Foundations of Biomedical Science (MEDS6448)

Biochemistry II

Ubiquitination and Cancer:
The p53 signaling pathway is a complex multi-component network central to cancer biology. Over 50% of all tumors have mutated tumor suppressor p53. The primary focus of my reasearch is structural and biochemical characterization of proteins and protein complexes of p53 pathway, especially, proteins responsible for maintenance of an appropriate level of p53 in the cell such as E3 ubiquitin ligase Hdm2 and ubiquitin-specific protease USP7. We use structural biology tools, NMR spectroscopy and X-ray crystallography, in conjunction with other biophysical and biochemical methods to determine 3D structures of proteins and characterize their interactions with specific binding partners. Detailed knowledge of protein structure provides the basis for rational design of new drugs suitable for anti-cancer therapies.

Ubiquitination and Epigenetics:
Epigenetic marks work as molecular switches that regulate expression of our genes without altering the DNA sequence itself. It is through epigenetic marks that environmental factors like diet, stress and prenatal nutrition can make an imprint on genes that is passed from one generation to the next. These marks include modifications of histone tails (methylation, acetylation, phosphorylation, ubiquitination, etc) and DNA methylation. Ubiquitination of residue K119 of the histone H2A, for example, is a hallmark of stably repressed developmental genes in stem cells and inactive X-chromosome.

We study Polycomb Repressive Complexes PRC1 and PRC2 responsible for developmental gene suppression and maintenance of “stemness” of a cell. PRC2 and PRC1 are multi-protein enzymatic complexes that methylate histone H3 and ubiquitinate histone H2A resulting in stable gene silencing. We are interested in structural organization of these complexes and molecular mechanism of gene recognition and gene silencing by these multi-subunit repressors.

Our lab studies structure, conformational dynamics and interactions of enzymes of ubiquitin-proteasome pathway relevant to human diseases. We use structural biology tools such as NMR spectroscopy and X-ray crystallography, in conjunction with other biophysical and biochemical methods to determine atomic resolution 3D structures of proteins, characterize their dynamic behaviour, and map their interactions with binding partners. Detailed knowledge of protein structure is used to develop new drugs suitable for anti-cancer therapies.

Rotation Project 1: Screening of small molecule inhibitors of de-ubiquitinating enzyme USP7. This project is part of current NIH-funded research in the lab and directly translates into development of new anti-cancer treatments. A rotation student will gain experience in bacterial expression of recombinant human proteins, many aspects of protein purification, including multiple chromatography techniques, and will be introduced to major structural biology methods such as biomolecular NMR spectroscopy and X-ray crystallography.

Rotation Project 2: The role of conformational dynamics in USP7 function. USP7 is a dynamic enzyme that can adopt active and inactive conformations in solution. Although structure of the enzyme is known it provides only a static snapshot of the enzyme in action.  The aim of this project is to characterize conformational dynamics of the enzyme in solution. This is part of a larger USP7 work that is currently funded by NIH and NSF. A rotating student will learn advanced protein biochemistry and biomolecular NMR.

Rotation Project 3: Analysis of mutations of patients with USP7-related diseases. This project will test the effect of know pathogenic mutations of USP7 on structure and function of the enzyme. During rotation a student will gain extensive experience in moleular biology, protein biochemistry and molecular modeling.

Rotation Project 4: Promyelocytic Leukemia and enzymatic function of PML protein. This project will focus on uncovering enzymatic function of a PML protein implicated in Promyelocytic Leukemia, a type of human cancer. It is a part of a larger NIH-funded project in the lab aimed at understanding molecular mechanism of PML action and discovery of new treatments for Promyelocytic Leukemia. A student is expected to learn advanced protein biochemistry techniques, develop enzymatic assays, become familiar with NMR spectroscopy, and molecular modeling.

Rotation Project 5: Angelman Syndrome and UBE3a enzyme. This project will focus on revealing structural and functional differences between protein isoforms of UBE3a enzyme implicated in Angelman syndrome and autism spectrum disorders. During rotation a student will be exposed to major protein biochemistry and biophysical methods as well as protein modeling approaches. This is a collaborative project with Dr. Chamberlain.

Accepting Lab Rotation Students: Fall Block 2024, Spring 1 and 2 Block 2025

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