1
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Dogra P, Mukhopadhyay S. Illuminating the interface: Protein aggregation at the condensate interface. Biophys J 2024; 123:1311-1313. [PMID: 37944533 PMCID: PMC11163285 DOI: 10.1016/j.bpj.2023.10.027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Revised: 10/24/2023] [Accepted: 10/25/2023] [Indexed: 11/12/2023] Open
Affiliation(s)
- Priyanka Dogra
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, Tennessee.
| | - Samrat Mukhopadhyay
- Centre for Protein Science, Design and Engineering, Indian Institute of Science Education and Research (IISER) Mohali, Punjab, India; Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Punjab, India; Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Punjab, India.
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2
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Roggeveen JV, Wang H, Shi Z, Stone HA. A calibration-free model of micropipette aspiration for measuring properties of protein condensates. Biophys J 2024; 123:1393-1403. [PMID: 37789618 PMCID: PMC11163300 DOI: 10.1016/j.bpj.2023.09.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Revised: 08/13/2023] [Accepted: 09/27/2023] [Indexed: 10/05/2023] Open
Abstract
There is growing evidence that biological condensates, which are also referred to as membraneless organelles, and liquid-liquid phase separation play critical roles regulating many important cellular processes. Understanding the roles these condensates play in biology is predicated on understanding the material properties of these complex substances. Recently, micropipette aspiration (MPA) has been proposed as a tool to assay the viscosity and surface tension of condensates. This tool allows the measurement of both material properties in one relatively simple experiment, in contrast to many other techniques that only provide one or a ratio of parameters. While this technique has been commonly used in the literature to determine the material properties of membrane-bound objects dating back decades, the model describing the dynamics of MPA for objects with an external membrane does not correctly capture the hydrodynamics of unbounded fluids, leading to a calibration parameter several orders of magnitude larger than predicted. In this work we derive a new model for MPA of biological condensates that does not require any calibration and is consistent with the hydrodynamics of the MPA geometry. We validate the predictions of this model by conducting MPA experiments on a standard silicone oil of known material properties and are able to predict the viscosity and surface tension using MPA. Finally, we reanalyze with this new model the MPA data presented in previous works for condensates formed from LAF-1 RGG domains.
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Affiliation(s)
- James V Roggeveen
- Department of Mechanical and Aerospace Engineering, Princeton University, Princeton, New Jersey
| | - Huan Wang
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey
| | - Zheng Shi
- Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey.
| | - Howard A Stone
- Department of Mechanical and Aerospace Engineering, Princeton University, Princeton, New Jersey.
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3
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Jahnke K, Pavlovic M, Xu W, Chen A, Knowles TPJ, Arriaga LR, Weitz DA. Polysaccharide functionalization reduces lipid vesicle stiffness. Proc Natl Acad Sci U S A 2024; 121:e2317227121. [PMID: 38771870 PMCID: PMC11145274 DOI: 10.1073/pnas.2317227121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Accepted: 04/15/2024] [Indexed: 05/23/2024] Open
Abstract
The biophysical properties of lipid vesicles are important for their stability and integrity, key parameters that control the performance when these vesicles are used for drug delivery. The vesicle properties are determined by the composition of lipids used to form the vesicle. However, for a given lipid composition, they can also be tailored by tethering polymers to the membrane. Typically, synthetic polymers like polyethyleneglycol are used to increase vesicle stability, but the use of polysaccharides in this context is much less explored. Here, we report a general method for functionalizing lipid vesicles with polysaccharides by binding them to cholesterol. We incorporate the polysaccharides on the outer membrane leaflet of giant unilamellar vesicles (GUVs) and investigate their effect on membrane mechanics using micropipette aspiration. We find that the presence of the glycolipid functionalization produces an unexpected softening of GUVs with fluid-like membranes. By contrast, the functionalization of GUVs with polyethylene glycol does not reduce their stretching modulus. This work provides the potential means to study membrane-bound meshworks of polysaccharides similar to the cellular glycocalyx; moreover, it can be used for tuning the mechanical properties of drug delivery vehicles.
