I was introduced to the art of protein crystallization during my work on master’s thesis that concentrated on optimization of recombinant expression and crystallization of receptor CD69, an activation marker of natural killer (NK) cells. Since then, I have keen interest in the field of structural biology and currently I am pursuing this interest through the work on preparation and structural studies of both rodent and human natural killer cell receptors involved in antiviral and antitumor immunity. During last years I have established an efficient expression system for these receptors based on transient transfection of HEK293 mammalian cell line. Receptors and their complexes formation are studied on structural and functional level by means of integrative structural biology and biochemistry. Now, I would like to focus on harnessing soluble forms of NK cell receptors and their ligands for the generation of novel anticancer immunotherapeutics.
RNDr. Ondřej Vaněk, Ph.D.
Date and place of birth: 17th October 1981, Opava, Czech Republic
Department of Biochemistry, Faculty of Science, Charles University in Prague
Hlavova 2030, CZ-12840 Prague
Education and awards:
2017 - Award for the best poster from the British Biophysical Society at AUC2017 international conference
2014 - Instruct Research & Development Award
2014 - Award “Velemlok” for the best teachers in the last academic year based on student questionnare
2010 - PhD in biochemistry at the Department of Biochemistry of the Charles University in Prague, doctoral thesis “Structure and function of C-type lectin NK cell receptors studied by recombinant expression and protein crystallography”
2006 - Award for the best diploma thesis in 2005 from the director of the Institute of Microbiology of the Academy of Sciences of Czech Republic; Award for the best oral presentation given in "Young Section" of the 10th Work Meeting of Biochemists and Molecular Biologists; selected participant of FEBS Young Scientist Forum for Czech Republic at 31st FEBS Congress
2005 - Graduated from the Faculty of Science of the Charles University in Prague, diploma thesis “Preparation and structural studies of protein CD69, receptor of human natural killer cells”
2001 - Award from The Ministry of Education of the Czech Republic for international representation
2000 - Bronze medal at the 32nd International Chemistry Olympiad; Award from The Learned Society of the Czech Republic
Special courses and workshops:
2017 - Proteins in Action (speaker) and Proteins for Life (main organizer) international conferences
2016 - Workshop for the hydrodynamic and thermodynamic analysis of biological macromolecules and their interactions with SEDFIT and SEDPHAT
2016 - FEBS Advanced Course – Ligand Binding and Theory (speaker)
2012 - EUKTS "Trans-national technology transfer manager junior / senior" certified courses
2011 - P-CUBE workshop "Advances in Protein Crystallization"
2009 SPINE2 Discussion workshop on Eukaryotic expression (main organizer), SPINE2 course New strategies for cloning & expression of protein complexes in E. coli and insect cells
2008 SPINE2 Biophysical Characterization of Macromolecular Complexes workshop, EMBO Practical Course on the Structural Characterization of Macromolecular Complexes
2007 TeachSG workshop on Biological macromolecules and their ligands, techniques in X-ray structure analysis and docking, HSC6 - Hercules Specialized Course on Advances and New Applications of Synchrotron Radiation for Structural Biology, SPINE2 Discussion workshop on protein co-expression
2004 FEBS Advanced course - Advanced methods in protein crystallization
Activities and positions:
Author or co-author of 102 contributions at scientific meetings, 1 patent and 31 publications in peer reviewed journals (WoS), 298 times cited (256 times without self-citations; WoS), H-index 11. Responsible for 6 research grants and 1 award, involved in 4 other projects, organizer of 1 international training workshop and 1 conference, supervisor of 28 bachelor, 17 diploma and 3 PhD. theses (5/3/2 ongoing), head of “Advanced practical course in biochemistry”, teacher of “Therapeutic proteins”, “Biology for biochemists”, “Cellular and molecular immunology” and “Introduction to knowledge and technology transfer” lectures.
