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PRF

Who eats whom and when? Zooming-in on alternative energy transfer pathways in planktonic food webs of hypertrophic shallow lakes

Principal investigator: Dagmara Sirová
(Co)investigator from the Department: Jaroslav Vrba
Funding provider: The Czech Science Foundation
Duration: 2019 to 2021

Project goals: 
To unravel complex interactions in planktonic food webs of the underexplored but important aquatic ecosystems at an unprecedented level of resolution, using a unique combination of molecular, epifluorescence, and chemical methods.

Project description: 
Freshwater planktonic food webs (FW) are crucial for understanding of energy and material flow among organisms in the water column. Though theory on FW structure and function is advancing rapidly, it remains poorly resolved and based on relatively simple systems in stratified lakes. Shallow polymictic ecosystems such as hypertrophic fishponds, however, seem to support more complex communities of immense biodiversity. Based on our preliminary results, we hypothesise that, contrary to the widely accepted plankton ecology paradigms, methane-oxidising bacteria, picocyanobacteria, and fungal zoospores are important players in the transfer of energy to higher trophic levels in hypertrophic lakes. The flow of energy from primary producers to higher trophic levels through the ‘classical FW’ is reduced here, the microbial FW is the main component, although likely less efficient due to more trophic levels and consequent energy losses. To unravel these complex interactions at a sufficient level of resolution, a combination of modern molecular methods and multidisciplinary skills is planned.

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Laboratory of Structural Chemistry

Macromolecular X-ray Crystallography is a technique used to study biological molecules such as proteins, viruses and nucleic acids (RNA and DNA) to an atomic resolution. This high resolution helps elucidate the detailed structure-based mechanism by which these macromolecules carry out their functions in living cells and organisms.

Laboratory description:

 The Laboratory of Structural Chemistry consists of three sub laboratories and one training part:

 MolBiol - is the laboratory of molecular biology designed for isolation and purification of proteins,

 XtallExp – is the laboratory for crystallization experiments aimed at production of diffractable crystals. Obtained crystals are measured at the synchrotron radiation sources and diffraction data are used for solving of protein structure,

 MolStruct – is the lab for molecular modeling and structural studies following by molecular dynamics studies,

 XtallTraining – offers other colleagues with the interest of crystallization of proteins possibility to crystallize own proteins by themselves or with the help of our specialists

Key activities:

  1. basic research in the field of isolation and purification of proteins and their crystallization
  2. solving of protein structures from diffraction data and structural studies of studied proteins
  3. development and testing of alternative and advanced crystallization techniques
  4. close cooperation with affiliated laboratories in the Czech Republic and abroad
  5. training of others about crystallization of own proteins
  6. teaching of Inorganic chemistry 1 (UCH/100), Inorganic chemistry 2 (UCH/101), Organic chemistry for biology (UCH/032) a Biocrystallization methods (UCH/253) in czech
  7. organization of international courses under auspices of FEBS named FEBS-INSTRUCT practical crystallization course „Advanced methods in macromolecular crystallization“

International cooperation:

Prof. Joseph Ng team University of Alabama in Huntsville, USA in the Department of Biological Science.

Dr. math. et dis. nat. Jeroen R. Mesters – a senior Researcher and Lecturer, Deputy of Universität zu Lübeck, Institut für Biochemie at Lübeck, Germany.

Dr. Monika Budayova-Spano – Assistant Professor – HDR, University Joseph Fourier Grenoble, Institut De Biologie Structurale, Umr5075 CEA-CNRS-UJF, Grenoble, France

Dr. José A. Gavira-Gallardo Research Scientist of Laboratorio de Estudios Cristalográficos

Instituto Andaluz de Ciencias de la Tierra, (CSIC-UGR) Armilla, Granada, Spain

Dr. Pavlina Rezacova a head of the Senior Research Group of Structural Biology at Institute of Organic Chemistry and Biochemistry AS CR

Doc. Radka Chaloupková, Ph.D. - Research Scientist at Loschmidt Laboratories, Department of Experimental Biology and Research Centre for Toxic Compounds in the Environment RECETOX, Masaryk University, Brno, Czech Republic

Infrastructure: 

 

Fully-equipped biochemical laboratories and Laboratory of Crystallogenesis and Macromolecular Crystallography (Assoc. Prof. Ivana Kuta-Smatanova, PhD) at University of South Bohemia (Faculty of Sciences, Ceske Budejovice), well-appointed with crystallization robotic system Oryx 3, Dynamic Light scattering instrument,  analytical balances, IWA distiller for redistilled water, deep-freeze, iceboxes, cold-room, incubators,  ice generator, pH-meters, SDS-PAGE and horizontal electrophoresis, Western blot system, PCR thermocycler, ultracentrifuge Beckman, low speed cooled centrifuges, table centrifuges, spectrophotometer, cells disintegrator, high-magnificence stereomicroscopes, photocameras, Eppendorf pipette sets, commercial crystallization and molecular kits, chemicals, crystallization plates and all necessary plastic and glass for the  cultivation, biochemical and crystallization experiments. 