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Affiliation(s)
- Kevin Jahnke
- School of Engineering and Applied Sciences, Harvard University, Cambridge, MA02138
| | - Marko Pavlovic
- School of Engineering and Applied Sciences, Harvard University, Cambridge, MA02138
| | - Wentao Xu
- School of Engineering and Applied Sciences, Harvard University, Cambridge, MA02138
| | - Anqi Chen
- School of Engineering and Applied Sciences, Harvard University, Cambridge, MA02138
| | - Tuomas P. J. Knowles
- Yusuf Hamied Department of Chemistry, University of Cambridge, CambridgeCB2 1EW, United Kingdom
| | - Laura R. Arriaga
- Department of Theoretical Condensed Matter Physics, Condensed Matter Physics Center and Instituto Nicolás Cabrera, Universidad Autónoma de Madrid, Madrid28049, Spain
| | - David A. Weitz
- School of Engineering and Applied Sciences, Harvard University, Cambridge, MA02138
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA02115
- Department of Physics, Harvard University, Cambridge, MA02138
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4
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Dormann D, Lemke EA. Adding intrinsically disordered proteins to biological ageing clocks. Nat Cell Biol 2024:10.1038/s41556-024-01423-w. [PMID: 38783141 DOI: 10.1038/s41556-024-01423-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Accepted: 04/12/2024] [Indexed: 05/25/2024]
Abstract
Research into how the young and old differ, and which biomarkers reflect the diverse biological processes underlying ageing, is a current and fast-growing field. Biological clocks provide a means to evaluate whether a molecule, cell, tissue or even an entire organism is old or young. Here we summarize established and emerging molecular clocks as timepieces. We emphasize that intrinsically disordered proteins (IDPs) tend to transform into a β-sheet-rich aggregated state and accumulate in non-dividing or slowly dividing cells as they age. We hypothesize that understanding these protein-based molecular ageing mechanisms might provide a conceptual pathway to determining a cell's health age by probing the aggregation state of IDPs, which we term the IDP clock.
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Affiliation(s)
- Dorothee Dormann
- Biocenter, Johannes Gutenberg University, Mainz, Germany.
- Institute for Molecular Biology, Mainz, Germany.
| | - Edward Anton Lemke
- Biocenter, Johannes Gutenberg University, Mainz, Germany.
- Institute for Molecular Biology, Mainz, Germany.
- Institute for Quantitative and Computational Biosciences, Johannes Gutenberg University, Mainz, Germany.
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5
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Mukherjee S, Poudyal M, Dave K, Kadu P, Maji SK. Protein misfolding and amyloid nucleation through liquid-liquid phase separation. Chem Soc Rev 2024; 53:4976-5013. [PMID: 38597222 DOI: 10.1039/d3cs01065a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/11/2024]
Abstract
Liquid-liquid phase separation (LLPS) is an emerging phenomenon in cell physiology and diseases. The weak multivalent interaction prerequisite for LLPS is believed to be facilitated through intrinsically disordered regions, which are prevalent in neurodegenerative disease-associated proteins. These aggregation-prone proteins also exhibit an inherent property for phase separation, resulting in protein-rich liquid-like droplets. The very high local protein concentration in the water-deficient confined microenvironment not only drives the viscoelastic transition from the liquid to solid-like state but also most often nucleate amyloid fibril formation. Indeed, protein misfolding, oligomerization, and amyloid aggregation are observed to be initiated from the LLPS of various neurodegeneration-related proteins. Moreover, in these cases, neurodegeneration-promoting genetic and environmental factors play a direct role in amyloid aggregation preceded by the phase separation. These cumulative recent observations ignite the possibility of LLPS being a prominent nucleation mechanism associated with aberrant protein aggregation. The present review elaborates on the nucleation mechanism of the amyloid aggregation pathway and the possible early molecular events associated with amyloid-related protein phase separation. It also summarizes the recent advancement in understanding the aberrant phase transition of major proteins contributing to neurodegeneration focusing on the common disease-associated factors. Overall, this review proposes a generic LLPS-mediated multistep nucleation mechanism for amyloid aggregation and its implication in neurodegeneration.
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Affiliation(s)
- Semanti Mukherjee
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India.
| | - Manisha Poudyal
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India.
| | - Kritika Dave
- Sunita Sanghi Centre of Aging and Neurodegenerative Diseases, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Pradeep Kadu
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India.
| | - Samir K Maji
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India.
