Publications

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Lysáková, K., Hlináková, K., Kutálková, K., Chaloupková, R., Žídek, J., Brtníková, J., & Vojtová, L., 2022: A novel approach in control release monitoring of protein-based bioactive substances from injectable PLGA-PEG-PLGA hydrogel. Express Polymer Letters 16: 798–811.

Vasina, M., Velecký, J., Planas-Iglesias, J., Marques, S. M., Skarupova, J., Damborsky, J., Bednar, D., Mazurenko, S., & Prokop, Z., 2022: Tools for Computational Design and High-throughput Screening of Therapeutic Enzymes. Advanced Drug Delivery Reviews: 183.

Marques, S. M., Slanska, M., Chmelova, K., Chaloupkova, R., Marek, M., Clark, S., Damborsky, J., Kool, E. T., Bednar, D., & Prokop, Z., 2022: Mechanism-Based Strategy for Optimizing HaloTag Protein Labeling. JACS Au 2: 1324–1337.

Vavra, O., Damborsky, J., & Bednar, D., 2022: Fast Approximative Methods for Study of Ligand Transport and Rational Design of Improved Enzymes for Biotechnologies. Biotechnology Advances: 60.

Krzyscik, M. A., Opaliński, Ł., Szymczyk, J., & Otlewski, J., 2022: Cyclic and Dimeric Fibroblast Growth Factor 2 Variants with High Biomedical Potential. International Journal of Biological Macromolecules, 218: 243–258.

2021

Markova, K., Kunka, A., Chmelova, K., Havlasek, M., Babkova, P., Marques, S. M., Vasina, M., Planas-Iglesias, J., Chaloupkova, R., Bednar, D., Prokop, Z., Damborsky, J., & Marek, M., 2021: Computational Enzyme Stabilization Can Affect Folding Energy Landscapes and Lead to Catalytically Enhanced Domain-Swapped Dimers. ACS Catalysis, 11: 12864–12885.

Muchová, J., Hearnden, V., Michlovská, L., Vištejnová, L., Zavaďáková, A., Šmerková, K., Kočiová, S., Adam, V., Kopel, P., & Vojtová, L., 2021: Mutual Influence of Selenium Nanoparticles and FGF2-STAB® on Biocompatible Properties of Collagen/Chitosan 3D Scaffolds: in vitro and ex ovo Evaluation. Journal of Nanobiotechnology 19.

Mazur, A., Grinkevich, P., Chaloupkova, R., Havlickova, P., Kascakova, B., Kuty, M., Damborsky, J., Smatanova, I. K., & Prudnikova, T., 2021: Structural Analysis of the Ancestral Haloalkane Dehalogenase anclinB-DmbA. International Journal of Molecular Sciences 22.

Vojtová, L., Pavliňáková, V., Muchová, J., Kacvinská, K., Brtníková, J., Knoz, M., Lipový, B., Faldyna, M., Göpfert, E., Holoubek, J., Pavlovský, Z., Vícenová, M., Blahnová, V. H., Hearnden, V., & Filová, E., 2021: Healing and Angiogenic Properties of Collagen/Chitosan Scaffolds Enriched with Hyperstable FGF2-stab® protein: In vitro, ex ovo and in vivo comprehensive evaluation. Biomedicines 9.

Krticka, M., Planka, L., Vojtova, L., Nekuda, V., Stastny, P., Sedlacek, R., Brinek, A., Kavkova, M., Gopfert, E., Hedvicakova, V., Rampichova, M., Kren, L., Liskova, K., Ira, D., Dorazilová, J., Suchy, T., Zikmund, T., Kaiser, J., Stary, D., Trunec, M., 2021: Lumbar Interbody Fusion Conducted on a Porcine Model with a Bioresorbable Ceramic/Biopolymer Hybrid Implant Enriched with Hyperstable Fibroblast Growth Factor 2. Biomedicines 9.

