CPB Seminar - Samrat Mukhopadhyay

9 June 2023

Samrat Mukhopadhyay

​Indian Institute of Science Education and Research (IISER) Mohali

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A Deep Dive into Biomolecular Condensates using Vibrational Raman and Single-Molecule FRET

Formation of biomolecular condensates via liquid-liquid phase separation of intrinsically disordered proteins/regions (IDPs/IDRs) and nucleic acids into membraneless organelles is involved in critical cellular functions and debilitating human diseases. We discovered that the prion protein (PrP) (well-known for its association with mad cow disease and Creutzfeldt-Jakob disease) can undergo phase separation via weak, multivalent, transient intermolecular interactions between the N-terminal IDR that resembles a yeast prion-like domain. An intriguing disease-associated amber stop codon mutation (Y145Stop) of PrP yields a C-terminally truncated intrinsically disordered fragment. We demonstrated that Y145Stop spontaneously phase-separates into highly dynamic liquid droplets under physiological conditions [1]. Upon aging, these highly dynamic liquid droplets undergo a liquid-to-solid phase transition into highly ordered, b-rich, amyloid-like aggregates that exhibit a characteristic autocatalytic self-templating behavior. The propensity for the aberrant phase transition is much lower for the full-length PrP indicating an evolutionarily conserved role of the folded C-terminal domain [1,2]. Our recent results also showed intriguing spatiotemporal modulations in complex coacervation of PrP with other neuronal IDPs (a-synuclein and tau) into heterotypic, multicomponent, multiphasic, multilayered condensates in the presence of RNA [3,4]. If time permits, I will also discuss our surface-enhanced Raman scattering (SERS) and single-molecule FRET (Förster resonance energy transfer) studies that capture exquisite molecular details of biomolecular condensates and dissect the crucial molecular events of phase separation [5, 6].

1. "An intrinsically disordered pathological prion variant Y145Stop converts into self-seeding amyloids via liquid-liquid phase separation". A. Agarwal, S.K. Rai, A. Avni & S. Mukhopadhyay. Proc. Natl. Acad. Sci. USA (2021) 118, 45, e2100968118. https://doi.org/10.1073/pnas.2100968118
2. "Prion Protein Biology Through the Lens of Liquid-Liquid Phase Separation". A. Agarwal & S. Mukhopadhyay. J. Mol. Biol.(2022) 434, 167368. https://doi.org/10.1016/j.jmb.2021.167368 
3. "Spatiotemporal Modulations in Heterotypic Condensates of Prion and α-Synuclein Control Phase Transitions and Amyloid Conversion" A. Agarwal, L. Arora, S.K. Rai, A. Avni & S. Mukhopadhyay. Nature Communications (2022) 13, 1154. https://www.nature.com/articles/s41467-022-28797-5
4. "Heterotypic electrostatic interactions control complex phase separation of tau and prion into multiphasic condensates and co-aggregates" S. K. Rai, R. Khanna, A. Avni & S. Mukhopadhyay. Proc. Natl. Acad. Sci. USA (2023) 120, e2216338120. https://doi.org/10.1073/pnas.2216338120 
5. "Single-Droplet Surface-Enhanced Raman Scattering Decodes the Molecular Determinants of Liquid-Liquid Phase Separation" A. Avni, A. Joshi, A. Walimbe, S. G. Pattanashetty & S. Mukhopadhyay. Nature Communications (2022) 13,4378. https://www.nature.com/articles/s41467-022-32143-0
6. "Single-Molecule FRET Illuminates Structural Subpopulations and Dissects Crucial Molecular Events During Phase Separation of a Prion-Like Low-Complexity Domain" A. Joshi, A. Walimbe, A. Avni, S. K. Rai, L. Arora, S. Sarkar & S. Mukhopadhyay. https://www.biorxiv.org/content/10.1101/2023.05.23.541917v1

Date: 9 June 2023 at 2 pm

Venue: Wolfson Lecture Theatre in the Yusuf Hamied Department of Chemistry

Biography

Professor Mukhopadhyay is the head of the Department of Biological Sciences at IISER Mohali and a Professor of Biology and Chemistry. His research group investigates a wide range of fascinating aspects of intrinsically disordered proteins/regions (IDPs/IDRs) that undergo biomolecular condensation via liquid-liquid phase separation (LLPS) and amyloid formation. For this, they utilize a diverse array of tools and concepts from physical chemistry to chemical biology to biophysics and molecular biology to study the intriguing behavior of IDPs.