Computational laboratory is well equipped by international standards for computational chemistry (Cluster of the Beowulf type with nodes connected by Myrinet, Graphics work stations with 3D, 2 computer labs, licenses for Gaussian09, Amber10, Gromacs, modeler, Yasara, autodock etc.) as well fully equipped lab to perform all tasks of structural analysis of biological macromolecules by X-ray crystallography with computational hardware and software necessary for the diffraction data processing, structure determination, macromolecular structure refinement, validation and analysis (XDS, XDSapp, CCP4 program package, Coot, PyMol, IMosflm and others).

For the diffraction quality crystals could be tested at home X-ray diffractometer D8 Venture source from Bruker at Institute of Institute of Nanobiology and Structural Biology, Institute of Microbiology, Academy of Sciences of the Czech Republic and later on will be prepared for the data collection experiments on the synchrotron. Diffraction measurements could be performed on synchrotron macromolecular beamlines BESSY (Berlin, Germany), DEZY (Hamburg, Germany) or ESRF (Grenoble, France) following standard application procedures.

Publications

2020

Brodsky K; Kutý M; Pelantová H; Cvačka J; Rebroš M; Kotik M; Kutá Smatanová I; Křen V; Bojarová P: Dual Substrate Specificity of the Rutinosidase from Aspergillus niger and the Role of Its Substrate Tunnel. Int. J. Mol. Sci. Volume 21, Issue 16, 5671 (2020). https://doi.org/10.3390/ijms21165671

Marek M., Chaloupkova, R., Prudnikova, T., Sato, Y., Rezacova, P., Nagata, Y., Kuta Smatanova, I., Damborsky, J.: Structural and catalytic effects of surface loop-helix transplantation within haloalkane dehalogenase family. Computational and Structural Biotechnology Journal 18, 1352-1362 (2020). https://doi.org/10.1016/j.csbj.2020.05.019

 

Kuta Smatanova I.: Data analytics for protein crystallization, Crystallography Reviews 26, 1, 58-61 (2020). DOI: 10.1080/0889311X.2019.1691174

 

2019

Aryafard M, Jahanshahi M, Harifi-Mood AR, Minofar B and Kuta Smatanova I.: J. Chem. Eng. Data 64 (12), 5755–5764 (2019). https://doi.org/10.1021/acs.jced.9b00719

Chrast, L., Tratsiak, K., Planas-Iglesias, J., Daniel, L., Prudnikova, T., Brezovsky, J., Bednar, D., Kuta Smatanova, I., Chaloupkova, R. and Damborsky, J.: Deciphering the Structural Basis of High Thermostability of Dehalogenase from Psychrophilic Bacterium Marinobacter sp. ELB17. Microorganisms 7, 498 (2019). doi:10.3390/microorganisms7110498 www.mdpi.com/journal/microorganisms

Havlickova, P., Brinsa, V., Brynda, J., Pachl, P., Prudnikova, T., Mesters, J. R., Kascakova B., Kuty, M., Pusey, M.L., Ng, J.D., Rezacova, P. and Kuta Smatanova, I.: A novel structurally characterized haloacid dehalogenase superfamily phosphatase from Thermococcus thioreducens with diverse substrate specificity. Acta Crystallographica Section D: Structural Biology, D75(8), 743-752 (2019). https://doi.org/10.1107/S2059798319009586

Prudnikova, T., Kascakova, B., Mesters, J. R., Grinkevich, P., Havlickova, P., Mazur, A., Shaposhnikova A., Chaloupkova, R.,  Damborsky, J., Kuty, M. and Kuta Smatanova, I.: Crystallization and crystallographic analysis of a Bradyrhizobium elkanii USDA94 haloalkane dehalogenase variant with an eliminated halide-binding site. Crystals 9(7), 375 (2019). https://doi.org/10.3390/cryst9070375, https://www.mdpi.com/2073-4352/9/7/375

Tratsiak, K., Prudnikova, T., Drienovska, I., Damborsky, J., Brynda, J., Pachl, P., Kuty, M., Chaloupkova, R., Rezacova P., and Kuta Smatanova I.: Crystal structure of cold-adapted haloalkane dehalogenase DpcA from Psychrobacter cryohalolentis K5. Acta Crystallographica Section F-Structural Biology Communications F75, 324-331(2019). DOI: 10.1107/S2053230X19002796

 

2018

Degtjarik O., Demo G., Wimmerova M., Kuta Smatanova I.: Chapter 11: X-ray Crystallography. In Plant Structural Biology: Hormonal Regulations. Pages 203-221. Edited by Hejatko J. and Hakoshima T. ISBN 978-3-319-91351-3. Springer IP AG part of Springer Nature (2018)   

 

 

2017

Sviridova E., Rezacova P., Bondar A., Veverka V., Novak P., Schenk G., Svergun D.I., Kuta Smatanova I. and Bumba L.: Structural basis of the interaction between the putative adhesion-involved and iron-regulated FrpD and FrpC proteins of Neisseria meningitides. Sci. Rep. 7, pages 14, 40408 (2017). DOI: 10.1038/srep40408.

