Education and Training

1993 B.Sc. (Vordiplom ‘pre-diploma’) in chemistry, Department of Chemistry, Eberhard-Karls-Universität, Tübingen, Germany
1998 Mgr. (corresponds to M.Sc.), Department of Physical Chemistry, Charles University, Prague Diploma thesis in physical and macromolecular chemistry: Chaperone-like Activity of Human Glycoproteins, supervisor: Prof. Z. Pavlíček
2002 Ph.D., Department of Physical Chemistry, Charles University, Prague; thesis: Human Haptoglobin: Structure and Interactions of a Tetrameric Chaperone-like Protein, supervisor: Prof. Z. Pavlíček
2002 RNDr., physical chemistry, Faculty of Sciences, Charles University, Prague
2006 Habilitation in biophysics – Habilitation defines the qualification to conduct self-contained university teaching and is the key for access to a professorship in Czech Republic

 

Employment and professional experience

12/2018 – current Larkin University, FL, USA, President/CEO
09/2018 – 12/2018: Larkin University, FL, USA, interim CEO/President
08/2018 – 12/2018: College of Biomedical Sciences, Larkin University, FL, USA, Dean of the College and Professor.
12/2018 – current: Department of Cellular Biology and Pharmacology, Wertheim College of Medicine, Florida International University – Community-based adjunct professor
08/2018 – 12/2019: Academy of Sciences of the Czech Republic (Institute of Microbiology), Prague, Czech Republic – senior research scientists
10/2016 – 4/2017: College of Ostheopatic Medicine and College of Medical Sciences, NOVA Southeastern University, Fl, USA, visiting faculty, Fulbright-Masaryk Scholar
2006-2018, responsible for the Nove Hrady branch (now Center for Nanobiology and Structural Biology, Institute of Microbiology) of the Academy of Sciences of the Czech Republic, including European integration and graduate studies.
01/2016 – 8/2018: Center for Nanobiology and Structural Biology, Institute of Microbiology) Academy of Sciences of the Czech Republic, Nové Hrady, Czech Republic – Head
6/2014 – 8/2018: C4SYS-Czech national research infrastructure for systems biology – Director
01/2011 – 12/2015: Institute of Nanobiology and Structural Biology, Global Change Research Center (from 01/2016 Center for Nanobiology and Structural Biology, Institute of Microbiology) Academy of Sciences of the Czech Republic, Nové Hrady, Czech Republic – Director
07/2003 – 8/2018: Center for Nanobiology and Structural Biology, Institute of Microbiology (formerly until 01/2016 Institute of Nanobiology and Structural Biology, Global Change Research Center, Academy of Sciences of the Czech Republic, until 12/2010 Institute of Systems Biology and Ecology ASCR), Nové Hrady, Czech Republic – Head of Department of Structure and Function of Proteins and group leader.
07/2003 – 8/2018: lecturer at the University of South Bohemia, since 2006 Professor (associate) in biophysics (doc.), since 2013 full professor in biophysics (Prof.)
07/2002 – 07/2003: Institute of Physical Biology, University of South Bohemia, Ceske Budejovice – post-doc, area of research: computational biology
7/1993 – 8/1995: research assistant, Chemistry, Universität Tübingen, Germany

Publications:

1. Pavlicek Z., Ettrich R.*:Chaperone-like Activity of Human Haptoglobin. Chemical Papers(1998) 52, 309-310.

2. Pavlicek Z., Ettrich R.:Chaperone-like Activity of Human Haptoglobin: Similarity with alpha-Crystallin. Collect.Czech.Chem.Commun.(1999) 64 (4), 717-725.

3.Ettrich R.*, Melichercik M., Teisinger J., Ettrichova O., Krumscheid R., Hofbauerova K., Kvasnicka P., Schoner W. and Amler E.:Three-dimensional structure of the large cytoplasmic H4-H5 loop of Na+/K+-ATPase deduced by restraint-based comparative modeling shows only one ATP binding site.Journal of Molecular Modeling (2001) 7, 184-192.

4. Hofbauerova K., Kopecky Jr. V, Ettrich R.,Ettrichova O. and Amler E.: Secondary and Tertiary Structure of the Nucleotide-Binding Domain of the alpha-Subunit of Na+/K+-ATPase.Biopolymers(2002), 67, 242-246.

5. Kubala M., Hofbauerova K., Ettrich R., Kopecky Jr. V., Krumscheid R., Plasek J., Teisinger J., Schoner W. and Amler E.:Phe475and Glu446but not Ser445parcticipate in ATP-binding to the alpha -subunit of Na+/K+-ATPase.Biochem.Biophys.Res.Commun. (2002) 297, 154-159.

6. Ettrich R.,Brandt W., Kopecky Jr. V, Baumruk V., Hofbauerova K. and Pavlicek Z.:Behaviour of the Chaperone-Like Protein Haptoglobin under Heat Shock Conditions.Biological Chemistry(2002) 383 (10), 1667-1676.

7. Kopecky V. Jr., Ettrich R., Hofbauerova K. and Baumruk V.:Structure of human acid  1-glycoprotein and its high-affinity binding site. Biochem.Biophys.Res.Commun.(2003) 300, 41-46.

8. Krumscheid R., Susankova K., Ettrich R., Teisinger J., Amler E. and Schoner W.:Localization of catalytic active sites in the large cytoplasmic domain of Na+/K+-ATPase.Annals of the New York Academy of Science(2003) 986, 242-244.

9. Vlachova V., Teisinger J., Susankova K., Lyfenko A., Ettrich R., Vyklicky L.:Functional role of C-terminal cytoplasmic tail of rat vanilloid receptor 1 (TRPV1). Journal of Neuroscience(2003), 23 (4), 1340-1350.

10.Ettrich R*.,Vlachova V., Teisinger J., Pavlicek J., Bezouska K., Kopecky Jr. V. and Stys D.:Molecular Modeling as a tool in molecular biology of membrane-bound receptors. Materials Structure(2003) 10 (3), 27-30.

11. Hofbauerova K., Kopecky Jr. V., Ettrich R.,Kubala M., Teisinger J., Ettrichova O. and Amler E.:Structural Biology on the sodium pump: a combined approach leading to a full characterization of the catalytic domain. Materials Structure(2003) 10 (3), 18-20 .

