Research focus

Targets

We perform structure-function analysis of proteins covering new enzymes or enzymes with the potential of novel applications, including sugar-nonspecific nucleases, metal-dependent oxidoreductases, flavin-dependent oxidoreductases and proteases. Most of these projects are targeted towards potential biotechnological applications (food industry, dry goods, waste remediation, etc. ) but some have also potential for utilization in medicine. In some projects we collaborate with the company Novozymes A/S, Denmark, and in other with the laboratory of Petra Lipovová (University of Chemistry and Technology, Prague).

We are also involved in research on natural killer cell surface receptors. In collaboration with the team of Ondrej Vanek (Charles University) we investigate structural properties and complex formation of mammalian NK receptors and their ligands. These results contribute to knowledge in mammalian immunology and have potential for treatment of cancer or viral infections.

Our efforts towards explanation of structure-function questions in bacterial transcription can be utilized in fight against bacteria causing human diseases (collaboration with Libor Krásný, Institute of Microbiology, Czech Academy of Sciences).

Other collaborative projects are aimed for example at explanation of function of sensor proteins (collaboration with M. Martínková, Charles University).

Tools

Atomic resolution analysis of protein structure uncovers important and sometimes intriguing details governing behaviour of biological molecules. Single crystal X-ray crystallography is a powerful tool for structure investigations of proteins, nucleic acids and molecular complexes. In high resolution studies nuances of effects caused by single atom replacement can be observed. For large molecular complexes (even if at low or intermediate resolution) it brings valuable information on fold, domains organization, oligomerization or intermolecular interactions. Crystallization of biomolecules and X-ray diffraction experiments are performed in the Centre of Molecular Structure at our Institute, using our D8 Venture diffractometer with MetalJet X-ray source and also using synchrotron radiation at a number of European sites.

Small angle X-ray scattering enables a relatively easy yet rich-in-information analysis of structure and dynamics of biomolecules. We use it to answer questions about exact oligomerization of our molecules, about overall molecular shape, changes connected with functional protein states or to address basic questions regarding protein-ligand or protein-protein complex formation. The experiments are performed at the Centre of Molecular Structure, using a SAXSPoint 2.0 with MetalJet X-ray source and Eiger X-ray detector. For more advanced SAXS experiments we utilize synchrotron radiation sources, such as PetraIII in Hamburg or Diamond Light Source in the United Kingdom.

Primary research areas

  • Determination of three-dimensional structure of biological macromolecules, mainly proteins and their complexes
  • Structure-function analysis
  • Novel enzymes for medicinal and biotechnological applications
  • Surface receptors of innate immune system
  • Bacterial transcription mechanisms
  • Development of methods of X-ray crystallography

Research tools

  • Bacterial and eukaryotic expression of proteins of interest, protein purification and characterization
  • X-ray crystallography
  • Biophysical techniques, including microscale thermophoresis, dynamic light scattering, surface plasmon resonance, circular dichroism, and other
  • Small angle X-ray scattering
  • Spectroscopic methods

Design and operation of the central structural biology facilities

Since 2008 our group has been involved in designing the Centre of Molecular Structure, IBT, Biocev - the central facilities with technology and expertise for structural biology research. Given our expertise we mainly contributed to design and setup of the crystallization and X-ray facility. We are also involved in operation, securing funding and heavy use of the CMS, as well as integration in the Czech Infrastructure for Integrative Structural Biology and European infrastructure Instruct-ERIC.