 

2016

Brezovsky* J., Babkova* P., Degtjarik O., Fortova A., Gora A., Iermak I., Rezacova P., Dvorak P., Kuta Smatanova I., Prokop Z., Chaloupkova R. and Damborsky J.: Engineering a de novo transport tunnel. ACS Catalysis 6, 7597-7610 (2016). DOI: 10.1021/acscatal.6b02081

Degtjarik O., Brynda J., Ettrichova O., Kuty M., Sinha D., Kuta Smatanova I., Carey J., Ettrich R., Řeha D.: Quantum calculations indicate effective electron transfer between FMN and benzoquinone in a new crystal structure of E. coli WrbA. Journal of Physical Chemistry B120 (22): 4867–4877 (2016). DOI: 10.1021/acs.jpcb.5b11958

 

2015

Einspahr H., Kuta Smatanova I., Betzel Ch. and Mesters J.: Introduction to selected articles from the 15th ICCBM. Acta Crystallographica Section F, Volume 71, Issue 7, page 805 (2015). DOI: 10.1107/S2053230X15012534

Iermak, I., Degtjarik, O., Steffler, F., Sieber, V. and Kuta Smatanova, I.: Crystallization behaviour of glyceraldehyde dehydrogenase from Thermoplasma acidophilum. Acta Cryst. F71, Volume 71, Part 12, pages. 1475-1480 (2015). DOI:10.1107/S2053230X15020270

Csefalvay E, Lapkouski M, Guzanova A, Csefalvay L, Baikova T, Shevelev I, Bialevich V, Shamayeva K, Janscak P, Kuta Smatanova I, Panjikar S, Carey J, Weiserova M, Ettrich R: Functional Coupling of Duplex Translocation to DNA Cleavage in a Type I Restriction Enzyme. PLoS ONE 10(6): e0128700 (2015).  DOI:10.1371/journal.pone.0128700

Liskova V., Bednar D., Prudnikova T., Rezacova P., Koudelakova T., Sebestova E., Kuta Smatanova I., Brezovsky J., Chaloupkova R., Damborsky J.: Balancing the stability-activity trade-off by fine-tuning dehalogenase access tunnels. ChemCatChem 7, 648 –659 (2015). DOI: 10.1002/cctc.201402792

 

2014

Chaloupkova R., Prudnikova T., Rezacova P., Prokop Z., Koudelakova T., Daniel L., Brezovsky J., Ikeda-Ohtsubo W., Sato Y., Kuty M., Nagata Y., Kuta Smatanova I., Damborsky J.: Structural and functional analysis of a novel haloalkane dehalogenase with two halide-binding sites, Acta Cryst. D70, 1884–1897 (2014). DOI:10.1107/S1399004714009018

Sykora J., Brezovsky J., Koudelakova T., Lahoda M., Fortova A., Chernovets T., Chaloupkova R., Stepankova V., Prokop Z., Kuta Smatanova I., Hof M., Damborsky J.: Dynamics and hydration explain failed functional transformation in dehalogenase design, Nature Chemical Biology, Vol. 10, No. 6, s. 428-430 (2014). ISSN 1552-4450, DOI:10.1038/nchembio.1502

Bumba L., Sviridova E., Kutá Smatanová I., Řezáčová P., Veverka V.: Backbone resonance assignments of the outer membrane lipoprotein FrpD from Neisseria meningitidis. Biomol NMR Assign 8, Issue 1, 53-55 (2014). ISSN 1874-2718, Published online 09 December 2012, DOI: 10.1007/s12104-012-9451-5

Lahoda M., Mesters J.R., Stsiapanava A., Chaloupkova R., Kuty M., Damborsky J., Kuta Smatanova I.: Crystallographic analysis of 1,2,3–trichloropropane biodegradation by haloalkane dehalogenase DhaA31. Acta Cryst. D70, 209-217 (2014). DOI:10.1107/S1399004713026254

 

2013

Kishko I., Carey J., Reha D., Brynda J., Winkler R., Harish B., Guerra R., Ettrichova O., Kukacka Z., Sheryemyetyeva O., Novak P., Kuty M., Kuta Smatanova I., Ettrich R, Lapkouski M.: 1.2 Å resolution crystal structure of Escherichia coli WrbA holoprotein. Acta Cryst. D69, Part 9, pages 1748-1757 (2013). DOI:10.1107/S0907444913017162

 Tratsiak K., Degtjarik O., Drienovska I., Chrast L., Rezacova P., Kuty M., Chaloupkova R., Damborsky J., Kuta Smatanova I.: Crystallographic analysis of new psychrophilic haloalkane dehalogenases: DpcA from Psychrobacter cryohalolentis K5 and DmxA from Marinobacter sp. ELB17. Acta Cryst. F69, 683-688 (2013). DOI:10.1107/S1744309113012979

