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Degree of protein structure disorder in prokaryotic and eukaryotic organisms
Nováková, Zuzana ; Vondrášek, Jiří (advisor) ; Feidakis, Christos (referee)
The structure-function paradigm of protein biology has been fundamentally changed in the last three decades by the discovery of intrinsically disordered proteins (IDPs) and regions (IDRs). These proteins have been identified as critical components in various cellular processes, including signaling, protein-protein interactions, and regulation. While it is apparent that IDPs/IDRs are vital in the function of living organisms, the study of their structure has posed a great challenge. Despite recent advancements in NMR spectroscopy and deep learning algorithms for protein structure prediction, IDPs/IDRs remain a relatively unnkown territory, with significant gaps in knowledge about their behavior and function in living systems. Although IDPs are present in all life forms, their abundance reveals a correlation between organismal complexity and degree of protein disorder. Prokaryotic organisms exhibit a much lower prevalence of IDPs than eukaryotic. Notably, a substantial degree of disorder is observed in unicellular parasitic protists, implying, that IDPs are fundamental in pathogenesis and the progression of diseases like malaria and toxoplasmosis. In humans, malfunctions in IDPs are linked to many conditions, including neurodegenerative diseases such as Parkinsons's, Alzheimer's as well as various...
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Specific heme interaction modulates the conformational dynamics and function of p53
Sergunin, Artur ; Martínková, Markéta (advisor) ; Dračínská, Helena (referee)
Tumor suppressor p53 is one of the most studied proteins in terms of cancer and the mechanism of its formation. The general function of p53 is based on the transcriptional regulation of various genes, which can differently influence numerous cellular processes. Recent studies revealed a relationship between p53 and iron homeostasis within the cell. In particular, p53 was shown to interact with a molecule of heme, and this interaction ultimately disrupts the DNA-binding ability of p53 and promotes its proteasomal degra- dation. This work focuses on a detailed description of heme binding to the p53. For this purpose, we isolated two forms of p53, heme-free and heme-bound. We discovered that conformational dynamics of heme-free and heme-bound p53 differ, with the latter exhibi- ting a higher degree of flexibility. We also confirmed previous reports that heme indeed interacts with a cysteine residue in a specific manner. However, heme binding does not disrupt the oligomeric state of p53 or its native zinc binding ability. Finally, we showed that heme-bound p53 exhibits severely impaired DNA-binding ability as opposed to the heme-free form. Keywords: heme, sensor proteins, p53 protein, transcription factor, intrinsically disor- dered proteins
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Structural characterization of selected random protein sequences with high disorder content
Ptáčková, Barbora ; Hlouchová, Klára (advisor) ; Šilhán, Jan (referee)
An infinitesimal fraction of the practically infinite sequence space has achieved enormous functional diversity of proteins during evolution. Intrinsically disordered proteins (IDPs) which lack a fully defined three-dimensional structure are the most likely precursors to today's proteins because of their flexible conformation and functional diversity. But how have these proteins evolved into often rigid and highly specialized protein structures? This evolutionary trajectory has the greatest support in the theory of induced fold whereby the development of the structure was mediated by the interaction and coevolution of primordial unstructured proteins with different cofactors or RNA molecules. Although some random sequences from the sequence space which is not used by nature are also able to form folded proteins the more suitable candidates for evolution of structure and function appear to be random sequences with a high content of disordered which have low aggregation propensity. The selected random protein sequences with high disorder content have been structurally characterized in this work for their further use in evolutionary studies. Three artificial proteins were selected from a random-sequence library based on previous study in our laboratory. In the present work they were purified and...
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