Mechanism of protein folding, phase-separation and aggregation

Protein molecules are the working unit of life. They perform numerous functions including chemical catalysis, gene regulation, molecular transport and cell signaling. In order to be functional, they fold into variety of structures by a poorly understood mechanism. Under stressful conditions, they demix and phase-separate into mesoscopic liquid-like assemblies that are metastable and reversible but can form amyloid-like fibers upon chronic stress. TDP-43 (transactive response DNA binding protein 43 kDa) is one such functionally vital protein which is implicated in amyotrophic lateral sclerosis (ALS) and a host of other neurodegenerative ‘TDP-43 proteinopathies’. Using TDP-43 as a model system, we are trying to understand the rules that govern the folding and function of proteins and how they begin to phase-separate and aggregate under disease-like conditions. We employ a highly interdisciplinary approach to address these problems by combining the tools of quantitative biophysical chemistry, protein engineering, molecular biology, and steady-state and time-resolved spectroscopic methods, including fluorescence resonance energy transfer technique, infrared spectroscopy, NMR, hydrogen-deuterium and thiol-disulfide exchange methodologies coupled to mass spectrometry. An understanding of the mechanism by which the structure and dynamics of proteins are altered in the functional and diseased states is essential for effective therapeutic interventions in a range of diseases that result from erroneous folding of proteins.

Selected publications:

1. Doke AA And Jha SK, Effect of in-vitro solvation condition on inter and intra-molecular assembly of full-length TDP-43, J. Phys. Chem. B., IN PRESS, (2022).

2. Patni D And Jha SK, Protonation-deprotonation switch controls the amyloid-like misfolding of nucleic acid binding domains of TDP-43, J. Phys. Chem. B., 125, 30, 8383 - 8394 (2021). 

3. Pillai M And Jha SK, The folding and aggregation energy landscapes of tethered RRM domains of human TDP-43 are coupled via a metastable molten globule-like oligomer, Biochemistry, 58, 608 - 620 (2019).

4. Mishra P And Jha SK, Slow motion protein dance visualized using red edge excitation shift of a buried fluorophore, J. Phys. Chem. B., 123, 1256 - 1264 (2019).

5. Acharya N, Mishra P And Jha SK, Evidence for Dry Molten Globule-Like Domains in the pH-Induced Equilibrium Folding Intermediate of a Multi-Domain Protein, J. Phys. Chem. Lett., 7, 173 - 179 (2016).

6. Jha SK And Marqusee S, Kinetic evidence for a two-stage mechanism of protein denaturation by guanidinium chloride, Proc. Natl. Acad. Sci. USA., 111, 4856 - 4861 (2014).