- Sunita Sanghi Centre of Aging and Neurodegenerative Diseases, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
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6
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Gil-Garcia M, Benítez-Mateos AI, Papp M, Stoffel F, Morelli C, Normak K, Makasewicz K, Faltova L, Paradisi F, Arosio P. Local environment in biomolecular condensates modulates enzymatic activity across length scales. Nat Commun 2024; 15:3322. [PMID: 38637545 PMCID: PMC11026464 DOI: 10.1038/s41467-024-47435-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Accepted: 03/28/2024] [Indexed: 04/20/2024] Open
Abstract
The mechanisms that underlie the regulation of enzymatic reactions by biomolecular condensates and how they scale with compartment size remain poorly understood. Here we use intrinsically disordered domains as building blocks to generate programmable enzymatic condensates of NADH-oxidase (NOX) with different sizes spanning from nanometers to microns. These disordered domains, derived from three distinct RNA-binding proteins, each possessing different net charge, result in the formation of condensates characterized by a comparable high local concentration of the enzyme yet within distinct environments. We show that only condensates with the highest recruitment of substrate and cofactor exhibit an increase in enzymatic activity. Notably, we observe an enhancement in enzymatic rate across a wide range of condensate sizes, from nanometers to microns, indicating that emergent properties of condensates can arise within assemblies as small as nanometers. Furthermore, we show a larger rate enhancement in smaller condensates. Our findings demonstrate the ability of condensates to modulate enzymatic reactions by creating distinct effective solvent environments compared to the surrounding solution, with implications for the design of protein-based heterogeneous biocatalysts.
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Affiliation(s)
- Marcos Gil-Garcia
- Department of Chemistry and Applied Biosciences, Institute for Chemical and Bioengineering, ETH Zurich, Zurich, Switzerland
| | - Ana I Benítez-Mateos
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Bern, Switzerland
| | - Marcell Papp
- Department of Chemistry and Applied Biosciences, Institute for Chemical and Bioengineering, ETH Zurich, Zurich, Switzerland
| | - Florence Stoffel
- Department of Chemistry and Applied Biosciences, Institute for Chemical and Bioengineering, ETH Zurich, Zurich, Switzerland
| | - Chiara Morelli
- Department of Chemistry and Applied Biosciences, Institute for Chemical and Bioengineering, ETH Zurich, Zurich, Switzerland
| | - Karl Normak
- Department of Chemistry and Applied Biosciences, Institute for Chemical and Bioengineering, ETH Zurich, Zurich, Switzerland
| | - Katarzyna Makasewicz
- Department of Chemistry and Applied Biosciences, Institute for Chemical and Bioengineering, ETH Zurich, Zurich, Switzerland
| | - Lenka Faltova
- Department of Chemistry and Applied Biosciences, Institute for Chemical and Bioengineering, ETH Zurich, Zurich, Switzerland
| | - Francesca Paradisi
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Bern, Switzerland
| | - Paolo Arosio
- Department of Chemistry and Applied Biosciences, Institute for Chemical and Bioengineering, ETH Zurich, Zurich, Switzerland.
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7
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Morelli C, Faltova L, Capasso Palmiero U, Makasewicz K, Papp M, Jacquat RPB, Pinotsi D, Arosio P. RNA modulates hnRNPA1A amyloid formation mediated by biomolecular condensates. Nat Chem 2024:10.1038/s41557-024-01467-3. [PMID: 38472406 DOI: 10.1038/s41557-024-01467-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Accepted: 01/30/2024] [Indexed: 03/14/2024]
Abstract
Several RNA binding proteins involved in membraneless organelles can form pathological amyloids associated with neurodegenerative diseases, but the mechanisms of how this aggregation is modulated remain elusive. Here we investigate how heterotypic protein-RNA interactions modulate the condensation and the liquid to amyloid transition of hnRNPA1A, a protein involved in amyothropic lateral sclerosis. In the absence of RNA, formation of condensates promotes hnRNPA1A aggregation and fibrils are localized at the interface of the condensates. Addition of RNA modulates the soluble to amyloid transition of hnRNPA1A according to different pathways depending on RNA/protein stoichiometry. At low RNA concentrations, RNA promotes both condensation and amyloid formation, and the catalytic effect of RNA adds to the role of the interface between the dense and dilute phases. At higher RNA concentrations, condensation is suppressed according to re-entrant phase behaviour but formation of hnRNPA1A amyloids is observed over longer incubation times. Our findings show how heterotypic nucleic acid-protein interactions affect the kinetics and molecular pathways of amyloid formation.