12. Hušáková L., Herkommerová-Rajnochová E., Semeňuk T., Kuzma M., Rauvolfová J., Přikrylová V., Ettrich R.,Plíhal O., Bezouška K., Křen V.: Enzymatic discrimination of 2-acetamido-2-deoxy-D-mannopyranose-containing disaccharides using beta -N-acetylhexosaminidases.Advanced synthesis and catalysis(2003) 345 (6+7), 735-742.

13. Kubala M., Teisinger J., Ettrich R.,Hofbauerova K., Kopecky Jr. V., Baumruk V., Krumscheid R., Plasek J., Schoner W. and Amler E.:Eight amino acids forming the ATP recognition site of of Na+/K+-ATPase. Biochemistry(2003) 42 (21), 6446-6452.

14. Pavlicek J., Sopko B., Ettrich R.,Kopecký Jr. V., Baumruk V., Man P., Havlíčková K., Vrbacký M., Křen V., Pospíšil M. and Bezouška K.: Molecular Characterization of Binding of Calcium and Carbohydrates by an Early Activation Antigen of Lymphocytes CD69. Biochemistry(2003) 42 (31), 9295-9306. (RETRACTED)

15. Hofbauerova K., Kopecky Jr. V., Ettrich R.,Kubala M., Teisinger J. and Amler E.:ATP is stabilized by an stacking interaction within the binding site of Na+/K+-ATPase. Biochem.Biophys.Res.Commun. (2003) 306, 325-329.

16. Fialova P., Weignerova L., Rauvolfova J., Prikrylova V., Pisvejcova A., Ettrich R.,Sedmera P. and Kren V.:Hydrolytic and Transglycosylation Reactions of Unnatural N-Acyl Modified Substrates Catalysed by beta -N-Acetylhexosaminidases.

17. Sovova Z., Mazna P., Teisinger J., Stys D., Obsil T. and Ettrich R.*:A structural model of human MT2 melatonin receptor and its melatonin recognition site.Materials Structure(2004) 11 (1), 12-14 .

18.Plíhal O., Mihok L., Ettrich R., Man P., Havlíček V., Byrtusová P., Pavlicek J. and Bezouška K .:The isoforms of rat natural killer cell receptor NKR-P1 display distinct binding of complex saccharide ligands. Collect.Czech.Chem.Commun.(2004) 69 (3), 631-644. (RETRACTED)

19. Kopecky V. Jr., Ettrich R., Hofbauerova K. and Baumruk V.:Vibrational spectroscopy and computer modeling of proteins: solving structure of alpha1-acid glycoprotein . Spectroscopy: An International Journal (2004) 18 (2), 323-330.

20. Lansky Z., Kubala M., Ettrich R.,Kuty M., Plasek J., Teisinger J., Schoner W. and Amler E.:The hydrogen bond between Arg423 and Glu472 and another key residues Asp443, Ser477 and Pro489 are responsible for forming and a different positioning of TNP-ATP and ATP within the nucleotide binding site of Na+/K+-ATPase. Biochemistry(2004) 43 (26), 8303-8311.

21. Mazna P., Obsilova V., Jelinkova J., Balik A., Berka K., Sovova Z.,Ettrich R.Svoboda P., Obsil T. and Teisinger J.: Molecular modeling of human MT2 melatonin receptor: the role of Val204, Leu272 and Tyr298 in ligand binding. Journal of Neurochemistry(2004) 91 (4), 836-842.

22. Krumscheid R., Ettrich R., Sovova Z., Susankova K., Lansky Z., Hofbauerova K., Linnertz H., Teisinger J., Amler E. and Schoner W.:The phosphatase activity of the isolated H4-H5-loop of Na+/K+-ATPase resides outside its ATP binding site. Eur. J. Biochem(2004) 271, 3923-3936.

23. Fialova P., Namdjou DJ., Ettrich R.,Prikrylova V., Rauvolfova J., Krenek K., Kuzma M., Elling L., Bezouška K. and Kren V.:Combined Application of Galactose Oxidase and b-N-Acetylhexosaminidase in the Synthesis of Complex Immunoactive N-Acetyl-d-galactosaminides. Advanced synthesis and catalysis(2005) 347 (7-8): 997-1006.

24. Štys D., Schoefberger W., Halbhuber Z., Ristvejova J., Müller M. and Ettrich R.*: Secondary structure estimation of recombinant psbHencoding a photosynthetic membrane protein of cyanobacterium Synechocystis sp. PCC 6803.Photosynthetica (2005) 43 (3): 421-424.

25. Fialova P., Carmona AT., Robina I., Ettrich R.,Sedmera P., Přikrylová V., Hušáková L., and Křen V.: Glycosyl Azides – Novel Substrates for Enzymatic Transglycosylations.Thetrahedronletters(2005), 46: 8715-8718.

26.Ristvejova J, Kopecky V, Sovova Z, Balsera M, Arrelano JB, Green M. and Ettrich R*:Structure and Dynamics of the N-terminal Loop Region of PsbQ from Photosystem II of Spinacia oleracea studied by the Means of Molecular Modeling and Vibrational Spectroscopy.Biochem Biophys Res Commun (2006) 345: 1. 287-291

27. Carmona AT., Fialová P. , Křen V., Ettrich R., Martínková L., Moreno-Vargas A. J., González C. and Robina I.: Cyanodeoxy-Glycosyl derivatives as substrates for enzymatic reactionsEur. J. Org. Chem (2006)8. 1876-1885

28.Ettrich R.*,Kopecký Jr., V.,Hofbauerová K.,Baumruk V.,Pompach P.,Man P.,Havlíček V.,Plíhal O.,Jan Sklenář J.,Pišvejcová A., Vladimír Křen V. and Bezouška K.: Structure of the dimeric N-glycosylated form of fungal beta-N-acetylhexosaminidase revealed by homology modeling, vibrational spectroscopy, biochemical and cross-linking studies. (2007) BMC Struct Biol 7: 05

