Finished grants:

  • Molecular mechanisms of DNA regulatory segment recognition by MADS box family transcription factors

    Grant agency: GAUK
    Identification number of grant: 402111
    Head of the project: Mgr. Barbora Řezáčová
    Vice-head of the project: Prof. RNDr. Josef Štěpánek, CSc., Mgr. Pavla Ottová, RNDr. Václav Profant

    Grant annotation
    This project is focused on study of physico-chemical properties and formation of complexes between the MADS-box family transcription factors and the DNA regulatory segment. The aim of the project is to elucidate the functional role of the MADS-box in the specific recognition of the CArG-box CC (A/T)6GG containing DNA segment. Geometry and dynamics of model oligomers, protein, and their complex will be characterized by spectroscopic techniques, in particular Raman and UV absorption spectroscopy, both stationary and time-resolved fluorescence measurements including stopped-flow method and fluorescence anisotropy decay. To complete the thermodynamic characteristics, microcalorimetric measurements (DSC) will be employed. Within the first year of the project, the effect of environmental conditions, mainly pH, temperature, and presence of selected cations, on the conformational stability of the model oligonucleotides, protein and protein-oligonucleotide complex will be determined and the impact of the MADS-box complex formation with the target DNA segment on its Raman spectrum, fluorescence emission and fluorescence anisotropy will be described. Next stage of the project solution will be devoted to dynamics study of the DNA segment, model proteins, and their complexes by fluorescence anisotropy decay measurement of both the intrinsic fluorophores (Tyr) and fluorescence labels and/or probes.

  • Application of Raman optical activity to dynamic peptide folding

    Grant agency: GAUK
    Identification number of grant: 126310
    Head of the project: Jana Hudecová (Institute of Organic Chemistry and Biochemistry AS CR, v.v.i.)
    Vice-head of the project: Prof. RNDr. Vladimír Baumruk, DrSc., RNDr. Petr Bouř, DSc. (Institute of Organic Chemistry and Biochemistry AS CR, v.v.i.), RNDr. Václav Profant, Mgr. Ivan Ivani ()

    Grant annotation
    Modern spectroscopic methods exploring the Raman optical activity provide enhanced information about the structure and dynamics of studied systems. The geometry and conformations of molecules can be deduced from the spectra using advanced simulation techniques that are being jointly developed by MFF UK and IOCB AS CR. In this project we will use and develop combined quantum and classical simulation techniques needed for simulations of flexible peptide structures. Such simulations are difficult, but they are important for many applications of the ROA technique in biochemistry. We will study namely model peptides with restricted conformational flexibility and continue to synthetic prion fragments studied as a model for neurodegenerative diseases, synthetized at IOCB AS CR.

  • Studium nanočástic v molekulových paprscích

    Grant agency: GAUK
    Identification number of grant: 257852
    Head of the project: RNDr. Václav Profant
    Vice-head of the project: Doc. RNDr. Juraj Dian, CSc. (), Mgr. Michal Fárník, Dr. (), Ing. Viktoriya Poterya, Dr. ()

    Grant annotation
    None