Electron microscopy (EM) became very competitive method for structure determination of large biomolecules or so called biomolecular machines, e.g. ribosome, during the last decade. Furthermore, it has been proven to be useful in studies of structures of middle-sized to small proteins. This effort has been crowned in the 2020 by reaching another milestone in resolution achieved by cryo-electron microscopy (cryoEM), namely atomic resolution of 1.25 Å achieved by the group of prof. Stark and his co-workers on apoferritin. For the purpose of structural studies, resolution sufficient for correct interpretation of side-chain is in the interval of 1.5-2.5 Å and for the main-chain conformations can be estimated from cryoEM structural data resolved to 3-4 Å.

The aim of this thesis will be determination of structures of proteins involved in transcription processing and interactions with RNA polymerase II – e.g. elongation factor Spt6, in RNA-induced silencing, and in DNA repair mechanisms. The student will use modern software and hardware tools for acquisition, processing, calculation and analysis of structural data acquired on the protein samples mentioned above to obtain high resolution structures of the studied proteins. The student will collaborate with the stuff of Cryo-Electron Microscopy and Tomography Core Facility to profound operation skills during the sample freezing and setting up measurements.

The thesis might be written in Czech, Slovak or English language.

1. Yip, K.M., Fischer, N., Paknia, E., Chari, A., Stark, H.: Atomic-resolution protein structure determination by cryo-EM. Nature 587(7832):157-161 (2020)
2. Punjani, A., Rubinstein, J.L., Fleet, D.J. & Brubaker, M.A.: cryoSPARC: algorithms for rapid unsupervised cryo-EM structure determination. Nature Methods 14, 290-296 (2017)
3. Scheres, S.H.W.: A Bayesian View on Cryo-EM Structure Determination. Journal of Molecular Biology 415(2), 406-418 (2012)
4. Scheres, S.H.W.: RELION: Implementation of a Bayesian approach to cryo-EM structure determination. Journal of Structural Biology 180(3), 519-530 (2012)