Laboratory of Structure and Function of Biomolecules

Application of structural and biophysical techniques on enzymes, receptors and bacterial transcription system.

Group leader: Ing. Jan Dohnálek, Ph.D.

Detailed laboratory website: https://sites.google.com/site/pragueprotein/

Physiological function of a biological macromolecule (protein, nucleic acid, complex), is tightly connected with its three-dimensional structure. We apply physical methods to determine the three-dimensional structure of such molecules and to measure other properties important for their function. In connection with functional data we aim at explaining the ultimate role of such molecules in the context of cell, tissue or organism. Where possible, conclusions are drawn towards biomedical or biotechnological applications.

Target molecular systems

We perform structure-function analysis of new enzymes or enzymes with the potential of novel applications, including sugar-nonspecific nucleases, metal-dependent oxidoreductases, flavin-dependent oxidoreductases and proteases. Most of these projects are targeted towards potential applications (food industry, dry goods, waste remediation, etc.), some have also potential for utilization in medicine. Our collaborators include Novozymes A/S, Denmark, and the laboratory of Petra Lipovová (University of Chemistry and Technology, Prague).

We are also involved in research on natural killer cell surface receptors. In collaboration with the team of Ondrej Vanek (Charles University) we investigate structural properties and complex formation of mammalian NK receptors and their ligands, with implications for mammalian immunology and potential treatment of cancer or viral infections.

Results of structure-function studies of bacterial transcription machinery can be utilized in fight against pathogenic bacteria (collaboration with Libor Krásný, Institute of Microbiology, Czech Academy of Sciences).

Our research tools

  • Recombinant production of proteins of interest, protein purification and characterization
  • X-ray crystallography, Cryo-electron microscopy, Small angle X-ray scattering (SAXS)
  • Biophysical techniques
  • Spectroscopic methods

 

Crystallization of biomolecules and X-ray diffraction experiments are performed in the Centre of Molecular Structure at our Institute, using our D8 Venture diffractometer with MetalJet X-ray source and SAXS experiments using a SAXSPoint 2.0 with MetalJet X-ray source and Eiger X-ray detector. More advanced experiments are done at European synchrotron radiation sources.

Methods development, teaching and central structural biology facilities

A part of our effort is dedicated towards development of X-ray crystallography methods (crystallization, data processing, phase problem solution, structure refinement, and model validation) and teaching at Prague universities, with the main focus on structural methods.

Since 2008 we have been involved in the design of the Centre of Molecular Structure, IBT, Biocev (central facilities for structural biology), its funding, operation, upgrades, and integration in the Czech Infrastructure for Integrative Structural Biology and the European infrastructure Instruct-ERIC.

More info:
https://sites.google.com/site/structuregallery/
https://sites.google.com/site/pragueprotein/

Adámková Kristýna, Ing.
Dohnálek Jan, Ing., Ph.D.
Dušková Jarmila, Mgr., Dr.
Hašek Jindřich, RNDr., DrSc.
Husťáková Blanka, Bc.
Kolenko Petr, doc. Ing., Ph.D.
Kovaľ Tomáš, Mgr., Ph.D.
Malý Martin, Ing.
Skálová Tereza, RNDr., Ph.D.
Strnad Michal, Ing.
Švecová Leona, Ing.
Trundová Mária, Mgr., Ph.D.

2021

  • Bondar, A., Rybakova, O., Melcr, J., Dohnalek, J., Khoroshyy, P., Tichacek, O., Timr, S., Miclea, P., Sakhi, A., Markova, V., Lazar, J. (2021). "Quantitative linear dichroism imaging of molecular processes in living cells made simple by open software tools." Commun Biol, 4(1), 189.

  • Pham, P. N., Huliciak, M., Biedermannova, L., Cerny, J., Charnavets, T., Fuertes, G., Herynek, S., Kolarova, L., Kolenko, P., Pavlicek, J., Zahradnik, J., Mikulecky, P., & Schneider, B. (2021, Jan 27). Protein Binder (ProBi) as a New Class of Structurally Robust Non-Antibody Protein Scaffold for Directed Evolution. Viruses, 13(2).

