Structural mechanism of intramembrane proteolysis by rhomboid proteases and its implications for inhibitor design

• Název práce v češtině: Strukturní mechanismus intramembránových proteas z rodiny rhomboidů a jeho implikace pro návrh inhibitorů
• Název v anglickém jazyce: Structural mechanism of intramembrane proteolysis by rhomboid proteases and its implications for inhibitor design
• Akademický rok vypsání: 2019/2020
• Typ práce: disertační práce
• Jazyk práce: angličtina
• Ústav: Katedra genetiky a mikrobiologie (31-140)
• Vedoucí / školitel: Ing. Kvido Stříšovský, Ph.D.
• Řešitel: skrytý - zadáno vedoucím/školitelem
• Datum přihlášení: 11.10.2019
• Datum zadání: 11.10.2019
• Datum odevzdání elektronické podoby: 19.11.2024
• Datum proběhlé obhajoby: 27.01.2025
• Oponenti: prof. Dr. Harald Steiner
• Ocenění: Práce byla navržena na ocenění

Předběžná náplň práce

Rhomboid intramembrane proteases are widespread and fulfil a number of important biological roles with medical potential, such as invasion of the malaria parasite Plasmodium into the host cells, maintenance of mitochondrial homeostasis, fine-tuning of EGF receptor signalling and others. However, the mechanism of these enzymes has not been fully understood and chemical tools for their study and targeting are scarce. My laboratory has been an international leader in both directions, and Ms. Kathrin Bach has an ideal background to advance the research in this area forward, while broadening her scientific horizons.
Kathrin Bach will be carrying out her doctoral research in my laboratory at the Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences in Prague. Kathrin will study the structural and mechanistic aspects of the mechanism of intramembrane proteolysis by rhomboid proteases, applying the mechanistic principles in the design of reversible inhibitors and activity based probes, and using the developed reagents in selected biological context in a chemical biology approach. The inhibitors are based on a platform recently developer in my group (Tichá et al., Cell Chem Biol 2017), and their synthesis and further development is completely feasible. Structural analysis will be carried out and training provided by the closely collaborating laboratories of Dr. Pavlína Řezáčová at IOCB and Prof. Rasmus Linser at the Ludwig-Maximilians-Universität in Munich, DE. Chemical synthesis will be fully provided by the collaborating laboratory of Dr. Pavel Majer at IOCB and Dr. Stanco Stancev therein. The cell biology will be carried out in my laboratory at IOCB and partially in collaboration with expert laboratories, such as that of Prof. Sinisa Urban at the Johns Hopkins University in Baltimore, Maryland, USA (Plasmodium rhomboid proteases). Short research stays in the collaborative laboratories, particularly that of Prof. Linser, are possible and likely, and will provide another level of training for Ms. Bach.
Methodologically, the project will entail expression and purification of recombinant membrane proteins from prokaryotic and eukaryotic expression systems, structural analysis (level of training flexible), enzymatic analysis, cell culture, fluorescence microscopy and others. The PhD project will inherently entail training in independent work with scientific literature, critical thinking, formulation and solving of scientific problems, and presentation of results in written and spoken form in English. All this will equip Ms. Bach with transferrable skills that will help her succeed in future career of her choice, particularly in science. The funding for Kathrin’s project will be provided by my group’s core funding from IOCB, aided by grants from the Czech Science Foundation (2018-2020, project no. 18-09556S), the National Sustainability Fund (project no. LO 1302), the Gilead Sciences Research Center in Prague III (2017-2021), and the European Regional Development Fund (OP RDE) (2018-2022, project no CZ.02.1.01/0.0/0.0/16_019/0000729). I am excited about and agree with acting as the doctoral thesis advisor of Ms. Kathrin Bach during her study in the Molecular and Cell Biology, Genetics and Virology at the Faculty of Science of Charles University in Prague.

Předběžná náplň práce v anglickém jazyce

Rhomboid intramembrane proteases are widespread and fulfil a number of important biological roles with medical potential, such as invasion of the malaria parasite Plasmodium into the host cells, maintenance of mitochondrial homeostasis, fine-tuning of EGF receptor signalling and others. However, the mechanism of these enzymes has not been fully understood and chemical tools for their study and targeting are scarce. My laboratory has been an international leader in both directions, and Ms. Kathrin Bach has an ideal background to advance the research in this area forward, while broadening her scientific horizons.
Kathrin Bach will be carrying out her doctoral research in my laboratory at the Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences in Prague. Kathrin will study the structural and mechanistic aspects of the mechanism of intramembrane proteolysis by rhomboid proteases, applying the mechanistic principles in the design of reversible inhibitors and activity based probes, and using the developed reagents in selected biological context in a chemical biology approach. The inhibitors are based on a platform recently developer in my group (Tichá et al., Cell Chem Biol 2017), and their synthesis and further development is completely feasible. Structural analysis will be carried out and training provided by the closely collaborating laboratories of Dr. Pavlína Řezáčová at IOCB and Prof. Rasmus Linser at the Ludwig-Maximilians-Universität in Munich, DE. Chemical synthesis will be fully provided by the collaborating laboratory of Dr. Pavel Majer at IOCB and Dr. Stanco Stancev therein. The cell biology will be carried out in my laboratory at IOCB and partially in collaboration with expert laboratories, such as that of Prof. Sinisa Urban at the Johns Hopkins University in Baltimore, Maryland, USA (Plasmodium rhomboid proteases). Short research stays in the collaborative laboratories, particularly that of Prof. Linser, are possible and likely, and will provide another level of training for Ms. Bach.
Methodologically, the project will entail expression and purification of recombinant membrane proteins from prokaryotic and eukaryotic expression systems, structural analysis (level of training flexible), enzymatic analysis, cell culture, fluorescence microscopy and others. The PhD project will inherently entail training in independent work with scientific literature, critical thinking, formulation and solving of scientific problems, and presentation of results in written and spoken form in English. All this will equip Ms. Bach with transferrable skills that will help her succeed in future career of her choice, particularly in science. The funding for Kathrin’s project will be provided by my group’s core funding from IOCB, aided by grants from the Czech Science Foundation (2018-2020, project no. 18-09556S), the National Sustainability Fund (project no. LO 1302), the Gilead Sciences Research Center in Prague III (2017-2021), and the European Regional Development Fund (OP RDE) (2018-2022, project no CZ.02.1.01/0.0/0.0/16_019/0000729). I am excited about and agree with acting as the doctoral thesis advisor of Ms. Kathrin Bach during her study in the Molecular and Cell Biology, Genetics and Virology at the Faculty of Science of Charles University in Prague.