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Affiliation(s)
- Chiara Morelli
- Department of Chemistry and Applied Biosciences, Institute for Chemical and Bioengineering, ETH Zurich, Zürich, Switzerland
| | - Lenka Faltova
- Department of Chemistry and Applied Biosciences, Institute for Chemical and Bioengineering, ETH Zurich, Zürich, Switzerland
| | - Umberto Capasso Palmiero
- Department of Chemistry and Applied Biosciences, Institute for Chemical and Bioengineering, ETH Zurich, Zürich, Switzerland
| | - Katarzyna Makasewicz
- Department of Chemistry and Applied Biosciences, Institute for Chemical and Bioengineering, ETH Zurich, Zürich, Switzerland
| | - Marcell Papp
- Department of Chemistry and Applied Biosciences, Institute for Chemical and Bioengineering, ETH Zurich, Zürich, Switzerland
| | - Raphaël P B Jacquat
- Department of Chemistry and Applied Biosciences, Institute for Chemical and Bioengineering, ETH Zurich, Zürich, Switzerland
| | - Dorothea Pinotsi
- Scientific Center for Optical and Electron Microscopy, ETH Zurich, Zürich, Switzerland
| | - Paolo Arosio
- Department of Chemistry and Applied Biosciences, Institute for Chemical and Bioengineering, ETH Zurich, Zürich, Switzerland.
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8
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Ray S, Buell AK. Emerging experimental methods to study the thermodynamics of biomolecular condensate formation. J Chem Phys 2024; 160:091001. [PMID: 38445729 DOI: 10.1063/5.0190160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Accepted: 02/15/2024] [Indexed: 03/07/2024] Open
Abstract
The formation of biomolecular condensates in vivo is increasingly recognized to underlie a multitude of crucial cellular functions. Furthermore, the evolution of highly dynamic protein condensates into progressively less reversible assemblies is thought to be involved in a variety of disorders, from cancer over neurodegeneration to rare genetic disorders. There is an increasing need for efficient experimental methods to characterize the thermodynamics of condensate formation and that can be used in screening campaigns to identify and rationally design condensate modifying compounds. Theoretical advances in the field are also identifying the key parameters that need to be measured in order to obtain a comprehensive understanding of the underlying interactions and driving forces. Here, we review recent progress in the development of efficient and quantitative experimental methods to study the driving forces behind and the temporal evolution of biomolecular condensates.
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Affiliation(s)
- Soumik Ray
- Department of Biotechnology and Biomedicine, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
| | - Alexander K Buell
- Department of Biotechnology and Biomedicine, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
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9
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Das T, Zaidi F, Farag M, Ruff KM, Messing J, Taylor JP, Pappu RV, Mittag T. Metastable condensates suppress conversion to amyloid fibrils. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.28.582569. [PMID: 38464104 PMCID: PMC10925303 DOI: 10.1101/2024.02.28.582569] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/12/2024]
Abstract
Stress granules form via co-condensation of RNA binding proteins with prion-like low complexity domains (PLCDs) and RNA molecules released by stress-induced polysomal runoff. Homotypic interactions among PLCDs can drive amyloid fibril formation and this is enhanced by ALS-associated mutations. We find that homotypic interactions that drive condensation versus fibril formation are separable for A1-LCD, the PLCD of hnRNPA1. These separable interactions lead to condensates that are metastable versus fibrils that are globally stable. Metastable condensates suppress fibril formation, and ALS-associated mutations enhance fibril formation by weakening condensate metastability. Mutations designed to enhance A1-LCD condensate metastability restore wild-type behaviors of stress granules in cells even when ALS-associated mutations are present. This suggests that fibril formation can be suppressed by enhancing condensate metastability through condensate-driving interactions.
