Laboratory of Structural Chemistry

Macromolecular X-ray Crystallography is a technique used to study biological molecules such as proteins, viruses and nucleic acids (RNA and DNA) to an atomic resolution. This high resolution helps elucidate the detailed structure-based mechanism by which these macromolecules carry out their functions in living cells and organisms.


Laboratory description: 

 The Laboratory of Structural Chemistry consists of three sub laboratories and one training part:

 MolBiol - is the laboratory of molecular biology designed for isolation and purification of proteins,

 XtallExp – is the laboratory for crystallization experiments aimed at production of diffractable crystals. Obtained crystals are measured at the synchrotron radiation sources and diffraction data are used for solving of protein structure,

 MolStruct – is the lab for molecular modeling and structural studies following by molecular dynamics studies,

 XtallTraining – offers other colleagues with the interest of crystallization of proteins possibility to crystallize own proteins by themselves or with the help of our specialists

Key activities:

  1. basic research in the field of isolation and purification of proteins and their crystallization
  2. solving of protein structures from diffraction data and structural studies of studied proteins
  3. development and testing of alternative and advanced crystallization techniques
  4. close cooperation with affiliated laboratories in the Czech Republic and abroad
  5. training of others about crystallization of own proteins
  6. teaching of Inorganic chemistry 1 (UCH/100), Inorganic chemistry 2 (UCH/101), Organic chemistry for biology (UCH/032) a Biocrystallization methods (UCH/253) in czech
  7. organization of international courses under auspices of FEBS named FEBS-INSTRUCT practical crystallization course „Advanced methods in macromolecular crystallization“

International cooperation:

Prof. Joseph Ng team University of Alabama in Huntsville, USA in the Department of Biological Science.

Dr. math. et dis. nat. Jeroen R. Mesters – a senior Researcher and Lecturer, Deputy of Universität zu Lübeck, Institut für Biochemie at Lübeck, Germany.

Dr. Monika Budayova-Spano – Assistant Professor – HDR, University Joseph Fourier Grenoble, Institut De Biologie Structurale, Umr5075 CEA-CNRS-UJF, Grenoble, France

Dr. José A. Gavira-Gallardo Research Scientist of Laboratorio de Estudios Cristalográficos

Instituto Andaluz de Ciencias de la Tierra, (CSIC-UGR) Armilla, Granada, Spain

Dr. Pavlina Rezacova a head of the Senior Research Group of Structural Biology at Institute of Organic Chemistry and Biochemistry AS CR

Doc. Radka Chaloupková, Ph.D. - Research Scientist at Loschmidt Laboratories, Department of Experimental Biology and Research Centre for Toxic Compounds in the Environment RECETOX, Masaryk University, Brno, Czech Republic

Infrastructure: 

 

Fully-equipped biochemical laboratories and Laboratory of Crystallogenesis and Macromolecular Crystallography (Assoc. Prof. Ivana Kuta-Smatanova, PhD) at University of South Bohemia (Faculty of Sciences, Ceske Budejovice), well-appointed with crystallization robotic system Oryx 3, Dynamic Light scattering instrument,  analytical balances, IWA distiller for redistilled water, deep-freeze, iceboxes, cold-room, incubators,  ice generator, pH-meters, SDS-PAGE and horizontal electrophoresis, Western blot system, PCR thermocycler, ultracentrifuge Beckman, low speed cooled centrifuges, table centrifuges, spectrophotometer, cells disintegrator, high-magnificence stereomicroscopes, photocameras, Eppendorf pipette sets, commercial crystallization and molecular kits, chemicals, crystallization plates and all necessary plastic and glass for the  cultivation, biochemical and crystallization experiments. 

Computational laboratory is well equipped by international standards for computational chemistry (Cluster of the Beowulf type with nodes connected by Myrinet, Graphics work stations with 3D, 2 computer labs, licenses for Gaussian09, Amber10, Gromacs, modeler, Yasara, autodock etc.) as well fully equipped lab to perform all tasks of structural analysis of biological macromolecules by X-ray crystallography with computational hardware and software necessary for the diffraction data processing, structure determination, macromolecular structure refinement, validation and analysis (XDS, XDSapp, CCP4 program package, Coot, PyMol, IMosflm and others).

For the diffraction quality crystals could be tested at home X-ray diffractometer D8 Venture source from Bruker at Institute of Institute of Nanobiology and Structural Biology, Institute of Microbiology, Academy of Sciences of the Czech Republic and later on will be prepared for the data collection experiments on the synchrotron. Diffraction measurements could be performed on synchrotron macromolecular beamlines BESSY (Berlin, Germany), DEZY (Hamburg, Germany) or ESRF (Grenoble, France) following standard application procedures.