Research in Samrat Mukhopadhyay's Lab at IISER Mohali

Broad area:

Biophysical Chemistry, Biological Chemistry, Molecular Biophysics, and Chemical Biology

Specific interests:

Intrinsically Disordered Proteins (IDPs), Prions, Amyloids, and Liquid Droplets; Conformational Characteristics, Membrane Binding, and Phase Transition of IDPs; Liquid-Liquid Phase Separation, Misfolding, and Aggregation; Ultrafast Spectroscopy; Fluorescence & Raman Spectroscopy and Microscopy; Single-Molecule/Nanoscale Biophysics and Super-resolution Imaging.

Summary:

Proteins are the workhorses of the living systems. Traditionally, protein function was thought to depend on a unique well-defined 3D structure that is encoded by the amino acid sequence. However, current investigations have revealed that a large fraction of the proteome consists of polypeptide segments that lack a well-defined structure under physiological conditions. They belong to a distinct class of proteins termed as intrinsically disordered proteins (IDPs) that challenge the tenets of the traditional structure-function paradigm. The intrinsic disorder in the proteins allows the complex organisms to carry out multiple functions from the same proteins by adopting different conformational states. However, the disorder-to-function relationship is poorly understood. Additionally, the dysfunction of many IDPs is associated with a range of deadly diseases such as Alzheime r's disease, Parkinson's disease, Amyotrophic lateral sclerosis (ALS), frontotemporal dementias (FTDs) and cancers. The overarching goal of our lab is to understand the fundamental conformational characteristics of IDPs that undergo phase separation and amyloid formation that are related to human physiology and disease. We utilize a diverse range of approaches involving biophysics, biochemistry, chemical biology, cell, and molecular biology, and advanced single-molecule and ultrafast spectroscopy to gain molecular insights into the conformational ensemble and dynamics, the protein hydration water, liquid-liquid phase separation, aggregation and amyloid formation from various IDPs containing low-complexity and prion-like domains. These studies are beginning to illuminate the unique molecular insights into the pivotal functional and pathological aspects of phase transition of IDPs. We are addressing the following specific aspects:

Specific areas, representative publications and current lab members involved on the project:

• Liquid-liquid phase separation of IDPs into liquid droplets: Implications in Alzheimer's disease and ALS

Publications:

"Intermolecular Charge-Transfer Modulates Liquid–Liquid Phase Separation and Liquid-to-Solid Maturation of an Intrinsically Disordered pH-Responsive Domain" P. Dogra, A. Joshi, A. Majumdar, & S. Mukhopadhyay* J. Am. Chem. Soc. 2019, 141, 20380-20389. Link

"Liquid-Liquid Phase Separation is Driven by Large-Scale Conformational Unwinding and Fluctuations of Intrinsically Disordered Protein Molecules" A. Majumdar, P. Dogra, S. Maity & S. Mukhopadhyay* J. Phys. Chem. Lett. 2019, 10, 3929-3936. Link

Lab members: Priyanka Dogra, Anupa Majumdar, Ashish Joshi, PG Swastik, Sandeep Rai and Anusha Sarbahi

• Interaction of conformationally distinct oligomers of amyloid-β peptides with the prion protein: Implications in Alzheimer's disease

Publication:

"Preferential Recruitment of Conformationally Distinct Amyloid-β Oligomers by the Intrinsically Disordered Region of the Human Prion Protein" P. Madhu & S. Mukhopadhyay* ACS Chem. Neurosci. 2020, 11, 86-98. Link

Lab member: Priyanka Madhu

• Mechanism of protein misfolding, aggregation, and amyloid formation: Implications in Alzheimer's, Parkinson's and prion diseases

Publications:

"Synergistic Amyloid Switch Triggered by Early Heterotypic Oligomerization of Intrinsically Disordered α-Synuclein and Tau" K. Bhasne, S. Sebastian, N. Jain, & S. Mukhopadhyay* J. Mol. Biol. 2018, 430, 2508-2520.

"Human Fibrinogen Inhibits Amyloid Assembly of Biofilm-Forming CsgA" H. M. Swasthi,* K. Bhasne, S. Mahapatra, & S. Mukhopadhyay* Biochemistry 2018, 57, 6270-6273.

"Electrostatic lipid-protein interactions sequester the curli amyloid fold on the lipopolysaccharide membrane surface" H.M. Swasthi & S. Mukhopadhyay* J. Biol. Chem. 2017, 292, 19861-19872.

"pH-Responsive Mechanistic Switch Regulates the Formation of Dendritic and Fibrillar Nanostructures of a Functional Amyloid" P. Dogra, M. Bhattacharya & S. Mukhopadhyay* J. Phys. Chem. B. 2017, 121, 412-419.

