum chemical benchmark energy and geometry database for molecular clusters and complex molecular systems (www.begdb.com): A users manual and examples. Collect. Czech. Chem. Commun., 73 (10), 1261-1270, 2008 (Collect. Czech. Chem. Commun.)
3. Rezac J, Berka K, Horinek D, Hobza P, Vondrasek J: The Stabilization Energy of the Glu-Lys Salt Bridge in the Protein/Water Environment: Correlated Quantum Chemical ab initio, DFT and Empirical Potential Studies. Collect. Czech. Chem. Commun, 73, 921-936, 2008 (Collect. Czech. Chem. Commun.)
4. Mazna P, Berka K, Jelinkova I, Balik A, Svoboda P, Obsilova V, Obsil T, Teisinger J: Ligand binding to the human MT2 melatonin receptor: The role of residues in transmembrane domains 3, 6, and 7. Biochem. Biophys. Res. Commun., 332, 726-734, 2005. (Elsevier)
5. Mazna P, Obsilova V, Jelinkova I, Balik A, Berka K, Sovova Z, Ettrich R, Svoboda P, Obsil T, Teisinger J: Molecular modeling of human MT2 melatonin receptor: the role of Val204, Leu272 and Tyr298 in ligand binding. J. Neurochem. 91, 836-842, 2004. (Wiley, Erratum - Wiley)

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