1
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De Luca G, Sancataldo G, Militello B, Vetri V. Surface-catalyzed liquid-liquid phase separation and amyloid-like assembly in microscale compartments. J Colloid Interface Sci 2024; 676:569-581. [PMID: 39053405 DOI: 10.1016/j.jcis.2024.07.135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2024] [Revised: 06/24/2024] [Accepted: 07/16/2024] [Indexed: 07/27/2024]
Abstract
Liquid-liquid phase separation is a key phenomenon in the formation of membrane-less structures within the cell, appearing as liquid biomolecular condensates. Protein condensates are the most studied for their biological relevance, and their tendency to evolve, resulting in the formation of aggregates with a high level of order called amyloid. In this study, it is demonstrated that Human Insulin forms micrometric, round amyloid-like structures at room temperature within sub-microliter scale aqueous compartments. These distinctive particles feature a solid core enveloped by a fluid-like corona and form at the interface between the aqueous compartment and the glass coverslip upon which they are cast. Quantitative fluorescence microscopy is used to study in real-time the formation of amyloid-like superstructures. Their formation results driven by liquid-liquid phase separation process that arises from spatially heterogeneous distribution of nuclei at the glass-water interface. The proposed experimental setup allows modifying the surface-to-volume ratio of the aqueous compartments, which affects the aggregation rate and particle size, while also inducing fine alterations in the molecular structures of the final assemblies. These findings enhance the understanding of the factors governing amyloid structure formation, shedding light on the catalytic role of surfaces in this process.
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Affiliation(s)
- Giuseppe De Luca
- Department Biological, Chemical and Pharmaceutical Sciences and Technologies (STEBICEF), University of Palermo, Viale delle Scienze, 16, 90128, Palermo, Italy; Department of Physics and Chemistry - Emilio Segrè, University of Palermo, Viale delle Scienze, 18, 90128, Palermo, Italy.
| | - Giuseppe Sancataldo
- Department of Physics and Chemistry - Emilio Segrè, University of Palermo, Viale delle Scienze, 18, 90128, Palermo, Italy.
| | - Benedetto Militello
- Department of Physics and Chemistry - Emilio Segrè, University of Palermo, Viale delle Scienze, 18, 90128, Palermo, Italy; INFN Sezione di Catania, Via Santa Sofia 64, 95123 Catania, Italy.
| | - Valeria Vetri
- Department of Physics and Chemistry - Emilio Segrè, University of Palermo, Viale delle Scienze, 18, 90128, Palermo, Italy.
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2
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Arad E, Levi T, Yosefi G, Kass I, Cohen-Erez I, Azoulay Z, Bitton R, Jelinek R, Rapaport H. A Matter of Charge: Electrostatically Tuned Coassembly of Amphiphilic Peptides. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2024:e2404324. [PMID: 39155426 DOI: 10.1002/smll.202404324] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2024] [Revised: 08/04/2024] [Indexed: 08/20/2024]
Abstract
Coassembly of peptide biomaterials offers a compelling avenue to broaden the spectrum of hierarchically ordered supramolecular nanoscale structures that may be relevant for biomedical and biotechnological applications. In this work coassemblies of amphiphilic and oppositely charged, anionic and cationic, β-sheet peptides are studied, which may give rise to a diverse range of coassembled forms. Mixtures of the peptides show significantly lower critical coassembly concentration (CCC) values compared to those of the individual pure peptides. Intriguingly, the highest formation of coassembled fibrils is found to require excess of the cationic peptide whereas equimolar mixtures of the peptides exhibited the maximum folding into β-sheet structures. Mixtures of the peptides coassembled sequentially from solutions at concentrations surpassing each peptide's intrinsic critical assembly concentration (CAC), are also found to require a higher portion of the cationic peptide to stabilize hydrogels. This study illuminates a systematic investigation of oppositely charged β-sheet peptides over a range of concentrations, in solutions and in hydrogels. The results may be relevant to the fundamental understanding of such intricate charge-driven assembly systems and to the formulation of peptide-based nanostructures with diverse functionalities.
