PROTEIN ENGINEERING

We educate leaders for Science and Business!

prof. Mgr. Jiří Damborský, Dr.

E-mail: jiri.damborsky@fnusa.cz

Key words

Alzheimer Disease, Biocatalysis, Bioinformatics, Computer Modelling, Lab-on-chip, Microfluidics, Protein Engineering, Metabolic Engineering, Mechanistic Enzymology.

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 200 original articles, 20 book chapters and filed 7 international patents and founded the biotechnology spin-off Enantis Ltd.
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 stabilization mutations
International Collaborations: 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

Main goals

Computational design and engineering of hyperstable proteins
Application of novel theoretical concepts for proteins engineering
Development of user-friendly software tools and microfluidic chips

Technological equipment

Computer cluster
Circular dichroism
Colony picking robot
Hardware and software for computer modeling
Microfluidics
Pipetting robot
Rapid quench-flow system
Stopped flow-kinetic system

Assistant

Mgr. Martina Damborská
E-mail: martina.damborska@fnusa.cz

Team members

prof. Mgr. Jiří Damborský, Dr.
Mgr. Martina Damborská
Mgr. Šárka Nevolová, Ph.D.
Mgr. David Bednář, Ph.D.
Ing. Veronika Blechová
Tadeja Gao, Ph.D.
Irena Halíková
Mgr. Marie Hamšíková
Ing. Tomáš Henek
prof. Ing. Lenka Hernychová, Ph.D.
Mgr. Jan Herudek, Ph.D.
Ing. Jiří Hon
Petr Kabourek
Rayyan Tariq Khan
Mgr. David Kovář, Ph.D.
Anthony Thomas Pascal Legrand, Ph.D. MSc.
Ing. Marika Majerová
RNDr. Ing. Martin Marek, Ph.D.
Sérgio Manuel Marques, Ph.D.
Stanislav Mazurenko, Ph.D.
Ing. Miloš Musil
Joan Planas Iglesias, Ph.D.
prof. RNDr. Zbyněk Prokop, Ph.D.
Mgr. Jan Štourač
Mgr. Martin Toul
Mgr. Michal Vašina
Mgr. Ondřej Vávra

Selected results

Stabilization of growth factors to study the stem cells

Patented technology for stabilization of proteins

Software CAVER, CAVER WEB, CAVERDOCK, CALFITTER, HOTSPOT WIZARD, and PREDICTSNP for protein design and prediction of mutation effects on human health

TOUL, M., NIKITIN, D., MAREK, M., DAMBORSKY, J., PROKOP, Z. Extended mechanism of the plasminogen activator staphylokinase revealed by global kinetic analysis: 1000-fold higher catalytic activity than that of clinically used alteplase. 2022. ACS Catalysis 12: 3807-3814.

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., SÝKORA, 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., ŠTĚPÁNKOVÁ, 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.

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.

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.