29. Klara Susankova,Rudiger Ettrich,Ladislav Vyklicky,Jan Teisinger,Viktorie Vlachova(2007)  Contribution of the putative inner-pore region to the gating of the transient receptor potential vanilloid subtype 1 channel (TRPV1).   J Neurosci 27: 28. 7578-7585

30. Zofie Sovova,Rudiger Ettrich* (2007)  Phylogenetic analysis of extrinstic proteins of Photosystem II.   Materials Structure14: 1. 8-12

31. Jannette Carey,Jiri Brynda,Julie Wolfová,Rita Grandori,Tobias Gustavsson,Rüdiger Ettrich,Ivana Kutá Smatanová(2007)  WrbA bridges bacterial flavodoxins and eukaryotic NAD(P)H:quinone oxidoreductases.   Protein Sci 16: 10. 2301-2305

32. Jan Benedikt,Abdul Samad,Rudiger Ettrich,Jan Teisinger,Viktorie Vlachova(2009)  Essential role for the putative S6 inner pore region in the activation gating of the human TRPA1 channel.   Biochimica et Biophysica Acta (BBA) – Molecular Cell Research 1793: 7. 1279-1288

33. Mikalai Lapkouski,Santosh Panjikar,Pavel Janscak,Ivana Kuta Smatanova,Jannette Carey,Rüdiger Ettrich*,Eva Csefalvay(2009)  Structure of the motor subunit of type I restriction-modification complex EcoR124I.   Nat Struct Mol Biol 16: 1. 94-95

34. J Kohoutová,I Kutá Smatanová,J Brynda,M Lapkouski,J L Revuelta,J B Arellano,R Ettrich*(2009)  Crystallization and preliminary crystallographic characterization of the extrinsic PsbP protein of photosystem II from Spinacia oleracea.   Acta Crystallogr Sect F Struct Biol Cryst Commun 65: Pt 2. 111-115

35. Julie Wolfova, Ivana Kuta Smatanova, Jiri Brynda, Jeroen R Mesters,Mikalai Lapkouski,Michal Kuty,Antonino Natalello,Neal Chatterjee,Sy-Yeu Chern,Erin Ebbel,Angela Ricci,Rita Grandori,Rüdiger Ettrich*,Jannette Carey(2009)  Structural organization of WrbA in apo- and holo-protein crystals   Biochimica et Biophysica Acta (BBA) – Proteins and Proteomics 1794: 9. 1288-1298

36. Rebecca Strawn, Milan Melichercik, Michael Green, Thomas Stockner, Jannette Carey, Rudiger Ettrich*(2010)  Symmetric allosteric mechanism of hexameric Escherichia coli arginine repressor exploits competition between L-arginine ligands and resident arginine residues   PLOS Computational Biology 6: 6. e1000801

37. Natallia Kulik, Lenka Weignerová, Tomáš Filipi, Petr Pompach, Petr Novák, Hynek Mrázek, Kristýna Slámová, Karel Bezouška, Vladimír Křen,Rüdiger Ettrich*(2010)  The α-galactosidase type A gene aglA from Aspergillus niger encodes a fully functional α-N-acetylgalactosaminidase  Glycobiology20: 11. 1410-1419.

38. Kristýna Slámová, Radek Gažák, Pavla Bojarová, Natallia Kulik, Rudiger Ettrich, Helena Pelantová, Petr Sedmera, Vladimír Křen (2010)  4-Deoxy-substrates for beta-N-acetylhexosaminidases: how to make use of their loose specificity   Glycobiology20: 8. 1002-1009.

39. R Strawn, T Stockner, M Melichercik, L Jin, W – F Xue, J Carey, R Ettrich*(2011)  CHAPTER FIVE: Synergy of molecular dynamics and isothermal titration calorimetry in studies of allostery.   In: Methods in Enzymology, Biothermodynamics, Part D Volume 492 Edited by:Michael L. Johnson, Jo M. Holt , Gary K. Ackers. pages 151-189 Academic Press – Elsevier Publishing Company, ISBN: 978-0-12-386003-3

40. M Horničáková, J Kohoutová, J Schlagnitweit, C Wohlschlager, R Ettrich, R Fiala, W Schoefberger, N Müller(2011)  Backbone assignment and secondary structure of the PsbQ protein from Photosystem II   Biomolecular NMR Assignments 5: 2. 169-175.

41. P Bojarova, K Slamova, K Krenek, R Gazak, N Kulik, R Ettrich, H Pelantova, M Kuzma, S Riva, D Adamek, K Bezouska, V Kren(2011)  Charged hexosaminides as new substrates for β-N-acetyl-hexosaminidase catalyzed synthesis of immunomodulatory disaccharides   Advanced Synthesis & Catalysis 353: 2409-2420.

42. Žofie Sovová, Vladimír Kopecký Jr, Tomáš Pazderka, Kateřina Hofbauerová, Daniel Rozbeský, Ondřej Vaněk, Karel Bezouška,Rüdiger Ettrich*(2011)  Structural analysis of natural killer cell receptor protein 1 (NKR-P1) extracellular domains suggests a conserved long loop region involved in ligand specificity Journal of Molecular Modeling 17: 6. 1353-1370.

43. Morteza Khabiri, Azadeh Nikouee, Lukasz Cwiklik, Stephan Grissmer, Rüdiger Ettrich*(2011)  Charybdotoxin unbinding from the mKv1.3 potassium channel: A combined computational and experimental study Journal of Physical Chemistry B 115: 39. 11490–11500.

44. Ryslava, Helena, Kalendova, Alzbeta, Doubnerova, Veronika, Skocdopol, Premysl, Hodkova, Anna, Kukacka, Zdenek, Slamova, Kristyna, Bojarova, Pavla, Pompach, Petr, Kumar, Vinay, Kulik, Natallia, Ettrich, Rudiger, Kren, Vladimir, Bezouška, Karel(2011)  Enzymatic characterization and molecular modeling of an evolutionarily interesting fungal beta-N-acetylhexosaminidase FEBS Journal 278: 2469-2484.

45. Jana Jirásková-Vaníčková, Rudiger Ettrich, Barbora Vorlová, Hillary Hoffman, Martin Lepšík, Petr Jansa, Jan Konvalinka (2011)  Inhibition of Human Serine Racemase, an Emerging Target for Medicinal Chemistry Current Drug Targets 12: 7. 1037-1055.

