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Proteomics for beginners
Hubálek, Martin ; Vrbacký, M. ; Křenková, Alena
Proteomic tutorial for the beginners will summarise and present current methods to analyse and evaluate proteomic samples. The tutorial will be divided into two parts. The first part will focus on data accquisition process and interpretation of spectra. The second part will focus on protein quantification.
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Structural characterization of dsDNA and transcription factor interactions
Kadavá, Tereza ; Novák, Petr (advisor) ; Hubálek, Martin (referee)
Transcription factors from TEAD protein family play an important role in various eukaryotic regulatory processes. They are partly responsible for cell differentiation and apoptosis due to their involvement in the Hippo signalling pathway. Scientific interest in this protein family is mainly because they are associated with carcinogenesis. DNA-binding domain of TEAD transcription factors interacts with M-CAT element of double-stranded DNA, which is present also in enhancer and exon of C-MYC gene. Interaction between TEAD1 DNA-binding domain and C-MYC dsDNA was investigated in this bachelor's thesis mainly by ion mobility in connection with mass spectrometry using native nESI ionization. For the further analysis of TEAD1-DBD and its complexes with dsDNA, the protein was firstly recombinantly expressed by the optimized protocol in our laboratory. Investigation of TEAD1-DBD and its complexes was done using two IM-MS activations. Firstly, the collision-induced unfolding was performed and afterwards perturbation of the sample by preheating nESI emitter was done. The first activation led to the collision- induced unfolding of some charge states of TEAD1-DBD protein and both protein-DNA complexes. The second activation performed by heating of nESI emitters led to temperature melting of both dsDNA and...
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