Transcription factors play central role in many biological processes that range from cell cycle progression to cell differentiation and organism development. Hence, it is not surprising that the functions of these proteins are under tight regulation and their disruption lead to several diseases raging from developmental disorders to cancer. Regulatory mechanisms of these proteins include post-translational modifications, protein partnerships and DNA-binding autoinhibition, which most often occur through intrinsically disordered regions (IDRs) appended to the DNA-binding domain .

In particular, we are investigating the molecular basis of function, regulation and specificity of HOX transcription factors. We are focussing on Drosophila and Human HOX factors. The Drosophila HOX factors have well-defined biological roles and are ideal systems to explore the molecular basis of their function and regulation. The Human HOX factors, on the other hand, are important therapeutic targets for cancer treatment. The longer range goals of this research are to help enable diagnostic and therapeutic strategies for HOX related cancers.

This project is concerned with engineering of intein proteins. Protein splicing is a unique post-translational process that involves the excision of an intervening sequence (intein) from a precursor protein, resulting in the ligation of the flanking sequences (exteins) into a single polypeptide chain. We are using solution NMR spectroscopy and other biophysical methods as well as molecular dynamics simulation to dissect the structural and dynamic basis of intein function. The overall goal of this project is to utilize these structural and dynamic studies to engineer intein proteins for novel applications. We are focusing on two specific applications:

1) design of split inteins with minimal cross reactivity with other split inteins;

2) design of highly specific proteases with minimal undesired cleavage at cryptic sites.

In eukaryotic cells, thousands of reactions occur involving thousands of molecules. To reduce the dilution of the reactants and cross-reactivity leading to undesired non-specific reactions, these molecules are segregated in various compartments, leading to the membrane-bound organelles in the cell. These membranes are impervious to most molecules and only allow passing of molecules across them via active transport mechanisms.

In recent times, it has been found that cells also contain membrane-less organelles termed as 'biomolecular condensates' or 'bio-condensates'. A few examples are nucleolus, p-bodies, cajal bodies and stress granules. Although these cellular entities were known for a long time, their physical characteristics have only recently been discovered. These are formed due to liquid-liquid phase separation (LLPS) and are composed of proteins and nucleic acids. In LLPS certain proteins form a separate liquid phase within the bulk solvent. This separate liquid phase is facilitated by multiple weak intermolecular interactions. Some of these bio-condensates are permanent in nature, such as the nucleolus, while others are condition dependent, such as the stress granules.

We are studying the phase separation behavior of an RNA-binding proteins named RBM3, which is a cold shock proteins.