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Affiliation(s)
- Tapojyoti Das
- Department of Structural Biology, St. Jude Children’s Research Hospital; Memphis, TN 38105, USA
| | - Fatima Zaidi
- Department of Structural Biology, St. Jude Children’s Research Hospital; Memphis, TN 38105, USA
| | - Mina Farag
- Department of Biomedical Engineering and Center for Biomolecular Condensates, Washington University in St. Louis; St. Louis, MO 63130, USA
| | - Kiersten M. Ruff
- Department of Biomedical Engineering and Center for Biomolecular Condensates, Washington University in St. Louis; St. Louis, MO 63130, USA
| | - James Messing
- Department of Cell and Molecular Biology, St. Jude Children’s Research Hospital; Memphis, TN 38105, USA
| | - J. Paul Taylor
- Department of Cell and Molecular Biology, St. Jude Children’s Research Hospital; Memphis, TN 38105, USA
| | - Rohit V. Pappu
- Department of Biomedical Engineering and Center for Biomolecular Condensates, Washington University in St. Louis; St. Louis, MO 63130, USA
| | - Tanja Mittag
- Department of Structural Biology, St. Jude Children’s Research Hospital; Memphis, TN 38105, USA
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10
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Wake N, Weng SL, Zheng T, Wang SH, Kirilenko V, Mittal J, Fawzi NL. Expanding the molecular grammar of polar residues and arginine in FUS prion-like domain phase separation and aggregation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.15.580391. [PMID: 38405719 PMCID: PMC10888811 DOI: 10.1101/2024.02.15.580391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
A molecular grammar governing low-complexity prion-like domains phase separation (PS) has been proposed based on mutagenesis experiments that identified tyrosine and arginine as primary drivers of phase separation via aromatic-aromatic and aromatic-arginine interactions. Here we show that additional residues make direct favorable contacts that contribute to phase separation, highlighting the need to account for these contributions in PS theories and models. We find that tyrosine and arginine make important contacts beyond only tyrosine-tyrosine and tyrosine-arginine, including arginine-arginine contacts. Among polar residues, glutamine in particular contributes to phase separation with sequence/position-specificity, making contacts with both tyrosine and arginine as well as other residues, both before phase separation and in condensed phases. For glycine, its flexibility, not its small solvation volume, favors phase separation by allowing favorable contacts between other residues and inhibits the liquid-to-solid (LST) transition. Polar residue types also make sequence-specific contributions to aggregation that go beyond simple rules, which for serine positions is linked to formation of an amyloid-core structure by the FUS low-complexity domain. Hence, here we propose a revised molecular grammar expanding the role of arginine and polar residues in prion-like domain protein phase separation and aggregation.
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Affiliation(s)
- Noah Wake
- Therapeutic Sciences Graduate Program, Brown University, Providence, RI 02912
| | - Shuo-Lin Weng
- Department of Chemistry, Texas A&M University, College Station, TX 77843
| | - Tongyin Zheng
- Department of Molecular Biology, Cell Biology & Biochemistry, Brown University, Providence, RI 02912
| | - Szu-Huan Wang
- Department of Molecular Biology, Cell Biology & Biochemistry, Brown University, Providence, RI 02912
| | - Valentin Kirilenko
- Department of Molecular Biology, Cell Biology & Biochemistry, Brown University, Providence, RI 02912
| | - Jeetain Mittal
- Department of Chemistry, Texas A&M University, College Station, TX 77843
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, TX 77843
- Interdisciplinary Graduate Program in Genetics and Genomics, Texas A&M University, College Station, TX 77843
| | - Nicolas L Fawzi
- Department of Molecular Biology, Cell Biology & Biochemistry, Brown University, Providence, RI 02912
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11
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Choi H, Hong Y, Najafi S, Kim SY, Shea J, Hwang DS, Choi YS. Spontaneous Transition of Spherical Coacervate to Vesicle-Like Compartment. ADVANCED SCIENCE (WEINHEIM, BADEN-WURTTEMBERG, GERMANY) 2024; 11:e2305978. [PMID: 38063842 PMCID: PMC10870063 DOI: 10.1002/advs.202305978] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Revised: 11/12/2023] [Indexed: 02/17/2024]
Abstract
Numerous biological systems contain vesicle-like biomolecular compartments without membranes, which contribute to diverse functions including gene regulation, stress response, signaling, and skin barrier formation. Coacervation, as a form of liquid-liquid phase separation (LLPS), is recognized as a representative precursor to the formation and assembly of membrane-less vesicle-like structures, although their formation mechanism remains unclear. In this study, a coacervation-driven membrane-less vesicle-like structure is constructed using two proteins, GG1234 (an anionic intrinsically disordered protein) and bhBMP-2 (a bioengineered human bone morphogenetic protein 2). GG1234 formed both simple coacervates by itself and complex coacervates with the relatively cationic bhBMP-2 under acidic conditions. Upon addition of dissolved bhBMP-2 to the simple coacervates of GG1234, a phase transition from spherical simple coacervates to vesicular condensates occurred via the interactions between GG1234 and bhBMP-2 on the surface of the highly viscoelastic GG1234 simple coacervates. Furthermore, the shell structure in the outer region of the GG1234/bhBMP-2 vesicular condensates exhibited gel-like properties, leading to the formation of multiphasic vesicle-like compartments. A potential mechanism is proposed for the formation of the membrane-less GG1234/bhBMP-2 vesicle-like compartments. This study provides a dynamic process underlying the formation of biomolecular multiphasic condensates, thereby enhancing the understanding of these biomolecular structures.