"Detergent-induced Aggregation of an Amyloidogenic Intrinsically Disordered Protein" S. Arya, P. Dogra, N. Jain & S. Mukhopadhyay* J. Chem. Sci. 2017, 129, 1817–1827.

"Characterization of Salt-Induced Oligomerization of Human β2-Microglobulin at Low pH" D. Narang, A. Singh, H.M. Swasthi & S. Mukhopadhyay* J. Phys. Chem. B. 2016, 120, 7815-7823.

"Structural and Dynamical Insights into the Molten-globule form of Ovalbumin" M. Bhattacharya & S. Mukhopadhyay* J. Phys. Chem. B 2012, 116, 520-531.

Lab members: Priyanka Dogra, Lisha Arora, Anamika Avni and Sandeep Rai

• Misfolding of the prion protein

Publications:

"Energy Migration Captures Membrane-Induced Oligomerization of the Prion Protein" A. Agarwal, D. Das, T. Banerjee & S. Mukhopadhyay* BBA - Proteins and Proteomics, 2020, 1868, 140324.

"Confined Water in Amyloid-Competent Oligomers of the Prion Protein" V. Dalal, S. Arya, & S. Mukhopadhyay* ChemPhysChem 2016, 17, 2804-2807.

"Conformational Switching and Nanoscale Assembly of Human Prion Protein into Polymorphic Amyloids via Structurally-Labile Oligomers" V. Dalal, S. Arya, M. Bhattacharya & S. Mukhopadhyay* Biochemistry 2015, 54, 7505−7513.

Lab members: Aishwarya Agarwal

• Membrane-interaction and aggregation of a-synuclein, a Parkinson's disease-associated IDP

Publications:

"Discerning Dynamic Signatures of Membrane-Bound α-Synuclein Using Site-Specific Fluorescence Depolarization Kinetics" K. Bhasne, N. Jain, R. Karnawat, S. Arya, A. Majumdar, A. Singh & S. Mukhopadhyay* J. Phys. Chem. B. 2020 (in press)

"Structural and Dynamical Insights into the Membrane-bound α-Synuclein" N. Jain, K. Bhasne, M. Hemaswasthi, and S. Mukhopadhyay* PLoS ONE 2013, 8(12):e83752.

Lab member: Anupa Majumdar and Lisha Arora

• Conformational characteristics of IDPs

Publications:

"Fluorescence Depolarization Kinetics to Study the Conformational Preference, Structural Plasticity, Binding, and Assembly of Intrinsically Disordered Proteins" A. Majumdar and S. Mukhopadhyay* Methods in Enzymology 2018, 611, 347-381.

"Direct Observation of the Intrinsic Backbone Torsional Mobility of Disordered Proteins" N. Jain, D. Narang, K. Bhasne, V. Dalal, S. Arya, M. Bhattacharya, & S. Mukhopadhyay* Biophys. J. 2016, 111, 768-774.

"Chain Collapse of an Amyloidogenic Intrinsically Disordered Protein" N. Jain, M. Bhattacharya & S. Mukhopadhyay* Biophys. J. 2011, 101, 1720-1729.

Lab members: Debapriya Das and Lisha Arora

• Biological water in IDPs: Role of hydration water in aggregation

Publications:

"Femtosecond Hydration Map of Intrinsically Disordered α-Synuclein" S. Arya, A. Singh, K. Bhasne, P. Dogra, A. Datta,* P. Das,* & S. Mukhopadhyay* Biophys. J. 2018, 114, 2540–2551.

"Water Rearrangements upon Disorder-to-Order Amyloid Transition" S. Arya, A. K. Singh, T. Khan, M. Bhattacharya, A. Datta,* & S. Mukhopadhyay* J. Phys. Chem. Lett. 2016, 7, 4105-4110.

"Confined Water in Amyloid-Competent Oligomers of the Prion Protein" V. Dalal, S. Arya, & S. Mukhopadhyay* ChemPhysChem 2016, 17, 2804-2807.

"Ordered Water within the Collapsed Globules of an Amyloidogenic Intrinsically Disordered Protein" S. Arya and S. Mukhopadhyay* J. Phys. Chem. B. 2014, 118, 9191–9198.

Lab members: Priyanka Dogra, Debapriya Das and Lisha Arora

• Functional prions and amyloids

Publications:

"Human Fibrinogen Inhibits Amyloid Assembly of Biofilm-Forming CsgA" H. M. Swasthi,* K. Bhasne, S. Mahapatra, & S. Mukhopadhyay* Biochemistry 2018, 57, 6270-6273.

