ITQB: IMAC - PhD Theses
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- Unravelling Protein InteractionsPublication . Paiva, Ana Catarina F.; Matias, Pedro; Bandeiras, Tiago"Protein-protein interactions (PPIs) are essential for almost all biological processes, orchestrating crucial cellular activities such as signal transduction, metabolic regulation, gene expression, and structural organization. These interactions enable proteins to dynamically coordinate complex cellular tasks. Consequently, key PPIs are implicated in numerous diseases, including cancer, neurodegenerative disorders and infections, highlighting their importance as therapeutic targets. However, despite their significance, studying PPIs can be challenging due to their transient and dynamic nature.(...)"
- Cellular Assembly Machineries: Integrated structural and biochemical studies of human AAA+ proteins RuvBL1 and RuvBL2Publication . do Espírito Santo, Paulo Filipe Ribeiro; Matias, Pedro; Bandeiras, Tiago"The work described in the present dissertation concerns the study of RuvBL1 and RuvBL2 from the AAA+ ATPases super family, which can be divided in three different parts. One part describes the study of the RuvBL1/RuvBL2 complex. The second part describes the study of the R2TP and an R2TP-like complex called R2SP, which integrate the RuvBL1/RuvBL2 complex, and work as molecular hubs for the assembly of multi protein complexes. The third part concerns two adaptor proteins which assist the hubs in their assembly activities(...)"
- Structural insights into the human multifunctional protein RuvBL2Publication . Silva, Sara Teresa Neves da; Matias, Pedro; Bandeiras, Tiago"RuvB-Like transcription factors, RuvBL1 and RuvBL2, function in cell cycle regulation and development. They have been attributed the functions of chaperone, transcription regulator and helicase, sometimes in an ATP-dependent fashion, but just how these functions are regulated in each protein is still a mystery, that many groups have been working to understand. There is already a vast, albeit scattered amount of knowledge gathered about RuvBL1 and RuvBL2 proteins.(...)"
- Structure-function relationships in a glycosyltransferase, a phosphatase and an oxidoreductasePublication . Gonçalves, Susana; Matias, P. M.Enzyme evolution is often constrained by aspects of catalysis. Mechanistically diverse enzymes evolved from a common ancestor still preserve those structural signatures essential to the core chemistry retained by all members of the superfamily. Indeed, these shared features allow superfamilies to be accurately classified, while derived features allow nested families and subfamilies to be identified in a hierarchical fashion. Accurate classification has helped elucidate mechanisms promoting functional diversification, for example catalytic promiscuity, and protein engineering by rational design. Nowadays, a holistic view of enzymes` regulatory mechanisms and catalytic proficiency is provided by the identification of conserved features of molecular architecture in combination with aspects of reaction dynamics. My work focused on the structural elucidation and analysis of three enzymes: a glycosyltransferase; a phosphatase and an oxidorreductase. “Snapshots” along the reaction coordinate of each enzyme were obtained by combining X-ray diffraction with “cryo-trapping” ligand-binding methods. These were used to characterize the molecular mechanisms involved in substrate recognition and binding. They were also used to distinguish between models proposed for the catalytic mechanisms of each enzyme, and provide insights into enzyme dynamics essential for catalysis and the stereo and regio-selective strategies at work.(...)