Research focus

The research group focuses on protein and metabolic engineering for biomedicine. The group develops new theoretical concepts, software tools and lab-on-chip technologies for protein engineering. It uses these newly developed tools for the design of proteins with improved properties for biocatalysis, biodegradation, biosensing, cell culturing and differentiation. The group has published more than 180 original articles, 19 book chapters and filed 7 international patents and founded the biotechnology spin-off Enantis Ltd.

Research objectives

  • Computational design and engineering of hyperstable proteins.
  • Establishing new theoretical concepts for proteins engineering.
  • Development of user-friendly software tools and microfluidic chips.

Main partners

  • ETH Zurich, Switzerland
  • Tohoku University, Katahira, Japan
  • University of Cambridge, Cambridge, UK
  • Novo Nordisk Foundation Center for Biosustainability (CFB), Copenhagen, Denmark
  • Spanish National Research Council (CSIC), Madrid, Spain

Technological equipment

  • Computer cluster
  • Circular dichroism
  • Colony picking robot
  • Microfluidics
  • Pipetting robot
  • Rapid quench flow system
  • Stopped flow kinetics system

Offered services and expertise

  • Bioinformatics – identification of interesting genes in genomic databases for molecular cloning and experimental characterization.
  • Lab-on-Chip Technologies – development of microfluidic lab-on-chip technologies for biochemical and biomedical research.
  • Pathway Engineering – design and construction of bacterial strains expressing newly assembled biochemical pathways.
  • Protein Stabilization – computational design of stabilizing mutations using evolutionary and energetic approach.

Top publications

  • GORA, A., BREZOVSKÝ, J., DAMBORSKÝ, J. Gates of Enzymes. Chemical Reviews. 2013, 113(8), 5871-5923.
  • ŠTOURAČ, J., VÁVRA, O., KOKKONEN, P., FILIPOVIČ, J., PINTO, G., BREZOVSKÝ, J., DAMBORSKÝ, J., BEDNÁŘ, D. Caver Web 1.0: Identification of tunnels and channels in proteins and analysis of ligand transport. 2019. Nucleic Acid Research gkz378.
  • KOKKONEN, P., SYKORA, J., PROKOP, Z., GHOSE, A., BEDNÁŘ, D., AMARO, M., BEERENS, K., BIDMANOVÁ, S., SLÁNSKÁ, M., BREZOVSKÝ, J., DAMBORSKÝ, J., HOF, M. Molecular gating of an engineered enzyme captured in real time. 2018. Journal of the American Chemical Society 140: 17999–18008.
  • MUSIL, M., ŠTOURAČ, J., BENDL, J., BREZOVSKÝ, J., PROKOP, Z., ZENDULKA, J., MARTÍNEK, T., BEDNÁŘ, D., DAMBORSKÝ, J. FireProt: Web server for automated design of thermostable proteins. 2017. Nucleic Acids Research 45: W393-W399.
  • LIŠKOVÁ, V., SŤEPÁNKOVÁ, V., BEDNÁŘ, D., BREZOVSKÝ, J., PROKOP, Z., CHALOUPKOVÁ, R., DAMBORSKÝ, J. Different structural origins of the enantioselectivity of haloalkane dehalogenases toward linear β-haloalkanes: Open–solvated versus occluded–desolvated active sites. 2017. Angewandte Chemie International Edition 56: 4719-4723
  • SÝKORA, J., BREZOVSKÝ, J., KOUDELÁKOVÁ, T., LAHODA, M., FORTOVÁ, A., CHERNOVETS, T., CHALOUPKOVÁ, R., ŠTĚPÁNKOVÁ, V., PROKOP, Z., KUTÁ SMATANOVÁ, I., HOF, M., DAMBORSKÝ, J. Dynamics and hydration explain failed functional transformation in dehalogenase design. Nature Chemical Biology. 2014, 10(6), 428–430.
  • AMARO, M., BREZOVSKÝ, J., KOVÁČOVÁ, S., SÝKORA, J., BEDNÁŘ, D., NĚMEC, V., LIŠKOVÁ, V., KURUMBANG, N., BEERENS, K., CHALOUPKOVÁ, R., PARUCH, K., HOF, M., DAMBORSKÝ, J. Site-specific analysis of protein hydration based on unnatural amino acid fluorescence. Journal of the American Chemical Society. 2015, 137(15), 4988-4992.
  • BREZOVSKÝ, J., CHOVANCOVÁ, E., GORA, A., PAVELKA, A., BIEDERMANNOVÁ, L., DAMBORSKÝ, J. Software tools for identification, visualization and analysis of protein tunnels and channels. Biotechnology Advances. 2013, 31(1), 38-49.
  • BENDL, J., ŠTOURAČ, J., ŠEBESTOVÁ, E., VÁVRA, O., MUSIL, M., BREZOVSKÝ, J., DAMBORSKÝ, J. HotSpot Wizard 2.0: automated design of site-specific mutations and smart libraries in protein engineering. Nucleic Acids Research 2016, 44(W1): W479-487.

Other selected results

  • Stabilization of growth factors for stem cells research.
  • Patented technology for protein stabilization.
  • Software CAVER, CAVER WEB, CAVERDOCK, CALFITTER, HOTSPOT WIZARD and PREDICTSNP for protein design and prediction of effects of mutations on human health.

Team members

  • prof. Dr. Mgr. Jiří Damborský
  • Mgr. Martina Damborská
  • Mgr. Jitka Sedláčková, Ph.D.
  • Mgr. Petra Babková
  • Mgr. David Bednář, Ph.D.
  • Andy Beier, Ph.D.
  • Ing. Klaudia Chmelová
  • Mgr. Tereza Ghazalová
  • Irena Halíková
  • Ing. Jiří Hon
  • Ing. Jana Hozzová, Ph.D.
  • Rayyan Tariq Khan
  • Mgr. Aneta Kohutová
  • Mgr. Zuzana Koledová, Ph.D.
  • Mgr. David Kovář, Ph.D.
  • Bc. Antonín Kunka
  • Mgr. Kateřina Kutálková
  • Mgr. Veronika Lásková
  • Sérgio Manuel Marques, Ph.D.
  • Mgr. Hana Moskalíková
  • Ing. Miloš Musil
  • Mgr. Lucie Ovčáčková
  • prof. RNDr. Zbyněk Prokop, Ph.D.
  • Jose Gaspar Rangel Pamplona Pizarro Pinto, Ph.D.
  • Ing. Andrea Schenkmayerová, Ph.D.
  • Mgr. Karel Souček, Ph.D.
  • Mgr. Jan Štourač
  • Mgr. Markéta Stuchlá
  • Jakub Sumbal
  • Mgr. Táňa Svobodová
  • Mgr. Martin Toul
  • Mgr. Pavel Vaňáček
  • Mgr. Ondřej Vávra

Principal Investigator

prof. Dr. Mgr. Jiří Damborský
prof. Dr. Mgr. Jiří Damborský
Principal Investigator

Assistant

Mgr. Martina Damborská
Mgr. Martina Damborská
Assistant