46. Ondrej Kaplan, Karel Bezouska, Ondrej Plihal, Rudiger Ettrich, Natallia Kulik, Ondrej Vanek, Daniel Kavan, Oldrich Benada, Anna Malandra, Ondrej Sveda, Alicja B Vesela, Anna Rinagelova, Kristyna Slamova, Maria Cantarella, Jurgen Felsberg, Jarmila Duskova, Jan Dohnalek, Vladimir Kren, Ludmila Martinkova (2011)  Heterologous expression, purification and characterization of nitrilase from Aspergillus niger K10   BMC Biotechnology 11: 2

47. Abdul Samad, Lucie Sura, Jan Benedikt, Rudiger Ettrich, Babak Minofar, Jan Teisinger, Viktorie Vlachova(2011)  The C-terminal basic residues contribute to the chemical and voltage-dependent activation of TRPA1 Biochemical Journal 433 (1): 197-204.

48. Azadeh Nikouee, Morteza Khabiri, Stephan Grissmer, Rüdiger Ettrich*(2012)  Charybdotoxin and margatoxin acting on the human voltage-gated potassium channel hKv1.3 and its H399N mutant: An experimental and computational comparison Journal of Physical Chemistry B, 116 (17): 5132-5140.

49. Vladimir Kopecky Jr, Jaroslava Kohoutova, Mikalai Lapkouski, Katerina Hofbauerova, Zofie Sovova, Olga Ettrichová, Sergio González-Pérezc, Alexandr Dulebo, David Kaftan, Ivana Kuta Smatanova, Jose L Revuelta, Juan B Arellano, Jannette Carey, Rudiger Ettrich*(2012)  Raman spectroscopy adds complementary detail to the high-resolution x-ray crystal structure of photosynthetic PsbP from Spinacia oleracea  PLOS One7 (10): e46694

50. Alexander Dulebo, Rüdiger Ettrich, Rudolf Lucas, David Kaftan(2012)  A Computational Study of the Oligosaccharide Binding Sites in the Lectin-Like Domain of Tumor Necrosis Factor and TIP Peptide. Current Pharmaceutical Design 18 (27): 4236-4243.

51. Iryna Kishko, Balasubramanian Harish, Vasilina Zayats, David Reha, Brian Tenner, Dhananjay Beri, Tobias Gustavsson, Rüdiger Ettrich*, Jannette Carey(2012)  Biphasic kinetic behavior of FMN-dependent NAD(P)H:quinone oxidoreductase WrbA from E. coli  PLOS One 7 (8): e43902

52. Vasilina Zayats, Abdul Samad, Babak Minofar, Katherine Roelofs, Thomas Stockner, Rudiger Ettrich(2013)  Regulation of the transient receptor potential channel TRPA1 by its N-terminal ankyrin repeat domain Journal of Molecular Modeling, 19:  4689–4700.

53. Morteza Khabiri, Babak Minofar, Jan Březovsky, Jiří Damborský, Rudiger Ettrich*(2013)  Interaction of Organic Solvents with Protein Structures at Protein-Solvent InterfaceJournal of Molecular Modeling, 19: 4701–4711.

54. Veronika Štěpánková, Morteza Khabiri, Jan Brezovský, Antonín Pavelka, Babak Minofar, Rudiger Ettrich, Radka Chaloupková, Jiří Damborský(2013)  Expansion of tunnels and active-site cavities influence catalytic activity of haloalkane dehalogenases in organic co-solvents ChemBioChem, (in the section: Very Important Paper (VIP)),  14:  890–897.

55.Daniel Rozbeský, Žofie Sovová, Julien Marcoux, Petr Man, Rüdiger Ettrich, Carol V Robinson, Petr Novák (2013)  Structural model of lymphocyte receptor NKR-P1C revealed by mass spectrometry and molecular modelling   Analytical Chemistry 85: 3. 1597–1604.

56. Tana Koudelakova, Radka Chaloupkova, Jan Brezovsky, Zbynek Prokop, Martina Pavlova, Martin Hessler, Morteza Khabiri, Maryia Plevaka, Daryna Kulik, Ivana Kuta Smatanova, Pavlina Rezacova, Rudiger Ettrich,Uwe T Bornscheuer, Jiri Damborsky (2013) Engineering Enzyme Stability and Resistance to an Organic Cosolvent by Modification of Residues in the Access Tunnel Angewandte Chemie (International Edition) 52: 1959 –1963.

57.Iryna Kishko, Jannette Carey, Jiri Brynda, Richard Guerra, Olga Ettrichova, Zdenek Kukacka, Petr Novak, Michal Kuty, Ivana Kuta Smatanova,Rudiger Ettrich*, Mikalai Lapkouski* (2013)  1.2 Å-resolution crystal structure of E.coli WrbA holoprotein.Acta Crystallographica Section D: Biological Crystallography: Biological Crystallography 69: 9. 1748-1757.

58. Kristýna Slámová, Natallia Kulik, Martin Fiala, Jana Krejzová-Hofmeisterová, Rüdiger Ettrich,Vladimír Křen (2014)  Expression, characterization and homology modeling of a novel eukaryotic GH84 β-N-acetylglucosaminidase from Penicillium chrysogenum Protein Expression and Purification 95:  204–210.

59. D Sinha, K Shamayeva, V Ramasubramani, D Reha, V Bialevich, M Khabiri, N Milbar, A Guzanova, M Weiserova, E Csefalvay, J Carey, R Ettrich* (2014)  Interdomain communication in the endonuclease/motor subunit of Type I restriction-modification enzyme EcoR124I Journal of Molecular Modeling 20 (7):  2334.

60. S K Pandey, D Reha, V Zayats, M Melichercik, J Carey, R Ettrich *(2014)  Binding-competent states for L-arginine in E. coli arginine repressor apoprotein. Journal of Molecular Modeling 20 (7): 2330.

