Ph.D. project areas:
1) Assembly of avian reovirus and rotavirus (primary contact Roman Tuma, rtuma(at)prf.jcu.cz)
Viruses are infectious agents causing many diseases of humans, animals as well as crop plants. Design of antiviral drugs that selectively target key steps in viral life cycle requires detailed knowledge of virus structure, replication and assembly in the host cell. Our interest is in the replication of dsRNA viruses belonging to Reoviridae family, avian reovirus and human rotavirus. The former causes significant losses for poultry farms while the latter is causative agent of severe diarrhea in children. Both viruses replicate and assemble inside viral inclusion bodies (VIB), also called viroplasms or viral factories, in the host cell cytoplasm. We have established that VIB are dense, liquid separated phases. Currently, nothing is known about how these liquid inclusions form and how the virus assembles within.
One project will focus on developing model systems and using combination of biophysical techniques (e.g. live cell interference tomography, super-resolution and Raman microscopy) to study formation and phase transitions of VIB which constitute novel target for antiviral therapies. Other projects will focus on the structural biology of reovirus proteins, e.g. the RNA dependent RNA polymerase, virion bound capping complex, various viroplasm forming viral proteins. The techniques used will encompass cryo-electron microscopy, X-ray crystallography, mass spectrometry and computer modelling.
2) TBEV replication (primary contact Zdenek Franta, (at)prf.jcu.cz)
3) Development of hybrid photoactive nanostructures for “green chemistry – light driven chemical nanoreactors
Research projects aim at engineering photosystems and redox enzymes for modular linkage, establishing a virus-based nanocontainer self-assembly system for the photosystems and coupling the photoconverting complexes with redox enzymes to create light driven chemical reactors and characterize their properties. We will utilize the type 2 purple bacterial reaction center from Rhodobacter sphaeroides that is stable under a wide range of conditions and can be genetically manipulated. Photosynthetic complexes will be expressed and purified by established protocols and characterized functionally by UV/VIS spectroscopy (steady state, light induced differential absorption spectra, fluorescence emission spectroscopy). Mass spectrometry and electron microscopy will be used to characterize the complexes for structural integrity.
(primary contact David Kaftan, (at)prf.jcu.cz)
– potential supervisors David Reha, David Kaftan, Roman Tuma
4) Membrane protein dynamics and allosteric regulation (primary contact Tomas Fessl, (at)prf.jcu.cz)
Allosterically modulated molecular machines mediate many of the key processes in all forms of life. The Sec translocon, a membrane bound protein complex, is the principal route for the efficient transport of heterogeneous polypeptides across or into lipid bilayers. The bacterial translocon consists of two main parts, a cytosolic ATPase SecA and membrane channel SecYEG. Based on our group’s recent findings we propose that the Sec translocon is a novel type of stochastically coupled hybrid molecular machine, where the processive SecA steers the energy landscape of a stochastic SecYEG channel allosterically dependent on nucleotide state. We present a research project to map the full allosteric network regulating different stages of protein translocation in the Sec complex using a combination of single-molecule, in silico methods and hydrogen-deuterium exchange mass spectrometry.
Supervision: Tomáš Fessl (single molecules and protein translocation), Joel Crossley (single molecules), David Řeha (computational techniques), Filip Dyčka (mass spectrometry), Alexey Bondar (membrane proteins) and Roman Tůma (macromolecular complexes).
5) Structure based enzyme mechanism (primary contact Ivana Kuta-Smatanova , (at)prf.jcu.cz)
Shorter versions of the above projects are also available as MSc projects
MSc projects:
1) Structure and assembly of light harvesting complexes from green photosythetic bacteria – theoretical approach – supervisors Roman Tuma and David Reha