Degtjarik O., Chaloupkova R., Rezacova P., Kuty M., Damborsky J., Kuta Smatanova I.: Differences in crystallization of two LinB variants from Sphingobium japonicum UT26. Acta Cryst F69, Part 3, 284-287 (2013). DOI:10.1107/S1744309113002467

Degtjarik O., Dopitova R., Puehringer S., Nejedla E., Kuty M., Weiss M., Hejatko J., Janda L., Kuta Smatanova I.: Cloning, Expression, Purification, Crystallization and Preliminary X-ray Diffraction Analysis of AHP2, a signal transmitter protein from Arabidopsis thaliana. Acta Cryst F69, 158-161 (2013). DOI:10.1107/S174430911205186X

Koudelakova, T., Chaloupkova, R., Brezovsky, J., Prokop, Z., Sebestova, E., Hesseler, M., Khabiri, M., Plevaka, M., Kulik, D., Kuta Smatanova, I., Rezacova, P., Ettrich, R., Bornscheuer, U. T., Damborsky, J.: Engineering Enzyme Stability and Resistance to Organic Co-solvent by Access Tunnel Modification. Angewandte Chemie International Edition 52, 1959-1963 (2013). DOI: 10.1002/anie.201206708

 

2012

Kopecky V Jr, Kohoutova J, Lapkouski M, Hofbauerova K, Sovova Z, Ettrichova, O., Gonzales-Perez, S., Dulebo, A., Kaftan, D., Kuta Smatanova, I., Revuelta, J.L., Arellano, J.B., Carey, J., Ettrich R.: Raman Spectroscopy Adds Complementary Detail to the High-Resolution X-Ray Crystal Structure of Photosynthetic PsbP from Spinacia oleracea. PLoS ONE 7(10): e46694 (2012). DOI:10.1371/journal.pone.0046694

Nemcovicova I. and Kuta Smatanova I.: Chapter 11: Alternative Crystallization Technique: Cross Influence Procedure (CIP). In the Crystallization and Materials Science of Modern Artificial and Natural Crystals, Pages 249-276, Edited by: Elena Borisenko, ISBN 978-953-307-608-9, Publisher: InTech (January 2012)

 

2011

Lahoda M., Chaloupkova R., Stsiapanava A., Damborsky J., Kuta Smatanova I.: Crystallization and crystallographic analysis of the Rhodococcus rhodochrous NCIMB 13064 mutant DhaA31 and its complex with 1, 2, 3-trichloropropane. Acta Cryst F67, 397-400 (2011). DOI: 10.1107/S1744309111001254

Stsiapanava A., Chaloupkova R., Fortova A., Brynda J., Weiss M., Damborsky J., Kuta Smatanova I.: Crystallization and preliminary X-ray diffraction analysis of the wild type haloalkane dehalogenase DhaA and the variant DhaA13 complexed with different ligands. Acta Cryst F67, 253-257 (2011). DOI: 10.1107/S1744309110051286

Prudnikova, T., Chaloupkova, R., Sato, Y., Nagata, Y., Degtjarik, O., Kuty, M., Rezacova, P., Damborsky, J., Kuta Smatanova, I.: Development of a Crystallization Protocol for the  DbeA1 Variant of Novel Haloalkane Dehalogenase from Bradyrhizobium elkani USDA94. Crystal Growth and Design 11, 516-519 (2011). DOI: 10.1021/cg1013363

 

2010

Sviridova E., Bumba L., Řezacova P., Prochazkova K., Kavan D., Bezouska K., Kuty M., Sebo P., Kuta Smatanova I.: Crystallization and preliminary crystallographic characterization of the iron-regulated outer membrane lipoprotein FrpD from Neisseria meningitidis. Acta Cryst F66, 1119-1126 (2010). DOI: 10.1107/S174430911003215X

Stsiapanava, A., Dohnalek, J.,  Gavira, J. A., Kuty, M., Koudelakova, T., Damborsky, J. and Kuta Smatanova, I.: Atomic resolution studies of haloalkane dehalogenases DhaA04, DhaA14 and DhaA15 with engineered access tunnels. Acta Cryst D66, 962-969 (2010).  DOI: 10.1107/S09074449100027101

Prudnikova T., Gavira J.A., Řezáčová P., Pineda Molina E., Hunalová I., Sviridova E., Shmidt V., Kohoutová J., Kutý M., Kaftan D., Vácha F., García-Ruiz J.M., Kutá Smatanová I.: Towards the crystallization of photosystem II core complex from Pisum sativum L. Cryst. Growth Des. 10 (8) 3391-3396 (2010). DOI: 10.1021/cg901593x

 

2009

Klvana M.; Pavlova M.; Koudelakova T.; Chaloupkova R.; Dvorak P.; Stsiapanava A.; Kuty M.; Kuta-Smatanova I.; Dohnalek J.; Kulhanek P.; Wade R.C.; Damborsky J.: Pathways and Mechanisms for Product Release in the Engineered Haloalkane Dehalogenases Explored using Classical and Random Acceleration Molecular Dynamics Simulations. J. Mol. Biol. 392, 1339-1356 (2009). DOI:10.1016/j.jmb.2009.06.076