61. Jana Krejzová, Kristýna Slámová, Petr Šimona, Lubica Kalachova, Natallia Kulik, Pavla Bojarová, Petr Marhol, Helena Pelantová, Josef Cvačka, Rüdiger Ettrich, Vladimír Křen (2014) Inhibition of GlcNAc-processing glycosidases by C-6-azido-NAG-thiazoline and its derivatives Molecules 19:  3471-3488.

62. 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.

63. Natallia Kulik, Kristyna Slamova, Rudiger Ettrich, Vladimir Kren (2015) Computational study of β-N-acetylhexosaminidase from Talaromyces flavus, a glycosidase with high substrate flexibility BMC Bioinformatics 16 (1):  28.

64. Vasilina Zayats, Thomas Stockner, Saurabh K Pandey, Katharina Wörz, Rüdiger Ettrich, Jost Ludwig(2015) A refined atomic scale model of the Saccharomyces cerevisiae K+-translocation protein Trk1p combined with experimental evidence confirms the role of selectivity filter glycines and other key residues. BBA-Biomembranes 1848 (5):  1183-1195.

65. Adriana Walnerová, Kousik Chandra, Petr Rathner, Michaela Horničáková, Judith Schlagnitweit, Jaroslava Kohoutová, Rüdiger Ettrich, Norbert Müller (2015) Resonance assignment of PsbP an extrinsic protein from Photosystem II of Spinacia oleracea Biomolecular NMR Assignments 9 (2):  341–346.

66. Eva Csefalvay, Mikalai Lapkouski, Alena Guzanova, Ladislav Csefalvay, Tatjana Baikova, Igor Shevelev, Vitali Bialevich, Katsiaryna Shamayeva, Pavel Janscak, Ivana Kuta Smatanova, Santosh Panjikar, Jannette Carey, Marie Weiserova, Rüdiger Ettrich*(2012)  Functional coupling of duplex translocation to DNA cleavage in a type I restriction enzyme  PLOS One, PLoS ONE 10 (6):  e0128700

67. Petr Rathner, Adriana Walnerova, Michaela Hornicakova, Christian Wohlschlager, Kousik Chandra, Jaroslava Kohoutova, Rüdiger Ettrich, Reinhard Wimmer, Norbert Mueller(2015) Solution Structure of PsbQ from Photosystem II of Higher Plants  PROTEINS: Structure, Function, and Bioinformatics 83 (9):  1677–1686.

68. Irene Frischauf, Vasilina Zayats, Michael Deix, Anna Hochreiter, Isaac Jardin Polo, Martin Muik, Barbara Lackner, Barbora Svobodova, Teresa Pammer, Monika Litvinukova, Amrutha Arumbakam Sridhar, Isabella Derler, Ivan Bogeski, Christoph Romanin, Rüdiger Ettrich*, Rainer Schindl* (2015) A calcium accumulating region, CAR, in the Orai1 channel enhances Ca2+- permeation and SOCE-induced gene transcription Science Signaling 8 (408):  ra131

69. Vladimír Kopecký Jr, Rüdiger Ettrich, Tomáš Pazderka, Kateřina Hofbauerová, David Řeha, Vladimír Baumruk (2016)  Influence of ligand binding on structure and thermostability of human alpha-1-acid glycoprotein Journal of Molecular Recognition 29 (2):  70–79.

70. Isabella Derler, Isaac Jardin, Peter B Stathopulos, Martin Muik, Marc Fahrner, Vaselina Zayats, Saurabh Pandey, Michael Poteser, Barbara Lackner, Marketa Absolonova, Klaus Groschner, Rüdiger Ettrich, Mitsu Ikura, Christoph Romanin (2016) Cholesterol binding modulates Orai1 channel function Science Signaling 9 (412):  ra10. Jan 26.

71. 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.

72. Pavel Grinkevich, Iuliia Iermak, Nicholas A Luedtke, Jeroen R Mesters,Rudiger Ettrich*, Jost Ludwig (2016) pHluorin(GFP)-assisted expression, purification, crystallization and X-ray diffraction data analysis of C-terminal domain of HsdR subunit from E. coli type I restriction-modification system EcoR124I. Acta Crystallographica Section F, 72 (9): 672- 676.

73. 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, Ivan Bogeski, Rüdiger Ettrich, Christoph Romanin, Rainer Schindl (2017) Transmembrane helix connectivity in Orai1 controls two gates for calcium-dependent transcription Science Signaling 10 (507): eaao0358. (Cover story)

74. Bialevich V, Sinha D, Shamayeva K, Reha D, Guzanova A, Csefalvay E, Carey J, Weiserova M and Ettrich R.*(2017) The helical domain of the motor subunit of EcoR124I participates in ATPase activity and dsDNA translocation, PeerJ, Volume 2017, Issue 1, 2017, Article number e2887.

75. Marc Fahrner, Saurabh K Pandey, Martin Muik, Lukas Traxler, Carmen Butorac, Michael Stadlbauer, Vasilina Zayats, Adéla Krizova, Peter Plenk, Irene Frischauf, Rainer Schindl, Hermann J Gruber, Peter Hinterdorfer, Rüdiger H Ettrich, Christoph Romanin, Isabella Derler (2018) Communication between N-terminus and Loop2 tunes Orai activation The Journal of Biological Chemistry 293: 1271-1285.

76. Dhiraj Sinha, Vitali Bialevich, Katsiaryna Shamayeva, Alena Guzanova, Alexandra Sisakova, Eva Csefalvay, Lumir Krejci, Jannette Carey, Marie Weiserova, Rüdiger H Ettrich*(2018) A residue of motif III positions the helicase domains of motor subunit HsdR in restriction-modification enzyme EcoR124I,Journal of Molecular Modeling 24 (7):  176.

77. Pavel Grinkevich, Dhiraj Sinha, Iullia Iermak, Alena Guzanova, Marie Weiserova, Jost Ludwig, Jeroen R. Mesters, Rudi H Ettrich* (2018) Crystal structure of a novel domain of the motor subunit of the Type I restriction-modification system EcoR124 involved in complex assembly and DNA binding, The Journal of Biological Chemistry 293 (39): 15043-15054.

