Chemical biology of protein post-translational modifications

The complex signaling pathways and biochemical processes in our cells arise from a relatively small number (~21,000) of protein-coding genes. This is achieved, in part, by the large number of reversible chemical reactions that occur on proteins, also called protein post-translational modifications (PTMs). PTMs enable one protein to perform multiple functions by changing its shape, charge, cellular location, or catalytic activity!

Dissecting biology with chemical precision

We are interested in understanding how reversible chemical modifications of therapeutically important proteins, such as histones and transcription factors, influences their biological functions. Understanding the normal functions of PTMs is critical toward understanding several human diseases where these PTMs are either missing, or overabundant. Our long-term goal is to uncover new therapeutic targets for treating human diseases.

The PTM Origins Of Cancer

We specifically study protein PTM by small ubiquitin-like proteins that exist in all kingdoms of life. By combining the powerful techniques of synthetic organic chemistry, molecular biology and protein semisynthesis, we produce chemically modified proteins. These modified proteins are investigated in a range of biochemical and biophysical experiments in order to understand how their function changes with changing PTMs. Three key biological processes that we are studying include:

The language of histone modifications: We would like to understand how different chemical modifications of the histone proteins in human chromatin contribute toward DNA-templated processes such as transcription, replication and repair. Biochemical and biophysical assays with homogeneously modified histones, enabled by chemical synthesis, allow us to simplify and interpret the complexity of signals arriving at and emanating from nuclear chromatin.

The Complex Language Of Histone PTMs

The molecular logic of bacterial protein degradation: We are studying how actinomycete bacteria, such as the dreaded human pathogen Mycobacterium tuberculosis, employ a primitive form of the eukaryotic ubiquitin-proteasome system to survive under conditions of nutrient and oxidative stress. We have developed a series of activity-based probes to investigate the functions and substrate-scope of enzymes associated with the prokaryotic ubiquitin-like protein (Pup). Another goal of the lab is to design inhibitors of protein Pupylation. This is accomplished by using a combination of rational design and high-throughput screening assays.

A Zip-code For Protein Degradation

The regulation of transcription factor activity: Transcription factors are the gatekeepers of cellular function. About 7% of the human proteome is made up of this one class of proteins. Transcription factors function by integrating extracellular signals into complex gene expression patterns. PTMs of transcription factors include acetylation, phosphorylation, glycosylation, ubiquitylation and sumoylation. These different PTMs orchestrate various aspects of transctiption factor function- from subcellular localization to sequence-specific DNA binding and proteasome-mediated degradation. We are using the tools of protein semisynthesis to study how each PTM contributes to the overall activity of a transcripition factor. This will allow us to understand how mutations of amino acids that are modified in key transcription factors contribute to the development and progression of human diseases.

Transcription Factor Binding DNA

To achieve our goals we apply the principles of physical organic chemistry and enzymology in combination with chemical and biological tools. Our research is truly multidisciplinary in nature and lab members have diverse expertise including organic synthesis, analytical and biochemistry. Members of our group gain experience in the synthesis, purification, and characterization of small molecules and proteins and learn how to perform biophysical, biochemical and cell-based assays.