Wolfova J., Kuta Smatanova I., Brynda J., Mesters J.R., Lapkouski M., Kuty M., Natalello A., Chatterjee N., Chern S-Y., Ebbel E., Ricci A., Grandori R., Ettrich R., Carey J.: Structural organization of WrbA in apo- and holoprotein crystals. Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics 1794, 1288-1298 (2009). DOI: 10.1016/j.bbapap.2009.08.001. (The cover picture of this issue was selected from our paper)

Kohoutová J., Kopecký Jr. V., Lapkouski M., Hofbauerová K., Sovová Ž, González-Pérezc S., Kutá Smatanová I., Revuelta J.L., Arellano J.B., Ettrich R.: Structural analysis of extrinsic PsbP protein of PSII from Spinacea oleracea and its interaction with the oxygen-evolving complex. FEBS Journal 276, 146-147 (2009).

Lapkouski M., Panjikar S., Janscak P., Kuta Smatanova I., Carey J., Ettrich R., Csefalvay E.: Structure of the motor subunit and translocation model for EcoR124I restriction-modification complex. Nature Structural & Molecular Biology 16(1), 94-5 (2009). Epub 2008 Dec 14. DOI: 10.1038/nsmb.1523

Prudnikova T., Mozga T., Rezacova R., Chaloupkova R., Sato Y., Nagata Y., Brynda J., Kuty M., Damborsky J. and Kuta Smatanova I.: Crystallisation and preliminary X-ray analysis of a novel haloalkane dehalogenase DbeA from Bradyrhizobium elkani USDA94. Acta Cryst. F65, 353-356 (2009). DOI: 10.1107/S1744309109007039

Kohoutová J., Kutá Smatanová I., Brynda J., Lapkouski M., Revuelta J.L., Arellano J.B., Ettrich R.: Crystallization and preliminary crystallographic characterization of the extrinsic PsbP protein of photosystem II from Spinacia oleracea. Acta Cryst. F65, 111-115 (2009). DOI: 10.1107/S1744309108040578

Wolfová J., Brynda J., Mesters J.R., Ettrich R., Carey J., Kutá Smatanová I.: Structural changes of tetrameric flavoprotein WrbA upon flavin binding. Materials Structure 16, 2a, k56-57 (2009).

 

2008

Wolfová J., Brynda J., Mesters J.R., Carey J., Grandori R. and Kutá Smatanová I.: Crystallographic study of Escherichia coli favoprotein WrbA, a new NAD(P)H-dependent guinine oxidoreductase. Materials Structure 15, 1, 55-57 (2008).

Stsiapanava A., Koudelakova T., Lapkouski M., Pavlova M., Damborsky J. and Kuta Smatanova I.: Crystals of DhaA mutants from Rhodococcus rhodochrous NCIMB 13064 diffracted to ultra high resolution: crystallization and preliminary diffraction analysis. Acta Cryst. F64, 137-140 (2008). DOI: 10.1107/S1744309108002066

 

2007-1997

Tomčová I. and Kutá Smatanová I.: Copper co-crystallization and divalent metal salts cross-influence effect – a new optimisation tool improving crystal morphology and diffraction quality. Journal of Crystal Growth 306, 383-389 (2007). DOI: 10.1016/j.jcrysgro.2007.05.054

Wolfová J., Mesters J.R., Brynda J., Grandori R., Natalello A., Carey J. and Kutá Smatanová I.: Crystallization and preliminary diffraction analysis of E. coli WrbA in complex with its cofactor flavin mononucleotide. Acta Cryst. F63, 571-575 (2007). DOI: 10.1107/S1744309107026103

Lapkouski M., Panjikar S., Kuta Smatanova I. and Csefalvay E.: Purification, crystallization and preliminary X-ray analysis of the HsdR subunit of the EcoR124I endonuclease from E. coli. Acta Cryst. F63, 582-585 (2007). DOI: 10.1107/S174430910702622X

Carey J., Brynda J., Wolfová J., Grandori R., Gustavsson T., Ettrich R.H., Kutá Smatanová I.: WrbA bridges bacterial flavodoxins and eukaryotic NAD(P)H:quinone oxidoreductases. Protein Science 16, 10, 2301-2305 (2007). DOI: 10.1110/ps.073018907. (The cover picture of this issue was selected from our paper)

Tomčová I. and Kutá Smatanová I.: Cross-crystallization as a new optimization tool of crystallization procedures. Materials Structure 14, 1, 3-5 (2007). (The cover picture of this issue was selected from our paper)

Prudnikova T., Kutý M., Gavira J.A., Palenčár P., Vácha F., Řezáčová P., Garcia-Ruiz J.M. and Kutá Smatanová I.: Crystallization and structure-functional study of the photosystem II from higher plants. Materials Structure 14, 1, 5-7 (2007).