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Affiliation(s)
- Hyunsuk Choi
- Department of Chemical Engineering and Applied ChemistryChungnam National UniversityDaejeon34134South Korea
| | - Yuri Hong
- Division of Environmental Science and EngineeringPohang University of Science and Technology (POSTECH)Pohang37673South Korea
| | - Saeed Najafi
- Department of Chemistry and BiochemistryUniversity of CaliforniaSanta BarbaraCA93106USA
| | - Sun Young Kim
- Department of Chemical Engineering and Applied ChemistryChungnam National UniversityDaejeon34134South Korea
| | - Joan‐Emma Shea
- Department of Chemistry and BiochemistryUniversity of CaliforniaSanta BarbaraCA93106USA
| | - Dong Soo Hwang
- Division of Environmental Science and EngineeringPohang University of Science and Technology (POSTECH)Pohang37673South Korea
| | - Yoo Seong Choi
- Department of Chemical Engineering and Applied ChemistryChungnam National UniversityDaejeon34134South Korea
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12
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Li T, Kambanis J, Sorenson TL, Sunde M, Shen Y. From Fundamental Amyloid Protein Self-Assembly to Development of Bioplastics. Biomacromolecules 2024; 25:5-23. [PMID: 38147506 PMCID: PMC10777412 DOI: 10.1021/acs.biomac.3c01129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Revised: 12/03/2023] [Accepted: 12/04/2023] [Indexed: 12/28/2023]
Abstract
Proteins can self-assemble into a range of nanostructures as a result of molecular interactions. Amyloid nanofibrils, as one of them, were first discovered with regard to the relevance of neurodegenerative diseases but now have been exploited as building blocks to generate multiscale materials with designed functions for versatile applications. This review interconnects the mechanism of amyloid fibrillation, the current approaches to synthesizing amyloid protein-based materials, and the application in bioplastic development. We focus on the fundamental structures of self-assembled amyloid fibrils and how external factors can affect protein aggregation to optimize the process. Protein self-assembly is essentially the autonomous congregation of smaller protein units into larger, organized structures. Since the properties of the self-assembly can be manipulated by changing intrinsic factors and external conditions, protein self-assembly serves as an excellent building block for bioplastic development. Building on these principles, general processing methods and pathways from raw protein sources to mature state materials are proposed, providing a guide for the development of large-scale production. Additionally, this review discusses the diverse properties of protein-based amyloid nanofibrils and how they can be utilized as bioplastics. The economic feasibility of the protein bioplastics is also compared to conventional plastics in large-scale production scenarios, supporting their potential as sustainable bioplastics for future applications.
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Affiliation(s)
- Tianchen Li
- School
of Chemical and Biomolecular Engineering and Sydney Nano, The University of Sydney, PNR Building, Darlington NSW 2008, Australia
| | - Jordan Kambanis
- School
of Chemical and Biomolecular Engineering and Sydney Nano, The University of Sydney, PNR Building, Darlington NSW 2008, Australia
| | - Timothy L. Sorenson
- School
of Chemical and Biomolecular Engineering and Sydney Nano, The University of Sydney, PNR Building, Darlington NSW 2008, Australia
| | - Margaret Sunde
- School
of Medical Sciences and Sydney Nano, The
University of Sydney, Sydney NSW 2006, Australia
| | - Yi Shen
- School
of Chemical and Biomolecular Engineering and Sydney Nano, The University of Sydney, PNR Building, Darlington NSW 2008, Australia
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13
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Moors TE, Milovanovic D. Defining a Lewy Body: Running Up the Hill of Shifting Definitions and Evolving Concepts. JOURNAL OF PARKINSON'S DISEASE 2024; 14:17-33. [PMID: 38189713 PMCID: PMC10836569 DOI: 10.3233/jpd-230183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2024]
Abstract
Lewy bodies (LBs) are pathological hallmarks of Parkinson's disease and dementia with Lewy bodies, characterized by the accumulation of α-synuclein (αSyn) protein in the brain. While LBs were first described a century ago, their formation and morphogenesis mechanisms remain incompletely understood. Here, we present a historical overview of LB definitions and highlight the importance of semantic clarity and precise definitions when describing brain inclusions. Recent breakthroughs in imaging revealed shared features within LB subsets and the enrichment of membrane-bound organelles in these structures, challenging the conventional LB formation model. We discuss the involvement of emerging concepts of liquid-liquid phase separation, where biomolecules demix from a solution to form dense condensates, as a potential LB formation mechanism. Finally, we emphasize the need for the operational definitions of LBs based on morphological characteristics and detection protocols, particularly in studies investigating LB formation mechanisms. A better understanding of LB organization and ultrastructure can contribute to the development of targeted therapeutic strategies for synucleinopathies.
