Ing. Tomáš Henek
Junior Researcher
Protein Engineering
Our team investigates fundamental mechanisms and translates findings from bench to bedside, combining preclinical models with clinical insight.
Researcher at ICRC with focus on translational medicine. Combines preclinical insights with clinical practice across cardiology, neurology, and oncology programs.
Currently leads / contributes to interdisciplinary projects bridging molecular biology, imaging, and patient care at St. Anne's University Hospital Brno.
Research Group
- Team size
- Team size: 49 Researchers
- Place
- Place: Building B1, 4th Floor
- Collaborates with
- Collaborates with Czech Academy of Sciences
Head of Research Group
- prof. Dr. Mgr. Jiří Damborský
Members
Ing. Pavel Kohout
Junior Researcher
Mgr. Hana Faldynová
Ph.D. Student
Mgr. Daniel Pluskal
Ph.D. Student
Naina Verma, MSc
Ph.D. Student
Faraneh Haddadi, MSc
Ph.D. Student
Mgr. Martin Havlásek
Ph.D. Student
Mgr. Martin Sitte
Ph.D. Student
Mgr. Kateřina Hrůzová
Ph.D. Student
Mgr. Bc. Milada Sára Poledňáková
Research Assistant
Mgr. Aneta Horáčková
Research Assistant
Mgr. Pavel Vaňáček, Ph.D.
Postdoctoral Researcher
Mgr. Josef Kučera, Ph.D.
Postdoctoral Researcher
Mgr. Šárka Nevolová, Ph.D.
Facility Specialist, Research Coordinator
prof. Dr. Mgr. Jiří Damborský
Principal Investigator, Senior Research Team Leader
prof. RNDr. Zbyněk Prokop, Ph.D.
Principal Investigator, Head Researcher, Senior IT Specialist
prof. Ing. Lenka Hernychová, Ph.D.
Senior Postdoctoral Researcher, Head Researcher
Sérgio Manuel Marques, Ph.D.
IT Specialist, Head Researcher
Mgr. Ondřej Vávra, Ph.D.
IT Specialist
Ing. Petr Kabourek
IT Specialist, Senior Application Developer
Bc. David Damborský
IT Specialist
Mgr. Karen Pailozian
IT Specialist
Mgr. Martina Damborská
Research Coordinator
Ing. Miloš Musil, Ph.D.
Application Developer, Senior IT Specialist
Mgr. Michal Vašina, Ph.D.
Application Developer
Saltuk Mustafa Eyrilmez, Ph.D.
Application Developer
Ing. Dávid Lacko
Application Developer
Ing. Monika Rosinská
Application Developer
Mgr. Bc. Alan Strunga
Application Developer
Mgr. Jana Horáčková
Application Developer
Tim Titus Hendrikus De Martines, MSc
Application Developer
Joan Planas Iglesias, Ph.D.
Senior Application Developer
Irena Halíková
Lab Technician
MUDr. Jan Česnek
Lab Technician
Mgr. Zuzana Mihal Juríková
Lab Technician
Mgr. Aliaksandra Kursit
Lab Technician
RNDr. Ing. Martin Marek, Ph.D., MBA
Head Researcher
Stanislav Mazurenko, Ph.D.
Head Researcher, Senior IT Specialist
RNDr. Lenka Šindlerová, Ph.D.
Senior Research Specialist
Mgr. Eva Hrubá, Ph.D.
Lab Specialist
Mgr. Aneta Kohutová, Ph.D.
Lab Specialist
Mgr. Karolina Sedláčková
Lab Specialist
Ing. Michaela Matlohová
Lab Specialist
Mgr. Zuzana Prášilová
Lab Specialist
Mgr. Nikola Neumeisterová
Lab Specialist
Mgr. Ajay Modi
Lab Specialist
doc. Mgr. David Bednář, Ph.D.
Senior IT Specialist
Mgr. David Kovář, Ph.D.
Senior IT Specialist
Ing. Marie Šulová
Research Technician Specialist
Team Assistant
Mgr. Martina Damborská
Administrative Support
Main Objectives
- Computational design and engineering of hyperstable proteins
- Application of novel theoretical concepts for proteins engineering
- Development of user-friendly software tools and microfluidic chips
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
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
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.