78. Saurabh Pandey, Daniel Bonhenry, Rudi H Ettrich(2019) Chapter 10: Ion Channel Simulations.In: Biomolecular Simulations in Drug Discovery Edited by: Francesco L. Gervasio, Vojtech Spiwok, Raimund Mannhold, Helmut Buschmann, Jörg Holenz.   pages 247-280, Book Series: Methods and Principles in Medicinal Chemistry, Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim, Germany, isbn:978-3-527-34265-5.

79. Daniel Bonhenry, Romana Schober, Tony Schmidt, Linda Waldherr, Rudi H Ettrich, Rainer Schindl (2019) Mechanistic insights into the Orai channel by molecular dynamics simulations Seminars in Cell & Developmental Biology 94 (October 2019): 50-58.

80. Romana Schober, Daniel Bonhenry, Victoria Lunz, Jinhui Zhu, Adela Krizova, Irene Frischau, Marc Fahrner, Linda Waldherr, Tony Schmidt, Isabella Derler, Peter B. Stathopulos, Christoph Romanin, Rudi H. Ettrich* and Rainer Schindl* (2019) Sequential activation of STIM1 links Ca2+ with luminal domain unfolding. Science Signaling 12: eaax3194.

Selected Invited Talks

“Computational modeling of 3’- Phosphoadenosine 5’-phoshosulfate synthase PAPS”, Visegrad Symposium, Sopron, Hungary, June 20-23. 2023 (invited plenary lecture)

“Cation translocation in human ORAI channels” Vienna BioCenter, invited CAPSID seminar 12.12.2018 (hosted by Dr. Peggy Stolt-Bergner):

“Modulation of human ORAI1 channels: modeling and simulations”, 15th International Life Science Meeting, Krems, Austria, 18.4.2018, (invited plenary lecture)

“Cation translocation in human ORAI channels” Biomedical Center of the Slovak Academy of Sciences (hosted by Dr. Ivana Nemcovicova), 11.12.2018

“Modulation of human ORAI1 channels: modeling and simulations” at the conference Cell Physics 2017, October 11-13, 2017, Saarbruecken, Germany (invited plenary lecture)

“Computational modeling of 3’- Phosphoadenosine 5’-phoshosulfate synthase PAPS”, SOFLACS -Chemical Sciences Symposium 2017 organized by the South Florida Chapter of the American Chemical Society, Ft. Lauderdale, FL, USA, February 26, 2017 (invited plenary lecture)

“Interdomain communication in Type I restriction-modification enzymes” at the conference MGMS (Molecular Graphics and Modeling Society) “Exploring Mechanisms in Biology: Theory and Experiment”, November 25-27, 2015, Biopolis, Singapore (invited lecture)

“Structure and function of the motor subunit of the EcoR124I restriction-modification complex” at the conference “Modelling Interactions in Biomolecules VII”, 14-18 September 2015, Pruhonice, Prague, Czech Republic.(invited plenary lecture)¨

“Functional coupling of duplex translocation to DNA cleavage in a type I restriction enzyme”, University of Kent, Canterbury, UK, 20.10. 2015 (invited seminar)

“Was binding of free amino acids an early innovation in the evolution of allostery?” at the “International Conference on Informatics & Integrative Biology (CIIB-2014)” Bose Institute 16.12-19.12.2014, University of Calcutta.

“Combined computational and experimental studies” at the 11th International Life Science Meeting, IMC FH KREMS, March 25-26, 2014. (invited lecture, conference fee and accommodation covered by the organizers)

“Functional coupling of duplex translocation to DNA cleavage in a type I restriction enzyme”, Centre of Biotechnology, Nehru Science Complex, University of Allahabad, 8.12. 2014

“Was binding of free amino acids an early innovation in the evolution of allostery?”, Dr. B.R. Ambedkar Center for Biomedical Research, University of Delhi, 11.12.2014

“Was binding of free amino acids an early innovation in the evolution of allostery?”, Centre for Computational Biology and Bioinformatics, School of Computational and Integrative Sciences, Jawaharlal Nehru University, New Dehli, 12.12.2014 (accommodation for 2 days provided by JNU)

“Was binding of free amino acids an early innovation in the evolution of allostery?” Global Perspectives on the Structure and Dynamics of Liquids and Mixtures: Experiment and Simulation, EMLG – JMLG annual meeting 2013, 9 – 13 September 2013, Lille, France (invited lecture)

“Was binding of free amino acids an early innovation in the evolution of allostery?” Astbury Seminar, University of Leeds, UK, 14th November 2013 (invited seminar).

“Charybdotoxin unbinding from the mKv1.3potassium channel: A Combined computational and experimental study”, Modeling interactions in Biolomolecules VI, 2013 at Marianske Lazne, Czech Republic (invited plenary lecture)

“Functional coupling of DNA duplex translocation to its cleavage in a type I restriction enzyme.”2nd World DNA and Genome Day-2011, Dalian, China, 25-29.4.2011 (invited lecture)

„Was binding of free amino acids an early innovation in the evolution of allostery?“, 8thDiscussions in Structural Molecular Biology, Nove Hrady, 18–20.3.2010 (invited plenary lecture)

„Structural and thermodynamic evidence for allosteric relaxed-state symmetry“,Hofmeisterfest, October 13 – 16  2010 Prague, Czech Republic (invited plenary lecture)

Molecular mechanism of allostery in hexameric E. coli arginine repressor, Modeling interactions in Biolomolecules IV, 2009 at Hrubá Skála, Czech Republic (invited plenary lecture)

DNA translocation by type I restriction-modification enzymes, 7th International Life Science Meeting, Krems, Austria, 2009 (invited plenary lecture)

Coupling of endonuclease and translocase functions in Type I restriction-modification complexes, National Institute of Health, Bethesda, Maryland, USA, 2009

Young Scientist Invited Talk, Structure of the motor subunit and model for translocation by the type I restriction enzyme EcoR124I, 22ndAnnual Symposium of the Protein Society, 2008, San Diego, California, USA

Structure of the motor subunit and translocation model for EcoR124I restriction-modification complex, 2008, Princeton University, New Jersey, USA

Structure, Function and Dynamics of fungal beta-N-Hexosaminidase, MOLECULAR LIFE SCIENCES 2007, Fall meeting of the GBM, Hamburg

Vibrational spectroscopy and computer modelling of proteins – building of interdisciplinary bridges. Biological Sciences, University of Calgary, June 2004, Canada.

