“Jiri is a great scientist.”
Jiri Damborsky
Professor, Loschmidt Laboratories, Masaryk University & Founder Enantis Ltd.
Brno, Jihomoravský, Česko
7 tis. sledujících uživatelů
Více než 500 spojení
Pár slov o mně
Mission
We will conduct interdisciplinary research in the field of protein engineering. We wish to understand the structure-function relationships of proteins and improve their functionalities for biotechnologies. We study molecular mechanisms of neurodegenerative diseases, including Alzheimer’s and Parkinson’s disease.
Our goal is to be recognized as one of the leading protein engineering groups in Europe. We will consistently strive to publish our findings in reputable scientific journals, develop new software tools and microfluidic platforms and apply research results to practice.
The key components of our daily activities will include collaboration between experimentalists and theoreticians, solidarity among the laboratory team and mentoring of young colleagues—all while maintaining a friendly and creative working environment to honour the name of Jan Josef Loschmidt.
Aktivita
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Today we launched NVIDIA’s virtual screening for drug discovery implemented via inference microservices or NIMs. Leading biotechnology software…
Today we launched NVIDIA’s virtual screening for drug discovery implemented via inference microservices or NIMs. Leading biotechnology software…
Dal(a) líbí se: Jiri Damborsky
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Když jste na schůzce, na kterou se delší dobu těšíte, tak jde vše skoro samo🙂🤝 A přesně takové bylo páteční setkání s Ondrej Votruba v Brně. Ondra…
Když jste na schůzce, na kterou se delší dobu těšíte, tak jde vše skoro samo🙂🤝 A přesně takové bylo páteční setkání s Ondrej Votruba v Brně. Ondra…
Dal(a) líbí se: Jiri Damborsky
Pracovní zkušenosti
Vzdělání
Publikace
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The impact of tunnel mutations on enzymatic catalysis depends on the tunnel-substrate complementarity and the rate-limiting step
Computational and Structural Biotechnology Journal 18: 805-813
Transport of ligands between bulk solvent and the buried active sites is a critical event in the catalytic cycle of many enzymes. The rational design of transport pathways is far from trivial due to the lack of knowledge about the effect of mutations on ligand transport. The main and an auxiliary tunnel of haloalkane dehalogenase LinB have been previously engineered for improved dehalogenation of 1,2-dibromoethane (DBE). The first chemical step of DBE conversion was enhanced by L177W mutation…
Transport of ligands between bulk solvent and the buried active sites is a critical event in the catalytic cycle of many enzymes. The rational design of transport pathways is far from trivial due to the lack of knowledge about the effect of mutations on ligand transport. The main and an auxiliary tunnel of haloalkane dehalogenase LinB have been previously engineered for improved dehalogenation of 1,2-dibromoethane (DBE). The first chemical step of DBE conversion was enhanced by L177W mutation in the main tunnel, but the rate-limiting product release was slowed down because the mutation blocked the main access tunnel and hindered protein dynamics. Three additional mutations W140A + F143L + I211L opened-up the auxiliary tunnel and enhanced the product release, making this four-point variant the most efficient catalyst with DBE. Here we study the impact of these mutations on the catalysis of bulky aromatic substrates, 4-(bromomethyl)-6,7-dimethoxycoumarin (COU) and 8-chloromethyl-4,4′-difluoro-3,5-dimethyl-4-bora-3a,4a-diaza-s-indacene (BDP). The rate-limiting step of DBE conversion is the product release, whereas the catalysis of COU and BDP is limited by the chemical step. The catalysis of COU is mainly impaired by the mutation L177W, whereas the conversion of BDP is affected primarily by the mutations W140A + F143L + I211L. The combined computational and kinetic analyses explain the differences in activities between the enzyme-substrate pairs. The effect of tunnel mutations on catalysis depends on the rate-limiting step, the complementarity of the tunnels with the substrates and is clearly specific for each enzyme-substrate pair.
Ostatní autořiZobrazit publikaci -
Fluorescent Substrates for Haloalkane Dehalogenases: Novel Probes for Mechanistic Studies and Protein Labeling
Computational and Structural Biotechnology Journal Volume 18, 2020, Pages 922-932
Highlights
• The first fluorescent substrates for haloalkane dehalogenases.
• Potent probes for kinetic analysis and high-throughput activity screening.
• Provide high specificity and efficiency for protein labelling.
• Probes for studying protein hydration and dynamics or markers for cell imaging.
• Offer a unique possibility to directly label the enzyme active site.
Ostatní autořiZobrazit publikaci -
Machine Learning in Enzyme Engineering
ACS CATALYSIS 10: 1210-1223
Enzyme engineering plays a central role in developing efficient biocatalysts for biotechnology, biomedicine, and life sciences. Apart from classical rational design and directed evolution approaches, machine learning methods have been increasingly applied to find patterns in data that help predict protein structures, improve enzyme stability, solubility, and function, predict substrate specificity, and guide rational protein design. In this Perspective, we analyse the state of the art in…
Enzyme engineering plays a central role in developing efficient biocatalysts for biotechnology, biomedicine, and life sciences. Apart from classical rational design and directed evolution approaches, machine learning methods have been increasingly applied to find patterns in data that help predict protein structures, improve enzyme stability, solubility, and function, predict substrate specificity, and guide rational protein design. In this Perspective, we analyse the state of the art in databases and methods used for training and validating predictors in enzyme engineering. We discuss current limitations and challenges which the community is facing and recent advancements in experimental and theoretical methods that have the potential to address those challenges. We also present our view on possible future directions for developing the applications to the design of efficient biocatalysts.
Ostatní autořiZobrazit publikaci
Přijatá doporučení
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Zaregistrujte se nyní a zobrazte si profilVíce aktivity od uživatele Jiri
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For the first time, by computing binding affinity changes of interacting proteins from sequence data, we reconstruct complex-informed mutational…
For the first time, by computing binding affinity changes of interacting proteins from sequence data, we reconstruct complex-informed mutational…
Dal(a) líbí se: Jiri Damborsky
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🎓 Last week, I had the privilege of being part of Cecília Castellví Domingo MSc Thesis defence, marking the graduation of our 2nd master student…
🎓 Last week, I had the privilege of being part of Cecília Castellví Domingo MSc Thesis defence, marking the graduation of our 2nd master student…
Dal(a) líbí se: Jiri Damborsky
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Cfold for exploration of conformational space
Cfold for exploration of conformational space
Sdílel(a): Jiri Damborsky
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🍖 Future of Food 🍖 Enantis is at the forefront of the cultured meat revolution. Our thermostable growth factors improve cell culture media, making…
🍖 Future of Food 🍖 Enantis is at the forefront of the cultured meat revolution. Our thermostable growth factors improve cell culture media, making…
Dal(a) líbí se: Jiri Damborsky
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Computational chemistry at GSU Chem: This is what happens when a bunch of the finest QM/MM chemists dare to venture to learn thermodynamic…
Computational chemistry at GSU Chem: This is what happens when a bunch of the finest QM/MM chemists dare to venture to learn thermodynamic…
Dal(a) líbí se: Jiri Damborsky
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Great to see our friends from WhiteLab Genomics leading the way! #Bayer #CoLab David Del Bourgo Nathan Lee
Great to see our friends from WhiteLab Genomics leading the way! #Bayer #CoLab David Del Bourgo Nathan Lee
Dal(a) líbí se: Jiri Damborsky