2020

  • Maly, M., Diederichs, K., Dohnalek, J., & Kolenko, P. (2020). "Paired refinement under the control of PAIREF." Iucrj, 7, 681-692.
  • Khakurel, K.P., Espinoza, S., Savko, M., Polovinkin, V., Dohnalek, J., Shepard, W., Angelova, A., Hajdu, J., Andreasson, J., Angelov, B. (2020) "Kilohertz Macromolecular Crystallography Using an EIGER Detector at Low X-ray Fluxes." Crystals, 10(12), 1146.

  • Kouba, T., Koval’, T. , Sudzinová, P., Pospíšil, J., Brezovská, B., Hnilicová, j., Šanderová, H., Janoušková, M., Šiková, M., Halada, P., Sýkora, M., Barvík, I., Nováček, J., Trundová, M., Dušková, J., Skálová, T., Murakami, K.S., Dohnálek, J., Krásný, L. (2020) "Mycobacterial HelD is a nucleic acids-clearing factor for RNA polymerase." Nat Comm, 11(6419).

  • Polovinkin, V., Khakurel, K., Babiak, M., Angelov, B., Schneider, B., Dohnalek, J., Adreasson, J., Hajdu, J. (2020) "Demonstration of electronic diffraction from membrane protein crystals grown in a lipidic mesophase after lamella preparation by focused ion beam milling at cryogenic temperatures." J Appl Crystallogr, 53(6), 1416-1424
  • Skalova, T., Lengalova, A., Dohnalek, J., Harlos, K., Mihalcin, P., Kolenko, P., Stranava, M., Blaha, J., Shimizu, T., & Martinkova, M. (2020). "Disruption of the dimerization interface of the sensing domain in the dimeric heme-based oxygen sensor AfGcHK abolishes bacterial signal transduction." J Biol Chem, 295(6), 1587-1597.
  • Skorepa, O., Pazicky, S., Kalouskova, B., Blaha, J., Abreu, C., Jecmen, T., Rosulek, M., Fish, A., Sedivy, A., Harlos, K., Dohnalek, J., Skalova, T., & Vanek, O. (2020). "Natural Killer Cell Activation Receptor NKp30 Oligomerization Depends on Its N-Glycosylation." Cancers (Basel), 12(7).

2019

  • Koval, T., L. Svecova, L. H. Ostergaard, T. Skalova, J. Duskova, J. Hasek, P. Kolenko, K. Fejfarova, J. Stransky, M. Trundova and J. Dohnalek (2019). "Trp-His covalent adduct in bilirubin oxidase is crucial for effective bilirubin binding but has a minor role in electron transfer." Scientific Reports 9: 13.

  • Kovaľ, T., P. Sudzinová, T. Perháčová, M. Trundová, T. Skálová, K. Fejfarová, H. Šanderová, L. Krásný, J. Dušková and J. Dohnálek (2019). "Domain structure of HelD, an interaction partner of Bacillus subtilis RNA polymerase." FEBS Letters 593(9): 996-1005.

  • Kovaľová, T., T. Kovaľ, E. Benešová, P. Vodičková, V. Spiwok, P. Lipovová and J. Dohnálek (2019). "Active site complementation and hexameric arrangement in the GH family 29; a structure–function study of α-l-fucosidase isoenzyme 1 from Paenibacillus thiaminolyticus." Glycobiology 29(1): 59-73.

  • Kuban, V., P. Srb, H. Stegnerova, P. Padrta, M. Zachrdla, Z. Jaseňáková, H. Šanderová, D. Vítovská, L. Krásný, T. Kovaľ, J. Dohnálek, J. Ziemska-Legiecka, M. Grynberg, P. Jarnot, A. Gruca, M. R. Jensen, M. Blackledge and L. Zidek (2019). "Quantitative Conformational Analysis of Functionally Important Electrostatic Interactions in the Intrinsically Disordered Region of Delta Subunit of Bacterial RNA Polymerase." Journal of the American Chemical Society 141(42): 16817-16828.

