Overview
Doctoral study program: Life Sciences (Faculty of Science, Masaryk University)
Department: CEITEC MU
Form of study: doctoral full time
Supervisor: prof. Mgr. Lukáš Žídek, Ph.D.
Annotation
The PhD project is a continuation of previous studies of the research group, in collaboration with the Libor Krasny of Institute of Microbiology, Academy of Sciences of The Czech Academy of Sciences. Krasny’s lab discovered several proteins of Gram-positive bacteria that play so far little understood roles in transcription regulation. The goal of the project is to combine structural biology approaches to establish relation between structure, biophysical properties, and function of these proteins and other poorly understood bacterial transcription factors. The particular aims include maping of transient interactions of the delta subunit with the RNA polymerase core of Bacillus subtilis, interplay between delta subunit and sigma factors, interactions of a recently discovered transcription factor MoaB2 with mycobacterial sigma factors and RNA polymerases. Cryo-electron microscopy will be used as a major tool to study structures of the proteins in complexes with RNA polymerase. A particular attention will be paid to dynamics of the proteins, that often contain large disordered regions, where cryo-EM data will be combined with results of NMR spectroscopy. As alternative methods, FRET (and potentially EPR in collaboration with V. Laguta) using advanced labelling techniques will be used. The project should result in publications in respected journals with the student being the (shared) first author.
Recommended literature
- Camacho-Zarco et al., Chem. Reviews. 2022, 122, 9331-9356
https://dx.doi.org/10.1021/acs.chemrev.1c01023
- Kubáň et al., J. Am. Chem. Soc. 2019, 141, 16817-16828.
https://dx.doi.org/10.1021/jacs.9b07837.
Research area: Bacterial transcription, proteins important for bacterial infection, structural biology
Keywords:Bacterial RNA polymerase, transcritpion factors, protein dynamics, intrinsically disordered proteins, cryo-electron microscopy, NMR spectroscopy
Funding of the PhD candidate:
Grant proposal submitted to Czech Science Foundation and/or institutional support of the research group.
Requirements for candidate:
Strong background in biophysics and/or physical chemistry, experience with electron microscopy or NMR spectroscopy is an advantage.
Information about the supervisor
https://www.ceitec.eu/prof-lukas-zidek-ph-d/u17604?page=publication
More information on Lukas Zidek Research Group: https://www.ceitec.eu/protein-structure-and-dynamics/rg110
Information about the application process: https://www.ceitec.eu/ls-mm-phd/
Application webpage:
