Protein Structure and Dynamics - Lukáš Žídek
Protein Structure and Dynamics - Lukáš Žídek


Prof. Lukáš Žídek, Ph.D. Prof. Lukáš Žídek, Ph.D.
Research Group Leader
Jozef Hritz, Ph.D. Jozef Hritz, Ph.D.
Senior Researcher

Research areas

  • Structure, dynamics and interactions of proteins
  • Intrinsically disordered proteins
  • Development and application of NMR methodology

Main objectives

  • Development of new methodologies for the investigation of biomolecular structures, interactions, and dynamics.
  • Investigations of the biomolecular structures and interactions and their relationship with physiological functions, diseases and therapies.
  • Production of pure and homogeneous proteins for the structural analysis.
  • Production of monoclonal antibodies, with emphasis on the quality of the antigen – antibody selection.  Selection of binding molecules from synthetic DNA libraries for diagnostic and therapeutic use.

Content of research

In collaboration with L. Krasný (Institute of Microbiology, Academy of Sciences of the Czech Republic, Prague, Czech Republic), we study subunits and sigma-factors unique for RNA polymerase of Gram-positive bacteria. We have determined structure of well-ordered N-terminal domain of delta subunit and characterized structural features of its intrinsically disordered C-terminal domain. In addition to the structural description, we characterized dynamics of both domains at various time scales using NMR relaxation. Investigation of other subunits and sigma-factors is in progress.

Multidisciplinary research of proteins involved in plant hormone signaling cascades is an example of a collaborative project within CEITEC (J. Hejtko, Functional Genomics and Proteomics of Plants). We have studied dynamics of receiver domain of the sensory kinase CKI1 and characterized its interactions with Mg(2+) ions and a phosphate analogue. We are involved in characterization of interactions of the CKI1 receiver domain with its down-stream partners and in structural studies of other sensory kinases (e.g. ETR1).

Traditionally, the strength of the group has been development of NMR methodology for atomic-resolution studies of proteins and nucleic acids. Recently, several fruitful collaborations witnessed that we are able to apply our know-how to solve real biological problems that were hard to attack by the conventional approaches. In the future, we would like to continue to develop in this direction and to complement the existing successful collaboration with our own projects. We plan to study dynamics, structural properties, function and regulation of Microtubule Associated Protein 2c (MAP2c), a cytoskeletal protein important for development of neuronal cells. The free form of the protein is disordered and relatively large (49 kDa), which makes it a challenging target for NMR. Our preliminary results show that the methodology developed in our group is sufficient for such a type of molecule.

3D structure of the delta subunit of RNA polymerase from Bacillus subtilis including disordered C-terminal tail determined by NMR spectroscopy.