The Chemical Biology of Human Gene Function

The Chatterjee lab applies chemical tools to study the mechanistic roles of key proteins found in biochemical pathways associated with human conditions, such as cancers and intellectual disability disorders.

A relatively small number of proteins contribute to the vast array of biochemical pathways underlying human health and development. This requires single proteins to undertake many different functions. Protein Post-Translational Modification (PTM) by structurally and chemically unique moieties that directly change a protein’s overall shape, charge, cellular location, or catalytic activity, enable diverse functions for single proteins.

Our lab applies the powerful tools of Chemical Synthesis, Molecular Biology and Tissue Culture to study how PTMs of disease-associated proteins, such as Histones and Transcription Factors, change their important cellular functions. We seek to uncover the mechanisms and molecular origins of human diseases that result from the mis-regulation of Histone and Transcription Factor function in cells.

Cracking The Histone Code For Health and Disease

Besides commonly studied small-molecule PTMs such as phosphorylation, methylation and acetylation, we also study lesser understood PTMs such as the Small Ubiquitin-like MOdifier protein (SUMO) that is conjugated to protein lysine side-chain amines. By combining the powerful and far-reaching techniques of synthetic organic chemistry and protein semi-synthesis, we produce numerous homogeneously and site-specifically modified proteins. These proteins are investigated in a range of biochemical and biophysical experiments in order to understand how their function changes with changing PTMs. Some biological questions that we are answering include:

Studying The Histone Code For Gene Regulation: We are driven to understand how reversible chemical modifications of the human histone proteins in nuclear chromatin contribute to the DNA-templated processes of gene transcription, replication and repair. Biochemical and biophysical assays with homogeneously modified histones allow us to learn the complex epigenetic code that controls human development and disease.

A Complex Code Of Histone PTMs For Human Gene Function

Studying Regulation of The Tumor Suppressor p53: The transcription factor p53 is a crucial tumor suppressor protein that plays a key role in regulating the cell cycle and preventing cancer. Often referred to as the guardian of the genome, p53responds to DNA damage by activating repair mechanisms, halting the cell cycle to allow for repair, or initiating apoptosis (programmed cell death) when the damage is irreparable. Mutations in the p53 gene are found in ~50% of human cancers, leading to the loss of its tumor-suppressing function and allowing damaged cells to proliferate uncontrollably. The essential activity of p53 in maintaining genomic stability and preventing cancer progression is regulated by a range of PTMs, such as phosphorylation, methylation and acetylation, in the 5 structural domains of p53. We are investigating how PTMs of p53, such as symmetric arginine dimethylation and lysine sumoylation, directly regulate the DNA-binding and transcriptional activity of p53. Our studies are underpinned by the ability to synthesize site-specifically modified full-length p53 using peptide synthesis.

The Regulation of Critical p53 Functions by PTMs

Engineering Novel Biomolecular Condensates: Biomolecular condensates are dense, membrane-less compartments within cells that form through a process called liquid-liquid phase separation. These condensates are made up of proteins, RNA, and other biomolecules that aggregate into liquid-like droplets or gel-like structures. The distinct biochemical environment of condensates allows them to concentrate specific molecules in cells, facilitating various processes such as signal transduction, gene expression, and stress response. Understanding and controlling the formation of biomolecular condensates could lead to novel therapeutic strategies for diseases like neurodegeneration, cancer, or infections. For example, targeting or modulating condensates that form around misfolded proteins would help in treating diseases like Alzheimer’s or Parkinson’s. Controlling the chromatin region undergoing condensate formation in the nucleus could enable selective gene activation or silencing for cancer therapy. Toward our goals, we use the SUMO protein and its engineered forms to generate condensates with well-defined properties in living cells and to study the activity of human enzymes recruited to engineered condensates.

Engineering Biomolecular Condensates In Living Cells

Studying the ZNF292 Protein in Autism Spectrum Disorders: The transcription factor Zinc Finger 292, ZNF292, has been implicated in a range of autism spectrum disorders (ASD) and intellectual disability (ID), as well as cancers. Most ASD/ID-associated mutations of ZNF292 are related to early termination in the last and largest exon, exon 8 that encodes 16 zinc fingers, by frameshift or missense mutations. These mutations lead to the lack of full-length ZNF292 in cells, which may impact its ability to bind DNA and RNA in its normal transcriptional regulatory capacity and prevent the transcription of developmentally important proteins. We are studying the role of the ZNF292 HEAT domain in gene regulation by ZNF292.

HEAT Domain of ZNF292 Transcription Factor

Developing New Reactions for Peptide Synthesis: The synthesis and semi-synthesis of specific modified forms of disease-associated proteins is, in principle, identical to the total organic synthesis of Natural Products such as the anti-cancer drugs Taxol and Vinblastine. Our final synthetic modified protein must be identical to the Natural Product found in living organisms. Synthetic challenges presented by a long stretch of hydrophobic amino acids, amino acids prone to dehydration/cyclization, and the chemical instability of some PTMs, must all be overcome with novel chemical strategies. Toward these goals, we are developing new chemistry to circumvent issues in chemoselectivity and regiospecificity during protein semisynthesis. This includes strategies to synthesize peptide C-terminal thioesters and the development of new selenium (Se) protecting groups for applications in thiol-orthogonal native chemical ligation chemistry.

New Chemical Strategies For Efficient Protein Semi-synthesis