Protein modularity : Structure and interactions by NMR and SPR

Abstract: Protein degradation is a fundamental cornerstone of regulation of protein levels in the human body. For proper function, numerous molecular processes rely on fine-tuned communication through specific interactions between proteins. Tagging proteins by a small protein ubiquitin, called ubiquitination, is mediated by set of ubiquitin-conjugating and transferring enzymes with ubiquitin as well as substrates. This process enables specific selection of  substrate modifications, which is directly coupled to biological activity.In this work, the E3 ligase enzyme TRIM21, a member of the TRIM (tripartite motif) protein family, and its interactions are explored. First, the three-dimensional solution structure of the TRIM21 B-box2 domain solved by nuclear magnetic resonance (NMR) spectroscopy is presented. The structure reveals how different surfaces of the B-box motif are employed for various modular interactions. Using NMR titration experiments, an exposed interaction surface is identified, described as a novel interaction patch where the B-box2 is likely to bind the RING domain. Taken together, this work establishes an extended understanding of the structural role of the B-box2 domain, and how this domain is related to flanking domains in multimodular TRIM proteins.which is conserved in other TRIMs. Additionally, solution scattering provides further information on the complexes and also confirms that TRIM21 RING1-91 is predominantly dimer. We also understand how the acceptor ubiquitin can be transferred to Lysine residue of TRIM211-91.Another highly regulated system is the RNA polymerase-II transcription, which is the first step for all protein synthesis. TATA-box Binding Protein (TBP) is an essential subunit for initiating the gene transcription, which is regulated by number of other transcription factors. Among these, the oncoprotein c-Myc regulates the transcription by directly mediating its interaction with TBP. The interplay of these interaction and competing binding of TBP and c-Myc is studied in this thesis.Conclusively, this thesis highlights TRIM molecular recognition and its interface with E2, and also provides the first glimpse of interaction between TBP and c-Myc.