2016 - Member of Management Committee for participation of the Czech Republic in COST Action CA15126 “MOBIEU: Molecular Biophysics in Europe”, member of Core Management group of the Action and short-term scientific mission (STSM) coordinator of the Action
2016 - Reviewer of grant applications submitted to INTER-EXCELLENCE program of Ministry of Education
2014 - Mentee program of the director of BIOCEV institute
2012 - Technological scout at the Charles University Centre for Knowledge&Technology Transfer (part time)
2011 - Supervision over the establishment of cell culture room at the Department of Biochemistry
2011 - Assistant at the Department of Biochemistry, Faculty of Science, Charles University (full time)
2009 - Main organizer of SPINE2 Discussion workshop on Eukaryotic expression
2008 - Introduction of eukaryotic recombinant protein expression in HEK293 cell line
2007 - Introduction of analytical ultracentrifugation at the Department of Biochemistry
2006 - Institute of Microbiology AS CR, structural biology of NK cell receptors
2005 - Member of Czech Society for Biochemistry and Molecular Biology
2004 - Department of Biochemistry, Faculty of Science, Charles University, research in the field of structural biology of NK cell lectin receptors, recombinant protein expression, in vitro refolding, chromatographic protein purification, protein characterization and crystallization
- New ligands for old receptors of human natural killer cells: structure, assembly within the immune synapse and potential for therapy. Czech Science Foundation (18-10687S), 2018-2020, principal investigator
- MOBIEU: Molecular Biophysics in Europe. COST Action (CA15126), 2016-2021, member of the Core Management group and short-term scientific mission (STSM) coordinator of the Action; supported by project LTC17065 from the INTER-EXCELLENCE program of the Ministry (MEYS CR), principal investigator
- Impact of NKp30 glycosylation and oligomerization on its complex formation - the key features for NK cells activation. Charles University (GAUK 927916), 2016-2018, project leader
- Utilization of a structural description of the interaction of human lymphocyte complex NKR-P1 and LLT1 for development of immunoactive fusion therapeutics. Charles University (GAUK 161216), 2016-2018, project leader
- Harnessing soluble forms of NK cell receptors and their ligands for the generation of novel anticancer immunotherapeutics. Czech Science Foundation (15-15181S), 2015-2017, principal investigator
- Participation in EU funded structural biology projects P-CUBE, BioStruct-X, Instruct and iNEXT, 2011-2017, more than 10 accesses to various facilities abroad were granted to my students, including one two month long Instruct internship and two Instruct R&D Pilot Project awards, principal investigator at all applications
- Interspecies comparison of nitrilases by using recombinant enzymes obtained by database-mining: their environmental impact and potential application. Czech Science Foundation (GAP504/11/0394), 2011-2014, principal co-investigator
- Innovation of instrumental equipment of Advanced practical course laboratory of Department of Biochemistry. High Education Development Fund (669/2013), 2013, project leader
- Modern technologies for identification and optimization of tumour drugs of new generation. Charles University (UNCE 204025/2012), 2012-2017, member of junior research team
- Glycomic and proteomic analysis of the molecular mechanisms of elimination of clinically relevant tumours by killer cells of the immune system. Czech Science Foundation (GA303/09/0477), 2009-2012, member of research team at Institute of Microbiology, AS CR
SPINE2:Complexes. Integrated project EC 6FP No. LSH-2005-031220, coordinator prof. D. Stuart, Oxford University, 2006-2010, member of research team at Institute of Microbiology, AS CR
(for full publication list please see my ORCID, ResearcherID or Research Gate profiles)
- Škerlová J., Bláha J., Pachl P., Hofbauerová K., Kukačka Z., Man P., Pompach P., Novák P., Otwinowski Z., Brynda J., Vaněk O., Řezáčová P. (2017): Crystal structure of native β-N-acetylhexosaminidase isolated from Aspergillus oryzae sheds light onto its substrate specificity, high stability, and regulation by propeptide. FEBS J. doi: 10.1111/febs.14360.
- Bláha J., Kalousková B., Skořepa O., Pažický S., Novák P., Vaněk O. (2017): High-level expression and purification of soluble form of human natural killer cell receptor NKR-P1 in HEK293S GnTI- cells. Protein Expr Purif 140, 36-43.
- Doležal M., Zábranský A., Dostál J., Vaněk O., Brynda J., Lepšík M., Hadravová R., Pichová I. (2016): Myristoylation drives dimerization of matrix protein from mouse mammary tumor virus. Retrovirology 13, 2.
- Lynn G. M., Laga R., Darrah P. A., Ishizuka A. S., Balaci A. J., Dulcey A. E., Pechar M., Pola R., Gerner M. Y., Yamamoto A., Buechler C. R., Quinn K. M., Smelkinson M. G., Vaněk O., Cawood R., Hills T., Vasalatiy O., Kastenmüller K., Francica J. R., Stutts L., Tom J. K., Ryu K. A., Esser-Kahn A. P., Etrych T., Fisher K. D., Seymour L. W., Seder R. A. (2015): In vivo characterization of the physicochemical properties of polymer-linked TLR agonists that enhance vaccine immunogenicity. Nat Biotechnol 33, 1201-1210.
- Skálová T., Bláha J., Harlos K., Dušková J., Kovaľ T., Stránský J., Hašek J., Vaněk O., Dohnálek J. (2015): Four crystal structures of human LLT1, a ligand for human NKR-P1, in varied glycosylation and oligomerization state. Acta Cryst D71, 578-591.
- Bláha J., Pachl P., Novák P., Vaněk O. (2015): Expression and purification of soluble and stable ectodomain of natural killer cell receptor LLT1 through high-density transfection of suspension adapted HEK293S GnTI- cells. Protein Expr Purif 109, 7-13.
- Machová I., Snášel J., Dostál J., Brynda J., Fanfrlík J., Singh M., Tarábek J.,Vaněk O., Bednárová L., Pichová I. (2015): Structural and functional studies of phosphoenolpyruvate carboxykinase from Mycobacterium tuberculosis. PLoS ONE 10(3):e0120682.