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Affiliation(s)
- Elad Arad
- Ilse Katz Institute (IKI) for Nanoscale Science and Technology, Ben-Gurion University of the Negev, Beer-Sheva, 8410501, Israel
- Department of Chemistry, Ben-Gurion University of the Negev, Beer-Sheva, 8410501, Israel
- Department of Chemical Engineering, Columbia University in the City of New York, New York, NY, 10027, USA
| | - Topaz Levi
- Avram and Stella Goldstein-Goren Department of Biotechnology Engineering, Ben Gurion University of the Negev, Beer Sheva, 8410501, Israel
| | - Gal Yosefi
- Department of Chemical Engineering, Ben-Gurion University of the Negev, Beer-Sheva, 8410501, Israel
| | - Itamar Kass
- Ilse Katz Institute (IKI) for Nanoscale Science and Technology, Ben-Gurion University of the Negev, Beer-Sheva, 8410501, Israel
| | - Ifat Cohen-Erez
- Avram and Stella Goldstein-Goren Department of Biotechnology Engineering, Ben Gurion University of the Negev, Beer Sheva, 8410501, Israel
| | - Ziv Azoulay
- Avram and Stella Goldstein-Goren Department of Biotechnology Engineering, Ben Gurion University of the Negev, Beer Sheva, 8410501, Israel
| | - Ronit Bitton
- Ilse Katz Institute (IKI) for Nanoscale Science and Technology, Ben-Gurion University of the Negev, Beer-Sheva, 8410501, Israel
- Department of Chemical Engineering, Ben-Gurion University of the Negev, Beer-Sheva, 8410501, Israel
| | - Raz Jelinek
- Ilse Katz Institute (IKI) for Nanoscale Science and Technology, Ben-Gurion University of the Negev, Beer-Sheva, 8410501, Israel
- Department of Chemistry, Ben-Gurion University of the Negev, Beer-Sheva, 8410501, Israel
| | - Hanna Rapaport
- Ilse Katz Institute (IKI) for Nanoscale Science and Technology, Ben-Gurion University of the Negev, Beer-Sheva, 8410501, Israel
- Avram and Stella Goldstein-Goren Department of Biotechnology Engineering, Ben Gurion University of the Negev, Beer Sheva, 8410501, Israel
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3
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Ziaunys M, Sulskis D, Veiveris D, Kopustas A, Snieckute R, Mikalauskaite K, Sakalauskas A, Tutkus M, Smirnovas V. Liquid-liquid phase separation of alpha-synuclein increases the structural variability of fibrils formed during amyloid aggregation. FEBS J 2024. [PMID: 39116032 DOI: 10.1111/febs.17244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Revised: 04/25/2024] [Accepted: 07/25/2024] [Indexed: 08/10/2024]
Abstract
Protein liquid-liquid phase separation (LLPS) is a rapidly emerging field of study on biomolecular condensate formation. In recent years, this phenomenon has been implicated in the process of amyloid fibril formation, serving as an intermediate step between the native protein transition into their aggregated state. The formation of fibrils via LLPS has been demonstrated for a number of proteins related to neurodegenerative disorders, as well as other amyloidoses. Despite the surge in amyloid-related LLPS studies, the influence of protein condensate formation on the end-point fibril characteristics is still far from fully understood. In this work, we compare alpha-synuclein aggregation under different conditions, which promote or negate its LLPS and examine the differences between the formed aggregates. We show that alpha-synuclein phase separation generates a wide variety of assemblies with distinct secondary structures and morphologies. The LLPS-induced structures also possess higher levels of toxicity to cells, indicating that biomolecular condensate formation may be a critical step in the appearance of disease-related fibril variants.
