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Biomolecular Interactions and Transport
Our laboratory focuses on resolving the molecular details of ligand transport processes in proteins mainly relying on structural bioinformatics and computational simulations.
![](https://ibmib.web.amu.edu.pl/wp-content/uploads/2024/02/Jan-Brezovsky.jpg)
Prof. AMU Jan Brezovsky
Principal Investigator
Research
The main research topic of the laboratory is focused on solving fundamental questions about mechanisms involved in a ligand transport through proteins, and implications of such processes for the functions of living cells. To do so, we primarily employ various flavours of molecular dynamics simulations. To obtain a more comprehensive picture, we also investigate the protein-ligands interactions at the functional sites as well as intra- and inter-protein interactions. To achieve these goals, we also develop new computational protocols and tools and apply them to the analysis and design of biomedical and biotechnologically relevant proteins.
Selected publications
- Brezovsky J, Thirunavukarasu AS, Surpeta B, Sequeiros-Borja CE, Mandal N, Sarkar DK, Dongmo Foumthuim CJ, Agrawal N, 2022: TransportTools: a library for high-throughput analyses of internal voids in biomolecules and ligand transport through them. Bioinformatics 38: 1752-1753.
- Surpeta B, Grulich M, Palyzová A, Marešová H, Brezovsky J, 2022: Common Dynamic Determinants Govern Quorum Quenching Activity in N-Terminal Serine Hydrolases. ACS Catalysis 12: 6359-6374.
- Sequeiros-Borja CE, Surpeta B, Marchlewski I, Brezovsky J, 2022: Divide-and-conquer approach to study protein tunnels in long molecular dynamics simulations, MethodsX, in press
- Sequeiros-Borja CE, Surpeta B, Brezovsky J, 2021: Recent advances in user-friendly computational tools to engineer protein function. Briefings in Bioinformatics 22: bbaa150.
- Brezovsky J, Babkova P, Degtjarik O, Fortova A, Gora A, Iermak I, Rezacova P, Dvorak P, Kuta Smatanova I, Prokop Z, Chaloupkova R, Damborsky J, 2016: Engineering a De Novo Transport Tunnel. ACS Catalysis 6: 7597-7610.
- Bendl J, Musil M, Stourac J, Zendulka J, Damborsky J, Brezovsky J, 2016: PredictSNP2: A Unified Platform for Accurately Evaluating SNP Effects by Exploiting the Different Characteristics of Variants in Distinct Genomic Regions. PLoS Computational Biology 12: e1004962.
- 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: W479-487.
- Amaro M, Brezovsky J, Kovacova S, Sykora J, Bednar D, Nemec V, Liskova V, Kurumbang NP, Beerens K, Chaloupkova R, Paruch K, Hof M, Damborsky J, 2015: Site-Specific Analysis of Protein Hydration Based on Unnatural Amino Acid Fluorescence. Journal of the American Chemical Society 137: 4988-4992.
- 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.
- 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.
More publications in PubMed.
Current group members
![Prof. AMU Jan Brezovsky](https://ibmib.web.amu.edu.pl/wp-content/uploads/2024/02/Jan-Brezovsky1.jpg)
Prof. AMU Jan Brezovsky
principal investigator
![Bartłomiej Surpeta, MSc](https://ibmib.web.amu.edu.pl/wp-content/uploads/2024/02/Bartlomiej-Surpeta.jpg)
Bartłomiej Surpeta, MSc
PhD student
![Carlos Eduardo, Sequeiros Borja, MSc](https://ibmib.web.amu.edu.pl/wp-content/uploads/2024/02/Carlos-Eduardo-Sequeiros-Borja.jpg)
Carlos Eduardo, Sequeiros Borja, MSc
PhD student
![Dheeraj Kumar Sarkar, MSc](https://ibmib.web.amu.edu.pl/wp-content/uploads/2024/02/Dheeraj-Kumar-Sarkar.jpg)
Dheeraj Kumar Sarkar, MSc
PhD student
![Aravind Selvaram Thirunavukarasu, MSc (MTech)](https://ibmib.web.amu.edu.pl/wp-content/uploads/2024/02/Aravind-Selvaram-Thirunavukarasu.jpg)
Aravind Selvaram Thirunavukarasu, MSc (MTech)
PhD student
![Nishita Mandal, MSc](https://ibmib.web.amu.edu.pl/wp-content/uploads/2024/02/Nishita-Mandal.jpg)
Nishita Mandal, MSc
PhD student