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Affiliation(s)
- Tim E Moors
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Dragomir Milovanovic
- Laboratory of Molecular Neuroscience, German Center for Neurodegenerative Diseases (DZNE), Berlin, Germany
- Einstein Center for Neuroscience, Charité-Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität Berlin, and Berlin Institute of Health, Berlin, Germany
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Hoffmann C, Milovanovic D. Dipping contacts - a novel type of contact site at the interface between membraneless organelles and membranes. J Cell Sci 2023; 136:jcs261413. [PMID: 38149872 PMCID: PMC10785658 DOI: 10.1242/jcs.261413] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2023] Open
Abstract
Liquid-liquid phase separation is a major mechanism for organizing macromolecules, particularly proteins with intrinsically disordered regions, in compartments not limited by a membrane or a scaffold. The cell can therefore be perceived as a complex emulsion containing many of these membraneless organelles, also referred to as biomolecular condensates, together with numerous membrane-bound organelles. It is currently unclear how such a complex concoction operates to allow for intracellular trafficking, signaling and metabolic processes to occur with high spatiotemporal precision. Based on experimental observations of synaptic vesicle condensates - a membraneless organelle that is in fact packed with membranes - we present here the framework of dipping contacts: a novel type of contact site between membraneless organelles and membranes. In this Hypothesis, we propose that our framework of dipping contacts can serve as a foundation to investigate the interface that couples the diffusion and material properties of condensates to biochemical processes occurring in membranes. The identity and regulation of this interface is especially critical in the case of neurodegenerative diseases, where aberrant inclusions of misfolded proteins and damaged organelles underlie cellular pathology.
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Affiliation(s)
- Christian Hoffmann
- Laboratory of Molecular Neuroscience, German Center for Neurodegenerative Diseases (DZNE), 10117 Berlin, Germany
- Whitman Center, Marine Biological Laboratory, Woods Hole, MA 02543, USA
| | - Dragomir Milovanovic
- Laboratory of Molecular Neuroscience, German Center for Neurodegenerative Diseases (DZNE), 10117 Berlin, Germany
- Whitman Center, Marine Biological Laboratory, Woods Hole, MA 02543, USA
- National Center for X-ray Tomography, Advanced Light Source, Berkeley, CA 94720, USA
- Einstein Center for Neuroscience, Charité-Universitätsmedizin Berlin, Freie Universität Berlin, Humboldt-Universität Berlin and Berlin Institute of Health, 10117 Berlin, Germany
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Joshi A, Walimbe A, Avni A, Rai SK, Arora L, Sarkar S, Mukhopadhyay S. Single-molecule FRET unmasks structural subpopulations and crucial molecular events during FUS low-complexity domain phase separation. Nat Commun 2023; 14:7331. [PMID: 37957147 PMCID: PMC10643395 DOI: 10.1038/s41467-023-43225-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2023] [Accepted: 11/03/2023] [Indexed: 11/15/2023] Open
Abstract
Biomolecular condensates formed via phase separation of proteins and nucleic acids are thought to be associated with a wide range of cellular functions and dysfunctions. We dissect critical molecular events associated with phase separation of an intrinsically disordered prion-like low-complexity domain of Fused in Sarcoma by performing single-molecule studies permitting us to access the wealth of molecular information that is skewed in conventional ensemble experiments. Our single-molecule FRET experiments reveal the coexistence of two conformationally distinct subpopulations in the monomeric form. Single-droplet single-molecule FRET studies coupled with fluorescence correlation spectroscopy, picosecond time-resolved fluorescence anisotropy, and vibrational Raman spectroscopy indicate that structural unwinding switches intramolecular interactions into intermolecular contacts allowing the formation of a dynamic network within condensates. A disease-related mutation introduces enhanced structural plasticity engendering greater interchain interactions that can accelerate pathological aggregation. Our findings provide key mechanistic underpinnings of sequence-encoded dynamically-controlled structural unzipping resulting in biological phase separation.