2020

Kuo, H. H., Gao, X., DeKeyser, J. M., Fetterman, K. A., Pinheiro, E. A., Weddle, C. J., Fonoudi, H., Orman, M. V., Romero-Tejeda, M., Jouni, M., Blancard, M., Magdy, T., Epting, C. L., George, A. L., & Burridge, P. W., 2020: Negligible-Cost and Weekend-Free Chemically Defined Human iPSC Culture. Stem Cell Reports 14: 256–270.

2019

Koledova, Z., Sumbal, J., Rabata, A., De La Bourdonnaye, G., Chaloupkova, R., Hrdlickova, B., Damborsky, J., & Stepankova, V., 2019: Fibroblast Growth Factor 2 Protein Stability Provides Decreased Dependence on Heparin for Induction of FGFR Signaling and Alters ERK Signaling Dynamics. Frontiers in Cell and Developmental Biology 7.

Nevolova, S., Manaskova, E., Mazurenko, S., Damborsky, J., & Prokop, Z., 2019: Development of Fluorescent Assay for Monitoring of Dehalogenase Activity. Biotechnology Journal 14.

Chrast, L., Tratsiak, K., Planas-Iglesias, J., Daniel, L., Prudnikova, T., Brezovsky, J., Bednar, D., Smatanova, I. K., Chaloupkova, R., & Damborsky, J., 2019: Deciphering the Structural Basis of High Thermostability of Dehalogenase from Psychrophilic Bacterium Marinobacter sp. ELB17. Microorganisms 7.

Chaloupkova, R., Liskova, V., Toul, M., Markova, K., Sebestova, E, Hernychova, L., Marek, M. Pinto. G. P., Pluskal, D., Waterman, J., Prokop, Z., Damborsky, J., 2019: Light-Emitting Dehalogenases: Reconstruction of Multifunctional Biocatalysts. ACS Catalysis 9: 4810–4823.

Musil, M., Konegger, H., Hon, J., Bednar, D., Damborsky, J., 2019: Computational Design of Stable and Soluble Biocatalysts. ACS Catalysis 9: 1033−1054.

2018

Mazurenko, S., Bidmanova, S., Kotlanova, M., Damborsky, J., & Prokop, Z. (2018). Sensitive operation of Enzyme-based Biodevices by Advanced Signal Processing. PLoS ONE, 13(6).

Beerens, K., Mazurenko, S., Kunka, A., Marques, S. M., Hansen, N., Musil, M., Chaloupkova, R., Waterman, J., Brezovsky, J., Bednar, D., Prokop, Z., Damborsky, J., 2018: Evolutionary Analysis is a Powerful Complement to Energy Calculations for Protein Stabilization. ACS Catalysis 8: 9420−9428.

Sumbalova, L., Stourac, J., Martinek, T., Bednar, D., Damborsky, J., 2018: HotSpot Wizard 3.0: Web Server for Automated Design of Mutations and Smart Libraries Based on Sequence Input Information. Nucleic Acids Research 46: W356-W362.

Jurcik, A., Bednar, D., Byska, J., Marques, S. M., Furmanova, K., Daniel, L., Kokkonen, P., Brezovsky, J., Strnad, O., Stourac, J., Pavelka, A., Manak, M., Damborsky, J., Kozlikova, B., 2018: CAVER Analyst 2.0: Analysis and Visualization of Channels and Tunnels in Protein Structures and Molecular Dynamics Trajectories. Bioinformatics 34: 3586-3588.

Kaushik, S., Marques, S. M., Khirsariya, P., Paruch, K., Libichova, L., Brezovsky, J., Prokop, Z., Chaloupkova, R., Damborsky, J., 2018: Impact of the Access Tunnel Engineering on Catalysis is Strictly Ligand-Specific. FEBS Journal 285: 1456-1476.