Kutá Smatanová I., Gavira J.A., Řezáčová P., Vácha F., García-Ruiz J.M.: New techniques for membrane protein crystallization tested on photosystem II core complex of Pisum sativum. Photosynthesis Research 90 (3), 255-259 (2006). DOI: 10.1007/s11120-007-9131-y

Tomčová I., Mamede Branca R.M., Bodó G., Bagyinka C. and Kutá Smatanová I.: Cross-crystallization and preliminary diffraction analysis of a novel di-heme cytochrome c4. Acta Cryst. F62, 820-824 (2006). DOI: 10.1107/S1744309106027710

Wolfova J., Grandori R., Kozma E., Chatterjee N., Carey J. and Kuta Smatanova I.: Crystallization of the flavoprotein WrbA optimized by using additives and gels. Journal of Crystal Growth 284, 3-4, 502-505 (2005). DOI: 10.1016/j.jcrysgro.2005.07.043

Hogg T., Kuta Smatanova I., Bezouska K., Ulbrich N. and Hilgenfeld R.: Sugar-mediated lattice contacts in crystals of a plant glycoprotein. Acta Cryst. D58, 1734-1739 (2002). DOI: 10.1107/S0907444902014506

Oakley A.J., Prokop Z., Bohac M., Kmunicek J., Jedlicka T., Monincova M., Kuta Smatanova I., Nagata Y., Damborsky J., Wilce M.C.J.: Exploring the structure and activity of Haloalkane Dehalogenase from Sphingomonas paucimobilis UT26: Evidence for product and water mediated inhibition. Biochemistry 41, 4847-4855 (2002). DOI: 10.1021/bi015734i

Marek, J., Vevodova, J., Kuta Smatanova, I., Nagata, J., Svensson, L.A, Newman, J., Takagi, M. and Damborsky, J.: Crystal Structure of the Haloalkane Dehalogenase from Sphingomonas paucimobilis UT26. Biochemistry 39, 14082-14086 (2000). DOI: 10.1021/bi001539c

Schwendt, P., Svancarek, P., Smatanova, I. and Marek, J.: Stereospecific formation of alpha-Hydroxylato Oxo Peroxo Complexes of Vanadium(V). Crystal Structure of  (NBu4)2[V2 O2(O2)2 (L-lact)2].2H2O and (NBu4)2[V2 O2(O2)2 (D-lact)(L-lact)].2H2O. Journal of Inorganic Biochemistry 80, 59-64 (2000). DOI: 10.1016/S0162-0134(00)00040-4

Smatanova, I.K., Marek, J., Svancarek, P., Schwendt, P. :Bis(tetra-n-butylammonium)Bis[(mandelato)oxo-(peroxo)vanadate(V)] mandelic acid solvate. Acta Cryst. C56, 154-155 (2000). DOI: 10.1107/S0108270199013475

Svancarek, P., Schwendt, P., Tatiersky, J., Smatanova, I. and Marek, J.: Oxo Peroxo Glycolato Complexes of Vanadium (V). Crystal Structure of  (NBu4)2[V2O2(O2)2(C2H2O3)2].H2O. Monatshefte für Chemie 131, 145-154 (2000). DOI: 10.1007/PL00010301

Smatanova, I., Nagata, Y., Svensson, L. A., Takagi, M. and Marek, J.: Crystallization and preliminary X-ray diffraction analysis of haloalkane dehalogenase LinB from Sphingomonas paucimobilis UT26. Acta Cryst. D55, 1231-1233 (1999). DOI: 10.1107/S090744499900459X

Smatanova, I., Marek, J., Svancarek, P., Schwendt, P. : Bis(tetra-n-butylammonium) Bis[(methyllactato) dioxo-vanadate(V)] Dihydrate. Acta Cryst. C54, 1249 1251 (1998). DOI: 10.1107/S0108270198003424

Svancarek, P., Smatanova, I., Schwendt, P., Marek, J.: Vanadium (V) peroxo complexes with alpha-hydroxycarboxylates as heteroligands. Chemické listy, 91 (9), 632-632 (1997).

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Laboratory of Single Molecule Research

Right now we are looking for motivated students of all levels (Bc, Mgr, PhD)!

Contact information

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Address:
Building C (room 01037) 
Faculty of Science
University of South Bohemia in České Budějovice
Branišovská 1760
370 05 České Budějovice


Phone: 00420387776237
GPS: 48.9772847N, 14.4451364E

Research Interests

Allosteric communication in membrane protein complexes linked to conformational transitions on multiple timescales

- Development of novel mechanistic models of molecular machines behind protein translocation

Motivation:

Allosterically modulated molecular machines mediate many of the key processes in all forms of life. The Sec translocon, a membrane bound protein complex, is the principal route for the efficient transport of heterogeneous polypeptides across or into lipid bilayers. The bacterial translocon consists of two main parts, a cytosolic ATPase SecA and membrane channel SecYEG. Based on our group’s recent findings we propose that the Sec translocon is a novel type of stochastically coupled hybrid molecular machine, where the processive SecA steers the energy landscape of a stochastic SecYEG channel allosterically dependent on nucleotide state. We present a number of research projects to map the full allosteric network regulating different stages of protein translocation in the Sec complex using a combination of mutagenesis, single-molecule and in silico methods.