  • Sechovcová, H., L. Kulhavá, K. Fliegerová, M. Trundová, D. Morais, J. Mrázek and J. Kopečný (2019). "Comparison of enzymatic activities and proteomic profiles of Butyrivibrio fibrisolvens grown on different carbon sources." Proteome Science 17:2: 1-12.

  • Skalová, T., A. Lengalová, J. Dohnálek, K. Harlos, P. Mihalcin, P. Kolenko, M. Stranava, J. Bláha, T. Shimizu and M. Martínková (2019). "Disruption of the dimerization interface of the sensing domain in the dimeric heme-based oxygen sensor AfGcHK abolishes bacterial signal transduction " Journal of Biological Chemistry.

  • Tishchenko, G., Morganti, P., Stoller, M., Kelnar, I., Mikešová, J., Kovářová, J., Hašek, J., Kužel, R., Netopilík, M., Kaprálková, L., Špírková, M., Pavlova, E., Chánová, E., Brožová, L., Pekárek, M., Kobera, L., Sedláková, Z., Kubies, D. (2019). Chitin nanofibrils-chitosan composite films: characterization and properties. Bionanotechnology to save the environment. Plant and fishery's biomass as alternative to petrol. P. Morganti. Basel: 191-226.

2018

  • Trundová, M., T. Kovaľ, R. J. Owens, K. Fejfarová, J. Dušková, P. Kolenko and J. Dohnálek (2018 ). "Highly stable single-strand-specific 3′-nuclease/nucleotidase from Legionella pneumophila." International Journal of Biological Macromolecules 114: 776-787.

  • Kovaľ, T. and J. Dohnálek (2018). "Characteristics and application of S1-P1 nucleases in biotechnology and medicine." Biotechnology Advances 36(3): 603-612.

  • Malý, M., T. Skálová, L. Švecová, J. Dohnálek, J. Bláha, O. Vaněk, K. Harlos and P. Kolenko (2018). "Paired refinement: Impact of reintegration and rescaling. ." Sborník Osmé Studentské vědecké konference fyziky pevných látek FJFI ČVUT, 17.- 21. 9. 2018, Sedliště: 8-10.

  • Podzimek, T., T. Přerovská, J. Šantrůček, T. Kovaľ, J. Dohnálek, J. Matoušek and P. Lipovová (2018). "N-glycosylation of tomato nuclease TBN1 produced in N. benthamiana and its effect on the enzyme activity." Plant Science 276: 152-161.

  • Švecová, L., T. Skálová, T. Kovaľ, L. H. Østergaard, P. Kolenko, M. Malý and J. Dohnálek (2018). "Thermal stability of FAD-dependent oxidoreductase CtAO from thermophilic fungus Chaetomium thermophilum." Sborník Osmé Studentské vědecké konference fyziky pevných látek FJFI ČVUT, 17.- 21. 9. 2018, Sedliště: 5-7.

  • Tishchenko, G., P. Morganti, M. Stoller, I. Kelnar, J. Mikešová, J. Kovářová, J. Hašek, R. Kužel, M. Netopilík, L. Kaprálková, M. Špírková, E. Pavlová, E. Chanová, L. Brožová, M. Pekárek, L. Kobera, Z. Sedláková and D. Kubies (2018). "Chitin Nanofibrils-Chitosan CompositeFilms: Characterization and Properties." Bionanotechnology to Save the Environment. Plant and Fishery’s Biomass as Alternative to Petrol;

  • Pierfrancesco Morganti, Ed.; MDPI: Basel, Switzerland, 2018; Page Range. ISBN 978-3-03842-692-9: 191-226.

  • Zahradnik, J., P. Kolenko, A. Palyzova, J. Cerny, L. Kolarova, E. Kyslikova, H. Maresova, M. Grulich, J. Nunvar, M. Sulc, P. Kyslik and B. Schneider (2018). "The crystal structure of XdpB, the bacterial old yellow enzyme, in an FMN-free form." Plos One 13(4): e0195299.