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Affiliation(s)
- Ashish Joshi
- Centre for Protein Science, Design and Engineering, Indian Institute of Science Education and Research (IISER) Mohali, Sector 81, SAS Nagar, Mohali, Punjab, 140306, India
- Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Sector 81, SAS Nagar, Mohali, Punjab, 140306, India
| | - Anuja Walimbe
- Centre for Protein Science, Design and Engineering, Indian Institute of Science Education and Research (IISER) Mohali, Sector 81, SAS Nagar, Mohali, Punjab, 140306, India
- Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Sector 81, SAS Nagar, Mohali, Punjab, 140306, India
| | - Anamika Avni
- Centre for Protein Science, Design and Engineering, Indian Institute of Science Education and Research (IISER) Mohali, Sector 81, SAS Nagar, Mohali, Punjab, 140306, India
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Sector 81, SAS Nagar, Mohali, Punjab, 140306, India
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, CA, 92037, USA
| | - Sandeep K Rai
- Centre for Protein Science, Design and Engineering, Indian Institute of Science Education and Research (IISER) Mohali, Sector 81, SAS Nagar, Mohali, Punjab, 140306, India
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Sector 81, SAS Nagar, Mohali, Punjab, 140306, India
| | - Lisha Arora
- Centre for Protein Science, Design and Engineering, Indian Institute of Science Education and Research (IISER) Mohali, Sector 81, SAS Nagar, Mohali, Punjab, 140306, India
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Sector 81, SAS Nagar, Mohali, Punjab, 140306, India
| | - Snehasis Sarkar
- Centre for Protein Science, Design and Engineering, Indian Institute of Science Education and Research (IISER) Mohali, Sector 81, SAS Nagar, Mohali, Punjab, 140306, India
- Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Sector 81, SAS Nagar, Mohali, Punjab, 140306, India
| | - Samrat Mukhopadhyay
- Centre for Protein Science, Design and Engineering, Indian Institute of Science Education and Research (IISER) Mohali, Sector 81, SAS Nagar, Mohali, Punjab, 140306, India.
- Department of Biological Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Sector 81, SAS Nagar, Mohali, Punjab, 140306, India.
- Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Sector 81, SAS Nagar, Mohali, Punjab, 140306, India.
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He C, Wu CY, Li W, Xu K. Multidimensional Super-Resolution Microscopy Unveils Nanoscale Surface Aggregates in the Aging of FUS Condensates. J Am Chem Soc 2023; 145:24240-24248. [PMID: 37782826 PMCID: PMC10691933 DOI: 10.1021/jacs.3c08674] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/04/2023]
Abstract
The intracellular liquid-liquid phase separation (LLPS) of biomolecules gives rise to condensates that act as membrane-less organelles with vital functions. FUS, an RNA-binding protein, natively forms condensates through LLPS and further provides a model system for the often disease-linked liquid-to-solid transition of biomolecular condensates during aging. However, the mechanism of such maturation processes, as well as the structural and physical properties of the system, remains unclear, partly attributable to difficulties in resolving the internal structures of the micrometer-sized condensates with diffraction-limited optical microscopy. Harnessing a set of multidimensional super-resolution microscopy tools that uniquely map out local physicochemical parameters through single-molecule spectroscopy, here, we uncover nanoscale heterogeneities in FUS condensates and elucidate their evolution over aging. Through spectrally resolved single-molecule localization microscopy (SR-SMLM) with a solvatochromic dye, we unveil distinct hydrophobic nanodomains at the condensate surface. Through SMLM with a fluorogenic amyloid probe, we identify these nanodomains as amyloid aggregates. Through single-molecule displacement/diffusivity mapping (SMdM), we show that such nanoaggregates drastically impede local diffusion. Notably, upon aging or mechanical shears, these nanoaggregates progressively expand on the condensate surface, thus leading to a growing low-diffusivity shell while leaving the condensate interior diffusion-permitting. Together, beyond uncovering fascinating structural arrangements and aging mechanisms in the single-component FUS condensates, the demonstrated synergy of multidimensional super-resolution approaches in this study opens new paths for understanding LLPS systems at the nanoscale.
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Affiliation(s)
- Changdong He
- Department of Chemistry, University of California, Berkeley, California 94720, United States
| | - Chun Ying Wu
- Department of Chemistry, University of California, Berkeley, California 94720, United States
| | - Wan Li
- Department of Chemistry, University of California, Berkeley, California 94720, United States
| | - Ke Xu
- Department of Chemistry, University of California, Berkeley, California 94720, United States
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