Dvorak, P., Bednar, D., Vanacek, P., Balek, L., Eiselleova, L., Stepankova, V., Sebestova, E., Kunova Bosakova, M., Konecna, Z., Mazurenko, S., Kunka, A. Vanova, T., Zoufalova, K., Chaloupkova, R., Brezovsky, J., Krejci, P., Prokop, Z., Dvorak, P., Damborsky, J., 2018: Computer-Assisted Engineering of Hyperstable Fibroblast Growth Factor 2. Biotechnology and Bioengineering 115: 850-862.

Vanacek, P., Sebestova, E., Babkova, P., Bidmanova, S., Daniel, L., Dvorak, P., Stepankova, V., Chaloupkova, R., Brezovsky, J., Prokop, Z., Damborsky, J., 2018: Exploration of Enzyme Diversity by Integrating Bioinformatics with Expression Analysis and Biochemical Characterization. ACS Catalysis 8: 2402–2412.

2017

Schwarte, A., Genz, M., Skalden, L., Nobili, A., Vickers, C., Melse, O., Kuipers, R., Joosten, H., Stourac, J., Bendl, J., Black, J., Haase, P., Baakman, C, Damborsky, J., Bornscheuer, U, Vriend, G., Venselaar, H., 2017: NewProt – a protein engineering portal. Protein Engineering, Design & Selection 30(6): 441-447.

Liskova, V., Stepankova, V., Bednar, D., Brezovsky, J., Prokop, Z., Chaloupkova, R., Damborsky, J., 2017: Different Structural Origins of the Enantioselectivity of Haloalkane Dehalogenases toward Linear β-Haloalkanes: Open–Solvated versus Occluded–Desolvated Active Sites. Angewandte Chemie International Edition 56(17):4719-4723.

Musil, M,, Stourac, J., Bendl, J., Brezovský, J., Prokop, Z., Zendulka, J., Martinek, T., Bednar, D., Damborsky, J., 2017: FireProt: Web Server for Automated Design of Thermostable Proteins. Nucleic Acids Research 45 (W1): W393–W399.

2016

Pavelka, A., Sebestova, E., Kozlikova, B., Brezovsky, J., Sochor, J., Damborsky, J., 2016: CAVER: Algorithms for Analyzing Dynamics of Tunnels in Macromolecules. IEEE/ACM Transactions on Computational Biology and Bioinformatics 13: 505-517.

Bendl, J., Stourac, J., Sebestova, E., Vavra, O., Musil, M., Brezovsky, J., Damborsky, J., 2016: HotSpot Wizard 2: Automated Design of Site-Specific Mutations and Smart Libraries in Protein Engineering. Nucleic Acids Research 44: W479-W487.

Bidmanova, S., Steiner, M.S., Stepan, M., Vymazalova, K., Gruber, M.A., Duerkop, A., Damborsky, J., Prokop, Z., Wolfbeis, O.S., 2016: Enzyme Based Test Stripes for the Visual or Photographic Detection and Quantitation of Gaseous Sulfur Mustard. Analytical Chemistry 88: 6044-6049.

Buryska, T. , Daniel, L., Kunka, A., Brezovsky, J., Damborsky, J., Prokop, Z., 2016: Discovery of Novel Haloalkane Dehalogenase Inhibitors. Applied and Environmental Microbiology 82: 1958-1965.

Bidmanova, S., Kotlanova, M., Rataj, T., Damborsky, J., Trtilek, M., Prokop, Z., 2016: Fluorescence-Based Biosensor for Monitoring of Environmental Pollutants: From Concept to Field Application. Biosensors and Bioelectronics 84: 97-105.

2015

Bednar, D., Beerens, K., Sebestova, E., Bendl, J., Khare, S., Chaloupkova, R., Prokop, Z., Brezovsky, J., Baker, D., Damborsky, J., 2015: FireProt: Energy- and Evolution-Based Computational Design of Thermostable Multiple-Point Mutants. PLOS Computational Biology 11: e1004556.

Shrivastava, N., Prokop, Z., Kumar, A., 2015: Novel LinA Type 3 δ-Hexachlorocyclohexane Dehydrochlorinase. Applied and Environmental Microbiology 81: 7553-7559.