"Electrostatic lipid-protein interactions sequester the curli amyloid fold on the lipopolysaccharide membrane surface" H.M. Swasthi & S. Mukhopadhyay* J. Biol. Chem. 2017, 292, 19861-19872.

"pH-Responsive Mechanistic Switch Regulates the Formation of Dendritic and Fibrillar Nanostructures of a Functional Amyloid" P. Dogra, M. Bhattacharya & S. Mukhopadhyay* J. Phys. Chem. B. 2017, 121, 412-419.

"Site-Specific Fluorescence Depolarization Kinetics Distinguishes the Amyloid Folds Responsible for Distinct Yeast Prion Strains" D. Narang, H.M. Swasthi, S. Mahapatra & S. Mukhopadhyay* J. Phys. Chem. B. 2017, 121, 8447-8453.

Lab members: Priyanka Dogra, Sayanta Maha Patra, Anusha Sarbahi and Ashish Joshi

• Method developments and adaptation of fluorescence and Raman spectroscopy/imaging and nanobiophysics

Publications:

"Intermolecular Charge-Transfer Modulates Liquid–Liquid Phase Separation and Liquid-to-Solid Maturation of an Intrinsically Disordered pH-Responsive Domain" P. Dogra, A. Joshi, A. Majumdar, & S. Mukhopadhyay* J. Am. Chem. Soc. 2019, 141, 20380-20389. Link

"Liquid-Liquid Phase Separation is Driven by Large-Scale Conformational Unwinding and Fluctuations of Intrinsically Disordered Protein Molecules" A. Majumdar, P. Dogra, S. Maity & S. Mukhopadhyay* J. Phys. Chem. Lett. 2019, 10, 3929-3936. Link

"Fluorescence Depolarization Kinetics to Study the Conformational Preference, Structural Plasticity, Binding, and Assembly of Intrinsically Disordered Proteins" A. Majumdar and S. Mukhopadhyay* Methods in Enzymology 2018, 611, 347-381.

"Direct Observation of the Intrinsic Backbone Torsional Mobility of Disordered Proteins" N. Jain, D. Narang, K. Bhasne, V. Dalal, S. Arya, M. Bhattacharya, & S. Mukhopadhyay* Biophys. J. 2016, 111, 768-774.

"Appearance of Annular Ring-like Intermediates during Amyloid Fibril Formation from Human Serum Albumin" S. Arya, A. Kumari, V. Dalal, M. Bhattacharya & S. Mukhopadhyay* Phys. Chem. Chem. Phys. 2015, 17, 22862-22871.

"Nanophotonics of Protein Amyloids" M. Bhattacharya & S. Mukhopadhyay* Nanophotonics 2014, 3, 51-59.

Dynamics and Dimension of an Amyloidogenic Disordered State of Human β2-Microglobulin" D. Narang, P.K. Sharma & S. Mukhopadhyay* Eur. Biophys. J. 2013, 42, 767-776.

"Nanoscopic Amyloid Pores formed via Stepwise Protein Assembly" M. Bhattacharya, N. Jain, P. Dogra, S. Samai and S. Mukhopadhyay* J. Phys. Chem. Lett. 2013, 4, 480-485.

"Nanoscale Fluorescence Imaging of Single Amyloid Fibrils" V. Dalal, M. Bhattacharya, D. Narang, P.K. Sharma and S. Mukhopadhyay* J. Phys. Chem. Lett. 2012, 3, 1783-1787.

"Structural and Dynamical Insights into the Molten-globule form of Ovalbumin" M. Bhattacharya & S. Mukhopadhyay* J. Phys. Chem. B 2012, 116, 520-531.

"Chain Collapse of an Amyloidogenic Intrinsically Disordered Protein" N. Jain, M. Bhattacharya & S. Mukhopadhyay* Biophys. J. 2011, 101, 1720-1729.

"Insights into the Mechanism of Aggregation and Fibril Formation from Bovine Serum Albumin" M. Bhattacharya, N. Jain & S. Mukhopadhyay* J. Phys. Chem. B. 2011, 115, 4195-4205.

"pH-induced Conformational Isomerization of Bovine Serum Albumin Studied by Extrinsic and Intrinsic Protein Fluorescence" M. Bhattacharya, N. Jain, K. Bhasne, V. Kumari & S. Mukhopadhyay* J. Fluorescence 2011, 21, 1083-1090.

"Kinetics of Surfactant-induced Aggregation of Lysozyme Studied by Fluorescence Spectroscopy" N. Jain, M. Bhattacharya & S. Mukhopadhyay* J. Fluorescence 2011, 21, 615-625.

Lab members: Priyanka Dogra, Anamika Avni, Anupa Majumdar, Debapriya Das and Lisha Arora