- Pechar M., Pola R., Laga R., Braunová A., Filippov S. K., Bogomolova A., Bednárová L., Vaněk O., Ulbrich K. (2014): Coiled coil peptides and polymer-peptide conjugates: synthesis, self-assembly, characterization and potential in drug delivery systems. Biomacromolecules 15, 2590-2599.
- Ryšlavá H., Doubnerová V., Kavan D., Vaněk O. (2013): Effect of posttranslational modifications on enzyme function and assembly. J Proteomics 92, 80-109.
- Mrázek H., Weignerová L., Bojarová P., Novák P., Vaněk O., Bezouška K. (2013): Carbohydrate synthesis and biosynthesis technologies for cracking of the glycan code: Recent advances. Biotechnol Adv 31, 17-37.
- Skálová T., Kotýnková K., Dušková J., Hašek J., Koval T., Kolenko P., Novák P., Man P., Hanč P., Vaněk O., Bezouška K., Dohnálek J. (2012): Mouse Clr-g, a ligand for NK cell activation receptor NKR-P1F: crystal structure and biophysical properties. J Immunol 189, 4881-4889.
- Grave L., Tůmová L., Mrázek H., Kavan D., Chmelík J., Vaněk O., Novák P., Bezouška K. (2012): Preparation of soluble isotopically labeled NKp30, a human natural cytotoxicity receptor, for structural studies using NMR. Protein Expr Purif 86, 142-150.
- Kolenko P., Rozbeský D., Vaněk O., Bezouška K., Hašek J., Dohnálek J. (2011): Crystal structure of H107R variant of extracellular domain of mouse NKR-P1A at 2.3-Å resolution. Acta Crystallogr Sect F Struct Biol Cryst Commun 67, 1519-1523.
- Mrázek H., Benada O., Man P., Vaněk O., Křen V., Bezouška K., Weignerová L. (2012): Facile production of Aspergillus niger α-N-acetylgalactosaminidase in yeast. Protein Expr Purif 81, 106-114.
- Pechar M., Pola R., Laga R., Ulbrich K., Bednárová L., Maloň P., Sieglová I., Král V., Fábry M., Vaněk O. (2011): Coiled coil peptides as universal linkers for the attachment of recombinant proteins to polymer therapeutics. Biomacromolecules 12, 3645-3655.
- Ryšlavá H., Kalendová A., Doubnerová V., Skočdopol P., Kumar V., Kukačka Z., Pompach P., Vaněk O., Slámová K., Bojarová P., Kulik N., Ettrich R., Křen V., Bezouška K. (2011): Enzymatic characterization and molecular modeling of an evolutionarily interesting fungal β-N-acetylhexosaminidase. FEBS J 278, 2469-2484.
- Kolenko P., Rozbeský D., Vaněk O., Kopecký V. Jr., Hofbauerová K., Novák P., Pompach P., Hašek J., Skálová T., Bezouška K., Dohnálek J. (2011): Molecular architecture of mouse activating NKR-P1 receptors. J Struct Biol 175, 434-441.
- Vaněk O., Brynda J., Hofbauerová K., Kukačka Z., Pachl P., Bezouška K., Řezáčová P. (2011): Crystallization and diffraction analysis of β-N-acetylhexosaminidase from Aspergillus oryzae. Acta Crystallogr Sect F Struct Biol Cryst Commun 67, 498-503.
- Rozbeský D., Kavan D., Chmelík J., Novák P., Vaněk O., Bezouška K. (2011): High-level expression of soluble form of mouse natural killer cell receptor NKR-P1C(B6) in Escherichia coli. Protein Expr Purif 77, 178-184.
- Sovová Ž., Kopecký V. Jr., Pazderka T., Hofbauerová K., Rozbeský D., Vaněk O., Bezouška K., Ettrich R. (2011): Structural analysis of natural killer cell receptor protein 1 (NKR-P1) extracellular domains suggests a conserved long loop region involved in ligand specificity. J Mol Model 17, 1353-1370.
- Kolenko P., Skálová T., Vaněk O., Štěpánková A., Dušková J., Hašek J., Bezouška K., Dohnálek J. (2009): The high-resolution structure of the extracellular domain of human CD69 using a novel polymer. Acta Crystallogr Sect F Struct Biol Cryst Commun 65, 1258-1260.
- Vaněk O., Nálezková M., Kavan D., Borovičková I., Pompach P., Novák P., Kumar V., Vannucci L., Hudeček J., Hofbauerová K., Kopecký V. Jr., Brynda J., Kolenko P., Dohnálek J., Kadeřávek P., Chmelík J., Gorčík L., Žídek L., Sklenář V., Bezouška K. (2008): Soluble recombinant CD69 receptors optimized to have an exceptional physical and chemical stability display prolonged circulation and remain intact in the blood of mice. FEBS J 275, 5589-5606.
Charles University, Faculty of Science, Department of Biochemistry
Hlavova 2030Prague 12840
Czech Republic50° 4' 5.844" N, 14° 25' 29.46" E