Buchtova, M., Chaloupkova, R., Zakrzewska, M., Vesela, I., Cela, P., Barathova, J., Gudernova, I., Zajickova, R., Trantirek, L., Martin, J., Kostas, M., Otlewski, J., Damborsky, J., Kozubik, A., Wiedlocha, A., Krejci, P., 2015: Instability Restricts Signaling of Multiple Fibroblast Growth Factors. Cellular and Molecular Life Sciences 72: 2445-2459.

Daniel, L., Buryska, T., Prokop, Z., Damborsky, J., Brezovsky, J., 2015: Mechanism-Based Discovery of Novel Substrates of Haloalkane Dehalogenases using in Silico Screening. Journal of Chemical Information and Modeling 55: 54-62.

2014

Kozlikova, B., Sebestova, E., Sustr, V., Brezovsky, J., Strnad, O., Daniel, L., Bednar, D., Pavelka, A., Manak, M., Bezdeka, M., Benes, P., Kotry, M., Gora, A., Damborsky, J., Sochor, J., 2014: CAVER Analyst 1.0: Graphic Tool for Interactive Visualization and Analysis of Tunnels and Channels in Protein Structures. Bioinformatics 30: 2684-2685.

Bidmanova, S., Hrdlickova, E., Jaros, J., Ilkovics, L., Hampl, A., Damborsky, J., Prokop, Z., 2014: Microscopic Monitoring Provides Information on Structure and Properties During Biocatalyst Immobilisation. Biotechnology Journal 9: 852-860.

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., 2014: Dynamics and Hydration Explain Failed Functional Transformation in Dehalogenase Design. Nature Chemical Biology 10: 428-430.

Stepankova, V., Vanacek, P., Damborsky, J., Chaloupkova, R., 2014: Comparison of Catalysis by Haloalkane Dehalogenases in Aqueous Solutions of a Deep Eutectic and Organic Solvents. Green Chemistry 16: 2754-2761.

2013

Stepankova, V., Bidmanova, S., Koudelakova, T., Prokop, Z., Chaloupkova, R., Damborsky, J., 2013: Strategies for Stabilization and Activation of Biocatalysts in Organic Solvents. ACS Catalysis 3: 2823-2836.

Stepankova, V., Paterova, J., Damborsky, J., Jungwirth, P., Chaloupkova, R., Heyda, J., 2013: Cation-Specific Effects on Enzymatic Catalysis Driven by Interactions at the Tunnel Mouth. Journal of Physical Chemistry B 117: 6394-6402.

Bidmanova, S., Damborsky, J., Prokop, Z., 2013: Immobilization of Haloalkane Dehalogenase LinB from Sphingobium japonicum UT26 for Biotechnological Applications. Journal of Biocatalysis & Biotransformation 2: 1-7.

Stepankova, V., Khabiri, M., Brezovsky, J., Pavelka, A., Sykora, J., Amaro, M., Minofar, B., Prokop, Z., Hof, M., Ettrich, R., Chaloupkova, R., Damborsky, J., 2013: Expansion of Access Tunnels and Active-Site Cavities Influence Activity of Haloalkane Dehalogenases in Organic Cosolvents. ChemBioChem 14: 890-897.

Stepankova, V., Damborsky, J., Chaloupkova, R., 2013: Organic Co-solvents Affect Activity, Stability and Enantioselectivity of Haloalkane Dehalogenases. Biotechnology Journal 8: 719-729.

Koudelakova, T., Bidmanova, T., Dvorak, P., Pavelka, A., Chaloupkova, R., Prokop, Z., Damborsky, J., 2013: Haloalkane Dehalogenases: Biotechnological Applications. Biotechnology Journal 8: 32-45.

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., 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.

Niharika, N., Moskalikova, H., Kaur, J., Khan, F., Sedlackova, M., Hampl, A., Damborsky, J., Prokop, Z., Lal, R., 2013: Sphingobium czechense sp. nov., Isolated from a Hexachlorocyclohexane (HCH) Dump Site. International Journal of Systematic and Evolutionary Microbiology 63: 673-678.

