Research
Time!
Simply known, proteins are the building blocks of life. In a healthy cell, proteins are involved in intricate networks, regulating several crucial cellular processes however, disruption of the protein homeostasis leads to the generation of aberrant cells and proteins, causing fatal diseases like neurodegeneration and cancer. Thus, understanding the structure-function relationship of natural proteins has developed as a major goal in therapeutic research.
My research work solely focuses on protein engineering to explore the structure based function of enzymes of the ubiquitin-proteasome system. Systematic mutational analysis followed by use of a yeast cellular model as well as invitro assays to decipher the effects of individual positions of proteins towards its binding partners are the key approaches carried out in my projects.
Employing Engineered Ubiquitin to investigate modulators of deubiquitinases
Ubiquitin, the central player of this proteasome system, interacts via a common binding surface with large, diverse surfaces of enzymes and target proteins with low binding affinity but high specificity. This paradigm led to the use of ubiquitin as a general scaffold to generate tight-binding inhibitors for any of the ubiquitin-binding proteins. Ataxin-3 is one of the best-characterized DUBs (deubiquitinating enzymes) in the family of Machado-Joseph deubiquitinases, with its implication in the progression of Spinocerebellar Ataxia 3 (SCA3). SCA3 results from an abnormal expansion of glutamine repeat in the coding region of gene encoding Ataxin-3, triggering the formation of Ataxin-3 aggregates. Moreover, deregulation of this DUB is also associated with multiple pathologies, including tumor progression and cancer metastasis. Hence, our first approach is to scan for interactive motifs between ubiquitin and Ataxin-3 with variable binding efficiency and further utilize them for the formulation of selective inhibitors.
What's more intriguing is the diversity of human DUBs and their deregulation causing several severe diseases like cancer and neurodegeneration. However, it is challenging to look for specific inhibitors for each of these abrogative DUBs. Ubiquitin, interacts with these DUBs through a unique patch of residues, thus being the sole candidate to be modulated for regulating DUB activity. The DUB-ubiquitin interface holds great value in defining the structure-function relationship of these two proteins and elucidating the strong binding ubiquitin variants for DUB inhibition. Thus, our next approach focuses on the understanding the critical ubiquitin binding interfaces to screen for ubiquitin variants involved in modulating specific DUB function in normal health and disease.
Conclusively, with these technologies, my goal is to better understand the structural and molecular basis of this small yet complicated protein ubiquitin, and to use this knowledge for development of specific therapeutic alternatives for treatment of fatal diseases.
