Investigating Molecular Mechanisms of Biological Phase Separation

In the Shakya lab, we seek to understand how the multitude of biochemical processes occurring inside a cell are organized in absence of lipid membranes, and how the mis-regulation of such membraneless organization lead to diseases. The concept of membraneless condensate formation is helping us explain how among the billions of proteins/RNA molecules in the cell binding partners with a shared function can efficiently colocalize. This concept also presents a potential alternative for combating diseases by designing drugs that target emergent properties of condensates instead of the protein/RNA molecules themselves. This has generated a lot of excitement in disease biology and biomedicine such as neurodegenerative disease and cancer research. To be successful in both understanding disease mechanisms and targeting biological condensates, we need a deeper understanding of condensate properties and function. Our lab aims to provide a foundational framework for condensate formation and stability based on protein native structure and nucleic acid structural features, which can be generally applied to understanding partitioning and concentration of proteins and nucleic acids into various nuclear/cytoplasmic condensates in normal or diseased cellular states. To achieve this, we employ a range of interdisciplinary skills such as thermodynamic analysis, database mining and computation, super-resolution and high-throughput imaging, along with in-vitro reconstitution assays and cell biological techniques.

We are developing innovative methods to uncover the properties of proteins and RNA/DNA that regulate phase separation in cells. Our ongoing research areas are: 1) uncovering the mechanism by which RNA/DNA structure modulates the function of condensates involved in transcription and chromatin remodeling, 2) predicting the phase behavior of proteins (their mutants and post translational modifications) in the presence of their nucleic acid binding partners using single-protein thermodynamics, and 3) developing new super-resolution microscopy methods to reveal the fine details of the multiphase architecture of biomolecular condensates/membraneless organelles in cells.