2012

Chovancova, E., Pavelka, A., Benes, P., Strnad, O., Brezovsky, J., Kozlikova, B., Gora, A., Sustr, V., Klvana, M., Medek, P., Biedermannova, L., Sochor, J., Damborsky, J., 2012: CAVER 3.0: A Tool for Analysis of Transport Pathways in Dynamic Protein Structures. PLOS Computational Biology 8: e1002708.

Drienovska, I., Chovancova, E., Koudelakova, T., Damborsky, J., Chaloupkova, R., 2012: Biochemical Characterization of a Novel Haloalkane Dehalogenase from a Cold-Adapted Bacterium. Applied and Environmental Microbiology 78: 4995-4998.

Bidmanova, S., Hlavacek, A., Damborsky, J., Prokop, Z., 2012: Conjugation of 5(6)-Carboxyfluorescein and 5(6)-Carboxynaphthofluorescein with Bovine Serum Albumin and Their Immobilization for Optical pH Sensing. Sensors and Actuators B: Chemical 161: 93-99.

2011

Koudelakova, T., Chovancova, E., Brezovsky, J., Monincova, M., Fortova, A., Jarkovsky, J., Damborsky, J., 2011: Substrate Specificity of Haloalkane Dehalogenases. Biochemical Journal 435: 345-354.

2010

Bidmanova, S., Chaloupkova, R., Damborsky, J., Prokop, Z., 2010: Development of an Enzymatic Fiber-Optic Biosensor for Detection of Halogenated Hydrocarbons. Analytical and Bioanalytical Chemistry 398: 1891-1898.

Prokop, Z., Sato, Y., Brezovsky, J., Mozga, T., Chaloupkova, R., Koudelakova, T., Jerabek, P., Stepankova, V., Natsume, R., Leeuwen, J. G. E., Janssen, D. B., Florian, J., Nagata, Y., Senda, T., Damborsky, J., 2010: Enantioselectivity of Haloalkane Dehalogenases and its Modulation by Surface Loop Engineering. Angewandte Chemie International Edition 49: 6111-6115.

2009

Pavlova, M., Klvana, M., Prokop, Z., Chaloupkova, R., Banas, P., Otyepka, M., Wade, R., Nagata, Y., Damborsky, J., 2009: Redesigning Dehalogenase Access Tunnels as a Strategy for Degrading an Anthropogenic Substrate. Nature Chemical Biology 5: 727-733.

Pavelka, A., Chovancova, E., Damborsky, J., 2009: HotSpot Wizard: a Web Server for Identification of Hot Spots in Protein Engineering. Nucleic Acids Research 37: W376-W383.

2007

Ito, M., Prokop, Z., Klvana, M., Otsubo, Y., Tsuda, M., Damborsky, J., Nagata, Y., 2007: Degradation of Beta-Hexachlorocyclohexane by Haloalkane Dehalogenase LinB from Hexachlorocyclohexane-Utilizing Bacterium Sphingobium sp. MI1205. Archives of Microbiology 188: 313-325.

Chovancova, E., Kosinski, J., Bujnicki, J.M., Damborsky, J., 2007: Phylogenetic Analysis of Haloalkane Dehalogenases. Proteins 67: 305-316.

2006

Prokop, Z., Oplustil, F., DeFrank, J., Damborsky, J., 2006: Enzymes Fight Chemical Weapons. Biotechnology Journal 1: 1370-1380.

Book chapters

Kokkonen, P., Koudelakova, T., Chaloupkova, R., Daniel, L., Prokop, Z., Damborsky, J., 2017: Structure-function Relationships and Engineering of Haloalkane Dehalogenases. In: Rojo, F., Handbook of Hydrocarbon and Lipid Microbiology Series. Aerobic Utilization of Hydrocarbons, Oils, and Lipids, Springer, Heidelberg, pp. 1-21.