 

Publications:

• Allen, W. J., et al (2016) Two-way communication between SecY and SecA suggests a Brownian ratchet mechanism for protein translocation, Elife. 5.
• Fessl, T., et al (2018) Dynamic action of the Sec machinery during initiation, protein translocation and termination, Elife. 7.
• Corey, R. A., et al (2019) ATP-induced asymmetric pre-protein folding as a driver of protein translocation through the Sec machinery, Elife. 8. 
• Fessl, T., et al (2020) Dynamics of Membrane Proteins Monitored by Single-Molecule Fluorescence Across Multiple Timescales, Methods in Molecular Biology

 

Studies of G protein signaling at the single molecule level

- Getting insights into non-canonical G protein signaling and development of signaling activity sensors  

Motivation:

The G protein signaling cascade is a major pathway responsible for cellular communication with the external environment. It is present in all eukaryotes from yeast to humans. G proteins transduce signals from a variety of chemical and physical stimuli including hormones, odorants, neurotransmitters, and light. Up to 50% of all modern prescription drugs target this signaling cascade. However, many aspects of G protein signaling remain unclear. Our goal is to gain insights into non-conventional properties of G protein signaling in mammalian and fungal cells. Particularly, we are interested in precoupling between G proteins and G protein-coupled receptors (GPCRs), dimerization and heteromerization of GPCSs, and development of signaling activity sensors (1-5). In our research we use advanced imaging techniques, including single-molecule imaging, combined with molecular biology, cell biology methods and advanced data processing. We strive to utilize cutting-edge techniques and multidisciplinary approaches to do excellent science.

 

Figure 1.  Outstanding questions in G protein signaling research

 

Figure 2. A snapshot of real time dual channel single-molecule imaging of interactions between G proteins and G protein-coupled receptors in a live cell

 

Publications:

  1. A. Bondar, J. Lazar, Optical sensors of heterotrimeric G protein signaling. FEBS J 288, 2570-2584 (2021).
  2. A. Bondar, O. Rybakova, J. Melcr, J. Dohnalek, P. Khoroshyy, O. Tichacek, S. Timr, P. Miclea, A. Sakhi, V. Markova, J. Lazar  Quantitative Linear Dichroism Imaging of Molecular Processes in Living Cells Made Simple by Open Software Tools Communications Biology 4, 189 (2021).
  3. A. Bondar, W. Jang, E. Sviridova, N. A. Lambert, Components of the Gs signaling cascade exhibit distinct changes in mobility and membrane domain localization upon beta2-adrenergic receptor activation. Traffic 21, 324-332 (2020).
  4. A. Bondar, J. Lazar, The G protein Gi1 exhibits basal coupling but not preassembly with G protein-coupled receptors. J Biol Chem 292, 9690-9698 (2017).
  5. A. Bondar, J. Lazar, Dissociated GalphaGTP and Gbetagamma protein subunits are the major activated form of heterotrimeric Gi/o proteins. J Biol Chem 289, 1271-1281 (2014).
 
   
   
   

Lab Members

 
Researchers:
Tomáš Fessl, Ph.D.
Dr Łukasz Bujak
Radek Litvín, Ph.D.
Prof. František Vácha, Ph.D.

Students:
Eva Sýkorová
Jiří Štangl
Jakub Strejc
 
 

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Laboratory of Applied Biochemistry

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Our laboratory focuses on the application of biochemical methods in various scientific fields. We apply biochemical, molecular biological, transcriptomic, genomic, proteomic techniques for the study glycobiology of ticks and tick-borne pathogens, tick-host-pathogen interactions, nanostructured surface functionalization, and the study of fish development.

Research

Laboratory of Applied Biochemistry participated in the C4SYS research infrastructure.

C4SYS is a priority infrastructure project on the national roadmap, and currently builds on close collaboration between the Academy of Sciences (Institute of Nanobiology and Structural Biology, Nove Hrady, Institute of Microbiology, Prague, Global Change Research Center, Brno), the University of South Bohemia and Masaryk University, Brno.

Services offered by the laboratory in the frame of C4SYS can be found here.

Published papers

by the laboratory team members can be found here.

 

Research focus

A) Interaction of tick-borne encephalitis virus with tick and host on the molecular and cellular level.

