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Research

Overview

The human body produces more than a million distinct protein products. Interestingly, it does so from only ~20,000 genes. For years I have been fascinated by how processes such as alternative splicing, post-translational modification, and even post-translational protein splicing contribute to this diversification of the proteome. Studying these processes has not only advanced our general understanding of protein chemistry, but more concretely has led to new strategies for cancer treatment, protein engineering, and disease profiling. Since coming to Tufts, my lab’s research has the common theme of understanding modulation of protein function through changes in protein structure. As part of this work we have uncovered novel mechanisms – both genetic and enzymatic – used by cells to diversify the chemical structure of proteins, and revealed how these alterations modulate protein function. Fundamentally, the research in my lab is guided by three overarching questions:

What cellular mechanisms for modulating protein function remain unexplained?
Investigations of some of the most esoteric molecular processes have led to the most significant advances in the last century. For example, studies of extremophiles led to the discovery of thermophilic DNA polymerases which are the cornerstone of PCR (polymerase chain reaction), a technique that has dramatically increased the progress of molecular sciences since the 1980s. More recently, investigations of the bacterial adaptive immune system were the origins of the CRISPR technology that is currently revolutionizing the field of genome editing. My graduate research arose from preexisting knowledge that Ribonuclease A (RNase A), a small digestive protein from cows, had some capacity to enter and kill human cancer cells. Over the next several years I went on to show that cell entry was a general feature of cationic proteins such as RNase A and their properties could be engineered into other proteins. Even ten years later these principles continue to be used for the engineering of cell-penetrating macromolecules.

My lab at Tufts is exploring the genomic region that encodes the repetitive C-terminal domain (CTD) of RNA polymerase II (RNAPII) because it is prone to genetic rearrangements, a phenomenon first described by Rick Young and colleagues nearly 30 years ago. Using Saccharomyces cerevisiae (baker’s yeast) as a model system, we have characterized genetic factors that contribute to this rearrangement, used this phenomenon to learn something about how the CTD interacts with its partners, and posited an evolutionary role for this genomic instability. We and others have proposed that genetic variation in repetitive protein regions, such as the RNAPII CTD, may provide a source of diversity that allows a cell to tune protein function in response to environmental stress.

What is the best tool to answer our question?
My lab employs traditional and recent approaches from molecular biology, biochemistry, chemistry, computer science and engineering, and, when necessary, we develop new research tools. For example, as a postdoc I was studying how protein factors recognized the protein tail regions of histones. These regions are often enzymatically modified such that in the cell they can exist in hundreds of chemical configurations. Working with a talented peptide chemist, I developed a peptide microarray-based approach to probe the function of discrete structures in high-throughput. Similarly, in my lab at Tufts we have developed several novel tools and techniques ranging from genetic tools that report on genomic rearrangements to microfluidics systems that quantify differences in cellular adhesion.

How can leverage our understanding of protein structure function to help society?
It has been said that a good experiment is "enabling", in that it allows us to do something, technologically or biologically, that we weren’t able to do before. For example, my graduate research on cationic protein transport allowed us to devise better ways to deliver proteins and therapeutics to cells. Likewise, the tools I developed to analyze combinatorial histone modifications have since been used by numerous groups to make more specific antibodies, to probe enzyme substrate specificity, and to elucidate the mechanisms of association for dozens of chromatin-associating proteins.
Studying mechanisms of protein regulation inherently lends itself to the development of resources – whether they are tools to better study protein function, or small molecules drugs that can alter biologically important interactions. We and others, have used our tools for understanding histone post-translational modifications and we have developed several additional tools to help characterize behaviors of yeast cells (e.g. quiescence and adhesion). We are continuing in this vein, concentrating on the evolution of repetitive peptides with novel functions.


Our research is currently funded by:

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