 

Foreign research stays

February 1999, Martin Luther Universität, Halle-Wittenberg, Germany, group of assoc. Prof. W. Brandt, Homology modelling of the haptoglobin heavy chain using COMPOSER and SYBYL, supported by the Volkswagen Foundation

December 1999 – April 2001, several short-term stays (altogether 10 weeks), Justus Liebig Universität, Giessen, Germany, group of Prof. W. Schoner, Molecular modelling of the large cytoplasmic loop of Na/K-ATPase, supported by the German and Czech governments

May 2000, Univerzita Komenského, Bratislava, Slovakia, group of Dr. P. Kvasnička, Fold recognition on P-type ATPases

August 2000, Justus Liebig Universität, Giessen, Germany, group of Dr. B. Boschek, Electron microscopy of chaperone-substrate complexes

March 2001, Justus Liebig Universität, Giessen, Germany, group of Dr. B. Boschek, Electron microscopy of hemoglobin-haptoglobin complexes

May 2001, Universita Degli Studi, Ancona, Italy, group of Prof. L. Mazzanti, Bioinformatics

June 2004, University of Calgary, group of Prof. P. Tieleman, Molecular dynamics of membrane proteins

April 2008, Princeton University, Chemistry department, group of Prof. J. Carey, Structure of the motor subunit and translocation model for EcoR124I restriction-modification complex

April 2009, Princeton University, Chemistry department, group of Prof. J. Carey, Interaction of photosystem proteins PsbP and PsbQ

February 2010, Princeton University, Chemistry department, group of Prof. J. Carey, Allostery in Argine repressor from e. coli.

November 2011, Princeton University, Chemistry department, group of Prof. J. Carey, Apo/holo WrbA simulations

Sept/Oct 2012, Princeton University, Chemistry department, group of Prof. J. Carey, Umbrella sampling in ArgR

February 2015, NOVA Southeastern University, Florida, USA, College of Medical Sciences, group of Prof. K.V. Venkatachalam

March 2016, NOVA Southeastern University, Florida, USA, College of Medical Sciences, group of Prof. K.V. Venkatachalam

Sept 2016- April 2017, NOVA Southeastern University, Florida, USA, College of Ostheopathic Medicine and College of Medical Sciences, Fulbright-Masaryk Scholar (Host: Dr. Cecilia Rokusek)

 

Seminar lectures given at universities or research institutes

Medical University Graz, Austria, February 8, 2018 (invited seminar on “Modulation of human ORAI1 channels: modeling and simulations”)

Larkin University, College of Pharmacy, Miami, Florida, October 10, 2017 (invited seminar on “Using Computational Modeling and Simulation in Understanding Gene Mutations”)

Barry University, Department of Chemistry, Miami Shores, Florida, March 22, 2017 (invited seminar on “Using Computational Modeling and Simulation in Understanding Protein Structure and Function”)

College of Medical Sciences, Nova Southeastern University, Ft. Lauderdale, Florida, February 17th, 2017(invited seminar)

College of Osteopathic Medicine, Nova Southeastern University, Ft. Lauderdale, Florida, November 11th, 2016 (COM Grand round)

College of Osteopathic Medicine, Nova Southeastern University, Ft. Lauderdale, Florida, February 16th, 2015 (invited seminar)

Biomolecular Science Institute, Florida International University, Miami, Florida, February 19th, 2015 (invited seminar)

School of Biosciences, University of Kent, UK, October 2015 (invited seminar)

Physics Department, Astbury Center, Leeds University, Leeds, UK, November 2013 (invited seminar)

Comenius University, November 2013, Bratislava, Slovakia (invited seminar talk, paid by Comenius University)

IZMB, Bonn University Germany 25.1.2012 (invited seminar)

Joint seminar of Fukuoka University and Kyushu University, sponsored by the Japanese Society for Physical Chemistry, Fukuoka, Japan 2.5.2011 (invited seminar)

Biochemistry Department, Lund University, Lund, Sweden 29.7.2011 (invited seminar) Molecular Biology Department, Princeton University, NJ, USA 17.11.2011 (invited seminar)

Chemistry Department, Princeton University, NJ, USA, 16.2.2010 (invited seminar)

La Jolla Institute for Allergy and Immunology, La Jolla, CA, USA 2.8.2010 (invited seminar)

Department of Chemical and Biochemical Engineering, University of Vanderbilt University, Nashville, TN, USA, 10.8.2010 (invited seminar)

Max Planck Institute for Mathmatics, Leipzig, Germany, 29.10.2010 (invited seminar)

National Institute of Health, Bethesda, Maryland, USA, 15.April 2009 (invited seminar talk, paid by NIDDK NIH)

Jagellonian University, 3.11.2009, Krakow, Polska (invited seminar , paid by Jagellonian University)

National Institute of Child Health and Human Development, National Institutes of Health, 15 th April 2008, Bethesda, Maryland, USA (Accomodation covered by NIH)

Princeton University, New Jersey, USA, 21st April 2008 (Accomodation and local expenses covered by Princeton University)

Biological Sciences, University of Calgary, June 2004, Canada.

Awards, Honors, and Editorial Activities

2002, Financial support for research from Sigma-Aldrich awarded for second-place finish in competition for young scientists

2005, Czech television presented a short segment on my research

2006, Otto Wichterle award for excellent young scientist, Academy of Sciences of the Czech Republic

2010, nominated by the Chemistry Department at Princeton University as a Princeton Global Scholar

2016, Fulbright-Masaryk Scholarship – senior category (2016)

 

Research grant awards (amounts are approximate after conversion to USD)

2017-2019 Ministry of Education, Science and Sports, LT-Inter Excellence, Strcuture and Function of Cation Tranlocating Systems, Total Award: 100,000 USD. Principal investigator Ettrich

2013-2018 Czech Science Foundation, Symmetric Allosteric Mechanism of Hexameric Escherichia coli Arginine Repressor using Computational Simulations, Total Award: 225,000 USD. Principal investigator Ettrich.