Tick-borne encephalitis virus is one of the most dangerous tick-transmitted pathogens in Europe and Asia. We aim to better characterize the replication of the tick-borne encephalitis virus, the interaction of viral proteins with host and tick molecules, the regulation of virus replication by the host anti-viral proteins on the molecular level, as well as the effects of viral replication on cellular mechanisms.

https://doi.org/10.1371/journal.pntd.0007745

https://doi.org/10.1016/j.dib.2019.105029

https://doi:10.1016/j.ttbdis.2020.101420

https://doi.org/10.1016/j.csbj.2022.05.052

 

B) Tick research

Fibrinogen-related proteins (FRePs) with lectin activity were studied in the Dermacentor and Rhipicephalus ticks. These proteins participate in the tick innate immune response. All of the proteins were found to be glycosylated and a cross-reaction of anti-FReP antibodies with the tick storage protein Hemelipoglycoprotein (HLGP) was discovered; however, the cross-reactivity is most probably dependent on the epitope similarity as sequence similarity was not found between fibrinogen and FRePs on one hand and HLGP on the other. The hemagglutination activity of Rhipicephalus ticks was inhibited by sialic acid and sialylated glycoproteins, GalNAc, and GlcNAc, suggesting similarity to another FReP from Ornithodoros moubata, the Dorin M protein. (Sterba et al., Parasite Vector 2011)

Mass spectrometric analysis of D. marginatus HLGP N-glycans in a collaborating Novotny laboratory (Indiana University, Bloomington, IN) showed the presence of high-mannose and complex type; paucimannosic type glycans were not observed. Furthermore, lectin-activity of HLGP was studied in collaboration with M. Wimmerova lab (Central European Institute of Technology, Masaryk University, Brno, Czech Republic). The highest binding activity was found for galactose. (Dupejova et al., Parasite Vector 2011).

Sialylated N-glycans were detected in Ixodes and Dermacentor ticks – both N-acetylneuraminic and N-glycosylneuraminic acid (NeuGc) were detected again in collaboration with Prof. Novotny's group in Bloomington, IN. Antibodies against NeuGc were utilized for tracking of sialylated glycans in tick tissues and thus we showed the route of sialylated host glycoproteins from the tick gut through the hemolymph to the salivary glands, where they are in part excreted back into the host. (Vancova et al., J. Insect Physiol. 2012).

Next, we used a combination of sialic acid quantitation and detection of metabolically incorporated sialic acid (Click-iT chemistry) to determine expression of sialylated glycoproteins by the ticks themselves. Using this approach we showed, that majority of sialic acid present in fed female Ixodes ricinus ticks is coming from the host and not the tick itself. This can be one of the immune system evasion strategies employed by ticks (Sterba et al., Carbohydr. Res. 2014).

Recently, we work on the determination of the importance of glycan moieties (NeuAc and NeuGc) for the infection of tick and host cells by the Anaplasma marginale MSP1a in collaboration with Prof. de la Fuente's laboratory (IREC, Universidad de Castilla-La Mancha, Ciudad Real, Spain). While it was previously shown, that Anaplasma infection of tick cells is dependent on the presence of core-fucosylated N-glycans, here we are showing for the first time the importance of sialic acid for the infection of tick cells. The presence of host sialylated molecules in tick tissues and on the surface of tick cells could explain these findings.

Our current knowledge on the tick glycobiology was published recently. https://doi.org/10.1186/s13071-018-3062-7

https://doi.org/10.1186/s13071-019-3460-5.

https://doi.org/10.1038/s41598-020-70330-5

https://doi.org/10.1186/s13071-020-04173-4

Various aspects of gene expression regulation are studied in our laboratory, primarily changes in the gene expression in the various tick life-stages and methyltransferases responsible for DNA and RNA methylation.

https://doi.org/10.1016/j.ttbdis.2019.101348

 

C) Functionalized and nanostructured surfaces, biosensors

Antimicrobial effects on various modified and functionalized materials are studied in collaboration with our colleagues from the Laboratory of Applied Plasma Physics, Department of Physics. Furthermore, biocompatibility of the newly prepared surfaces for the growth of human cells is studied. It is important to mention, that we are entirely changing from the usually used cancer cell lines to primary human cells in this research field to better model the in vivo system.

http://dx.doi.org/10.1002/ppap.201900003

https://doi.org/10.1016/j.matlet.2018.07.082

https://doi.org/10.1016/j.apsusc.2019.07.135

https://doi.org/10.1007/s00216-019-02329-5

https://doi.org/10.1016/j.surfcoat.2020.125805

https://doi.org/10.1021/acsami.1c16930

https://doi.org/10.1021/acs.langmuir.1c01409

 

D) Fish gametes and fertilization

We participate in research oriented on various aspects of gametes development and preservation in collaboration with several laboratories from the Faculty of Fisheries and Water Protection.

https://doi.org/10.1007/s10695-018-0538-5

https://doi.org/10.1016/j.anireprosci.2018.03.025

https://doi.org/10.3390/ani9100753

https://doi.org/10.1111/raq.12355

https://doi.org/10.3390/ijms22115925

https://doi.org/10.3389/fmars.2021.736087

https://doi.org/10.1016/j.theriogenology.2019.02.029

 

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Contacts

Master's in Ecology

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