  • Zahradnik, J., L. Kolarova, H. Parizkova, P. Kolenko and B. Schneider (2018). "Interferons type II and their receptors R1 and R2 in fish species: Evolution, structure, and function." Fish Shellfish Immunol 79: 140-152.

2017

  • Malý, M., J. Dušková, L. H. Østergaard, J. Stránský, L. Švecová, P. Kolenko and J. Dohnálek (2017). "Difrakční limit v makromolekulární krystalografii. ." Sborník Sedmé Studentské vědecké konference fyziky pevných látek FJFI ČVUT, 18.- 22. 9. 2017, Sedliště: 50-52.

  • Stranava, M., P. Man, T. Skálová, P. Kolenko, J. Bláha, V. Fojtíková, V. Martínek, J. Dohnálek, A. Lengalová, M. Rosůlek, T. Shimizu and M. Martínková (2017). "Coordination and redox state-dependent structural changes of the heme-based oxygen sensor AfGcHK associated with intraprotein signal transduction." Journal of Biological Chemistry 292(51): 20921-20935.

  • Švecová, L., T. Koval, T. Skálová, L. H. Østergaard and J. Dohnálek (2017). "Spektroskopické studie bilirubin oxidázy a jejího mutantu. ." Sborník Sedmé Studentské vědecké konference fyziky pevných látek FJFI ČVUT, 18.- 22. 9. 2017, Sedliště: 47-49.

2016

  • Agirre, J., A. Ariza, W. A. Offen, J. P. Turkenburg, S. M. Roberts, S. McNicholas, P. V. Harris, B. McBrayer, J. Dohnálek, K. D. Cowtan, G. J. Davies and K. S. Wilson (2016). "Three-dimensional structures of two heavily N-glycosylated Aspergillus sp. family GH3 beta-D-glucosidases." Acta crystallographica. Section D, Structural biology 72(Pt 2): 254-265.

  • Dohnálek, J., McAuley, K. E., Brzozowski, A. M., Ostergaard, P. R., Svendsen, A., Wilson, K. S. (2016). Stabilization of enzymes by metal binding: structures of two alkalophilic Bacillus subtilases and analysis of the second metal-binding site of the subtilase family. Understanding Enzymes: Function, Design, Engineering and Analysis. A. Svendsen. Singapore, Pan Stanford Publishing Pte. Ltd.: 203-265.

  • Fejfarová, K., A. Kádek, H. Mrázek, J. Hausner, V. Tretyachenko, T. Kovaľ, P. Man, J. Hašek and J. Dohnálek (2016). "Crystallization of nepenthesin I using a low-pH crystallization screen." Acta Crystallographica Section F-Structural Biology Communications 72: 24-28.

  • Koval, T., L. H. Ostergaard, J. Lehmbeck, A. Norgaard, P. Lipovova, J. Duskova, T. Skalova, M. Trundova, P. Kolenko, K. Fejfarova, J. Stransky, L. Svecova, J. Hasek and J. Dohnalek (2016). "Structural and Catalytic Properties of S1 Nuclease from Aspergillus oryzae Responsible for Substrate Recognition, Cleavage, Non-Specificity, and Inhibition." Plos One 11(12): 25.

  • Malý, M., J. Dušková, Ø. L. H, J. Stránský, L. Švecová, P. Kolenko and J. Dohnálek (2016). "Optimalizace parametrů zpracování difrakčních dat oxidázy z Microdochium nivale." Sborník  Šesté Studentské vědecké konference fyziky pevných látek FJFI ČVUT, 27.6 - 1. 7. 2016, Sedliště: 5-9.

  • Mikulecky, P., J. Zahradnik, P. Kolenko, J. Cerny, T. Charnavets, L. Kolarova, I. Necasova, P. N. Pham and B. Schneider (2016). "Crystal structure of human interferon-gamma receptor 2 reveals the structural basis for receptor specificity." Acta Crystallogr D Struct Biol 72(Pt 9): 1017-1025.

  • Stránský, J., L. Švecová, P. Kolenko and J. Dohnálek (2016). "Analýza vlivu expozice na difrakční data a model struktury proteinu." Sborník  Šesté Studentské vědecké konference fyziky pevných látek FJFI ČVUT, 27.6 - 1. 7. 2016, Sedliště: 10-15.