Stepankova, V., Damborsky, J., Chaloupkova, R., 2015: Hydrolases in Non-Conventional Media: Implications for Industrial Biocatalysis. In: Peter Grunwald, Industrial Biocatalysis, Pan Stanford Publishing, pp. 583-620.

Bidmanova, S., Hrdlickova, E., Koudelakova, T., Damborsky, J., Prokop, Z., 2013: On-line Monitoring of Biodegradation Processes using Enzymatic Biosensors. In: Nojiri, H., Tsuda, M., Fukuda, M., Kamagata, Y., (Eds.), Biodegradative Bacteria, Springer, Japan, pp. 155-180.

Prokop, Z., Stepankova, V., Hasan, K., Chaloupkova, R., Damborsky, J., 2012: Preparation of Optically Pure Haloalkanes and Alcohols by Kinetic Resolution using Haloalkane Dehalogenases. In: John Whittall and Peter Sutton (Eds.), Practical Methods for Biocatalysis and Biotransformations, 2nd ed., John Wiley & Sons, Chichester, pp. 307-313.

Prokop, Z., Gora, A., Brezovsky, J., Chaloupkova, R., Stepankova, V., Damborsky, J., 2012: Engineering of Protein Tunnels: Keyhole-lock-key Model for Catalysis by the Enzymes with Buried Active Sites. In: Lutz, S., Bornscheuer, U.T. (Eds.), Protein Engineering Handbook, Wiley-VCH, Weinheim, pp. 421-464.

Damborsky, J., Chaloupkova, R., Pavlova, M., Chovancova, E., Brezovsky, J., 2009: Structure-Function Relationships and Engineering of Haloalkane Dehalogenases. In: Kenneth N. Timmis (Ed.), Handbook of Hydrocarbon and Lipid Microbiology, Springer, Berlin, Heidelberg, pp. 1081-1098.

Patents

Chaloupkova, R., Stepankova, V., Horackova, A., Bednar, D., Kutalkova, K., 2023: Hermostable Fgf10 Polypeptide or Fragment Thereof and Use Thereof. Enantis s.r.o., Brno, Czech Republic. Patent WO/ 2023/089157.

Dvorak, P.,Krejci, P., Balek, L., Eiselleova, L., Konecna, Z., Dvorak, P., Bednar, D., Brezovsky, J., Sebestova, E., Chaloupkova, R., Stepankova, V., Vanacek, P., Prokop, Z., Damborsky, J., Bosakova, M., 2017: Thermostable Fgf2 Polypeptide, Use Thereof. Masaryk University, Brno, Czech Republic. Enantis s.r.o., Brno, Czech Republic. Patent WO/2017/089016.

Damborsky, J., Nikulenkov, F., Sisakova, A., Havel, S., Krejci, L., Carbain, B., Brezovsky, J., Daniel, L., Paruch, K., 2015: Pyrazolotriazines as Inhibitors of Nucleases. Masaryk University, Brno, Czech Republic. Patent WO 2015/192817 A1.

Damborsky, J., Prokop, Z., Koudelakova, T., Stepankova, V., Chaloupkova, R., Gora, A., Chovancova, E., Brezovsky, J., 2013: Method of Thermostabilization of a Protein and/or Stabilization Towards Organic Solvents. Masaryk University, Brno, Czech Republic. Patent US 8,580,932.

Prokop, Z., Damborsky, J., Oplustil, F., Jesenska, A., Nagata, Y., 2005: Method of Detoxification of Yperite by using Haloalkane Dehalogenases. Masaryk University, Brno, Czech Republic. Patent WO 2006/128390 A1.

Prokop, Z., Damborsky, J., Nagata, Y., Janssen, D.B., 2004: Method of Production of Optically Active Hydrocarbons and Alcohols Using Hydrolytic Dehalogenation Catalysed by Haloalkane Dehalogenases. Masaryk University, Brno, Czech Republic. Patent WO 2006/079295 A2.

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