2012-2018 Czech Science Foundation, Cleavage and translocation by Type I restriction-modification complexes, Total Award: 879,600 USD. Principal investigator Ettrich.

2011-2014 Czech Science Foundation, Thiazolinové inhibitory ß-N-acetylhexosaminidas založené na nových, nepřirozených substrátech Total Award: 116,000 USD. Co-Principal investigator Ettrich.

2010-2016Czech Science Foundation, Structural insight into E. coli protein WrbA, the founding member of a family of proteins implicated in defense of cells against oxidative stress, Total Award: 405,400 USD. Principal investigator Ettrich.

2009-2013 Grant Agency of the Czech Republic, Specific ion effects of proteins in solution and similar relevant biological systems, Total Award: 171,667 USD; 50,000 USD to co-principal investigator Ettrich.

2006-2010 Ministry of Education, Science and Sports, Research center grant, Centre of biocatalysis and biotransformation, Total Award: approximately 3M USD (600,000 USD/year), 800,000 USD total (160,000 USD/year) to Ettrich, principal investigator at ISBE ASCR.

2003-2006 Grant Agency of the Czech Republic, Study of the oxygen evolving complex of photosystem II by molecular modeling and vibrational spectroscopy, Total Award: 70,000 USD. Principal investigator Ettrich.

2004-2005 Ministry of Education, Science and Sports, Aktion Austria-Czech Republic, NMR investigations of recombinant PsbH protein in Escherichia coli, Total award: 40,000 USD. Principal investigator Ettrich.

2005-2007 Grant Agency of the Czech Republic, a-N Acetylgalactosaminidase and a-galactosidase – structural and functional characterization, its aplication in synthesis of biological active glycoconjugates, Total Award: 50,000 USD to Co-Principal Investigator Ettrich.

 

Large institutional network grants:

2016-2019 Ministry of Education, Youth and Sports of the Czech Republic, LM – Large RDI infrastructures projects: LM2015055 – Center for Systems Biology, Coordinator and Principal Investigator

2012-2015FP7:INFRA-2012-2.2.4. – ISBE – Infrastructure for Systems Biology-Europe-preparatory phase, Delegate on behalf of the Czech Republic and steering committee member

2005-2012Ministry of Education, Youth and Sports of the Czech Republic, Physical Biology – new approach in biological research, Total Award: 560,000 USD (80,000 USD/year) to Ettrich. Principal investigator F.Vacha.

2005-2012 Academy of Sciences of the Czech Republic, Institutional research concept: Spatial and functional dynamics of biological, ecological and socio-ecological systems, Total Award: 0.6M USD (100,000 USD/year) to Ettrich. Principal investigator Institute of Systems Biology and Ecology.

 

Bi- or multilateral grants:

2016-2019 INTERREG V-A: ATCZ14 – Czech-Austrian Center for Supracellular Medical Research (CAC-SuMeR)
2015-2019 COST Action BM1406: Ion Channels and Immune Response toward a global understanding of immune cell physiology and for new therapeutic approaches (IONCHAN-IMMUNRESPON)

2016-2020 COST Action CA15110 Harmonising standardisation strategies to increase efficiency and competitiveness of European life-science research (CHARME)

2011-2012 Aktion Austria-Czech Republic (No. 60p21) Study of photosynthetic PsbI protein’s interaction with the thylakoid membrane

2011 HPC-Europa2 Transnational Access programme, joint grant with Groningen University to gain access to the pan-european infratructure on high performance computing cluster for 2011

2004-2005 Aktion Austria-Czech Republic (No. 40p2) NMR investigations of recombinant PsbH protein in Escherichia Coli.

2006-2007 WTZ A/CZ 20-6-06-14, Optimization of Expression and Isotope Enrichment od Photosynthetic Proteins for NMR, Czech Republic-Austria

 

Editorial Activities

Editorial Board Member, PeerJ

Reviewer for PLOS Computational Biology, Journal of Physical Chemistry B, Proteins: Structure, Function & Bioinformatics, European Biophysics Journal, Chemical Biology & Drug Design, Journal of Biolmolecular Structure & Dynamics, Nucleic Acid Research, Journal of Molecular Modeling,Chemistry Central Journal, Collection of Czechoslovak Chemical Communications, Biologia Plantarum, Materials Structure, Ceskoslovensky casopis pro fyziku

Service in advisory councils and committees

Reviewer/Evaluator for the Southern Association of Colleges and Schools Commission on Colleges (SACSCOC)

Member of the International Evaluation Panel of Palacky University, Faculty of Medicine. (2023).

Chair of the International Evaluation Panel of Masaryk University, Faculty of Pharmacy. (2022).

Chair of the International Evaluation Panel appointed by the Ministry of Youth and Education of the Czech Republic and the rector of the University to chair the external evaluation of the University of Veterinary and Pharmaceutical University Brno (2020).

External foreign expert in the Technical Review Panel (TRP) formed by the Department of Bio-sciences, COMSATS University Islamabad (Pakistan), 2018 and 2021 review of promotion dossiers of faculty

Elected member of the general assembly of the Academy of Sciences of the Czech Republic (since 2010, elected until 2018)

Member of the scientific councils of: Global Change Research Center (former Institute of Systems Biology and Ecology, Academy of Sciences (2007-2015); Institute of Microbiology, Academy of Sciences (2007-2015); Institute of Physical Biology, University of South Bohemia (until 2011); Czech Center of Excellence for Fluorescence Spectroscopy (2006- 2011) and Czech Center of Excellence for Biocatalysis and Biotransformation (2006 -2011)

Member of the educational board of the Faculty of Sciences (2011-2018) and the Institute of Physical Biology (until 2011), University of South Bohemia, Ceske Budejovice

Member of the grant review panel of ERAnet Neuron (2009 and 2012)

Member of the steering committee of the European Infrastructure for Systems Biology ESFRI-ISBE that connects approx. 50 research centers in Europe in the field of Systems Biology (2009-2018)

Member of the steering committee of the regional science infrastructure Upper Austria-South Bohemia (current)

Member of the grant review panel 207 (biochemical reactions) of the Czech Science Foundation 2011-2012