2015

  • Pekarova, M., A. Koudelka, H. Kolarova, G. Ambrozova, A. Klinke, A. Cerna, J. Kadlec, M. Trundova, L. Sindlerova Svihalkova, R. Kuchta, Z. Kuchtova, A. Lojek and L. Kubala (2015). "Asymmetric dimethyl arginine induces pulmonary vascular dysfunction via activation of signal transducer and activator of transcription 3 and stabilization of hypoxia-inducible factor 1-alpha." Vascular Pharmacology 73: 138-148.

  • Skalova, T., J. Blaha, K. Harlos, J. Duskova, T. Koval, J. Stransky, J. Hasek, O. Vanek and J. Dohnalek (2015). "Four crystal structures of human LLT1, a ligand of human NKR-P1, in varied glycosylation and oligomerization states." Acta Crystallographica Section D-Structural Biology 71: 578-591.

  • Stransky, J., T. Koval, T. Podzimek, A. Tycova, P. Lipovova, J. Matousek, P. Kolenko, K. Fejfarova, J. Duskova, T. Skalova, J. Hasek and J. Dohnalek (2015). "Phosphate binding in the active centre of tomato multifunctional nuclease TBN1 and analysis of superhelix formation by the enzyme." Acta Crystallographica Section F-Structural Biology Communications 71: 1408-1415.

  • Stránský, J. and J. Dohnálek (2015). "Zanedbávaný parametr difrakcního experimentu: expozicní cas." Sborník Páté Studentské vědecké konference fyziky pevných látek FJFI ČVUT, 14. - 19. 9. 2015, Byňov 22-27.

  • Švecová, L., T. Koval, T. Skálová, L. H. Østergaard and J. Dohnálek (2015). "Krystalová struktura Bilirubin oxidázy z Myrothecium verrucaria s ligandem v aktivním místě. ." Sborník Páté Studentské vědecké konference fyziky pevných látek FJFI ČVUT, 14. - 19. 9. 2015, Byňov: 28-32.

2014

  • Mikešová, J., J. Hašek, G. Tishchenko and P. MorganticaInstitute (2014). "Rheological study of chitosan acetate solutions containing chitinnanofibrils." Carbohydrate Polymers 112: 753-757.

  • Stránský, J. and J. Dohnálek (2014). "Optimalizace parametrů pro řešení fázového problému metodou S-SAD." Sborník Čtvrté Studentské vědecké konference fyziky pevných látek FJFI ČVUT, 23. - 27. 6. 2014, Penzion Kamínek: 67-72.

2013

  • Skalova, T., P. Kolenko, J. Duskova, T. Koval, J. Hasek, J. Stransky and J. Dohnalek (2013). "NK receptors and ligands with C-type lectine-like fold: Structure and function." Acta Crystallographica a-Foundation and Advances 69: S302-S302.

H2020: INFRAIA-2020-1: 101004806, Jan Dohnálek: MOlecular-Scale Biophysics Research Infrastructure (MOSBRI), 2021-2024

GACR: GA20-12109S, Dohnálek: The Unique Mycobacterial Transcription Machinery: Insights into its Composition, Structure & Functioning. 2020-2022.

MEYS: LM2018127, Dohnálek: Czech infrastructure for integrative structural biology. 2020-2022.

GACR: GA18-10687S, Skálová: New ligands for old receptors of human natural killer cells: structure, assembly within the immune synapse and potential for therapy. 2018-2020.

MEYS: LM2015043, Dohnálek: Czech infrastructure for integrative structural biology. 2016-2019.

GACR: GA15-05228S, Dohnálek: Deciphering the cellular role of HelD, a helicase-like protein associated with bacterial RNA polymerase. 2015-2017.

MEYS (programme INGO II): LG14009, Dohnálek: Structure and function of proteins for biotechnologies and drug design. 2014-2016.

GACR: GAP302/11/0855, Dohnálek: RNA polymerase: The “meeting point” of regulatory networks. 2011-2014.