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Affiliation(s)
- Mantas Ziaunys
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Lithuania
| | - Darius Sulskis
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Lithuania
| | - Dominykas Veiveris
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Lithuania
| | - Aurimas Kopustas
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Lithuania
- Department of Molecular Compound Physics, Center for Physical Sciences and Technology, Vilnius, Lithuania
| | - Ruta Snieckute
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Lithuania
| | | | - Andrius Sakalauskas
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Lithuania
| | - Marijonas Tutkus
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Lithuania
- Department of Molecular Compound Physics, Center for Physical Sciences and Technology, Vilnius, Lithuania
| | - Vytautas Smirnovas
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Lithuania
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4
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Wasim A, Menon S, Mondal J. Modulation of α-synuclein aggregation amid diverse environmental perturbation. eLife 2024; 13:RP95180. [PMID: 39087984 PMCID: PMC11293868 DOI: 10.7554/elife.95180] [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: 08/02/2024] Open
Abstract
Intrinsically disordered protein α-synuclein (αS) is implicated in Parkinson's disease due to its aberrant aggregation propensity. In a bid to identify the traits of its aggregation, here we computationally simulate the multi-chain association process of αS in aqueous as well as under diverse environmental perturbations. In particular, the aggregation of αS in aqueous and varied environmental condition led to marked concentration differences within protein aggregates, resembling liquid-liquid phase separation (LLPS). Both saline and crowded settings enhanced the LLPS propensity. However, the surface tension of αS droplet responds differently to crowders (entropy-driven) and salt (enthalpy-driven). Conformational analysis reveals that the IDP chains would adopt extended conformations within aggregates and would maintain mutually perpendicular orientations to minimize inter-chain electrostatic repulsions. The droplet stability is found to stem from a diminished intra-chain interactions in the C-terminal regions of αS, fostering inter-chain residue-residue interactions. Intriguingly, a graph theory analysis identifies small-world-like networks within droplets across environmental conditions, suggesting the prevalence of a consensus interaction patterns among the chains. Together these findings suggest a delicate balance between molecular grammar and environment-dependent nuanced aggregation behavior of αS.
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Affiliation(s)
- Abdul Wasim
- Tata Institute of Fundamental ResearchHyderabadIndia
| | - Sneha Menon
- Tata Institute of Fundamental ResearchHyderabadIndia
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5
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Bokros M, Balukoff NC, Grunfeld A, Sebastiao M, Beurel E, Bourgault S, Lee S. RNA tailing machinery drives amyloidogenic phase transition. Proc Natl Acad Sci U S A 2024; 121:e2316734121. [PMID: 38805292 PMCID: PMC11161805 DOI: 10.1073/pnas.2316734121] [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: 09/26/2023] [Accepted: 04/18/2024] [Indexed: 05/30/2024] Open
Abstract
The RNA tailing machinery adds nucleotides to the 3'-end of RNA molecules that are implicated in various biochemical functions, including protein synthesis and RNA stability. Here, we report a role for the RNA tailing machinery as enzymatic modifiers of intracellular amyloidogenesis. A targeted RNA interference screen identified Terminal Nucleotidyl-transferase 4b (TENT4b/Papd5) as an essential participant in the amyloidogenic phase transition of nucleoli into solid-like Amyloid bodies. Full-length-and-mRNA sequencing uncovered starRNA, a class of unusually long untemplated RNA molecules synthesized by TENT4b. StarRNA consists of short rRNA fragments linked to long, linear mixed tails that operate as polyanionic stimulators of amyloidogenesis in cells and in vitro. Ribosomal intergenic spacer noncoding RNA (rIGSRNA) recruit TENT4b in intranucleolar foci to coordinate starRNA synthesis driving their amyloidogenic phase transition. The exoribonuclease RNA Exosome degrades starRNA and functions as a general suppressor of cellular amyloidogenesis. We propose that amyloidogenic phase transition is under tight enzymatic control by the RNA tailing and exosome axis.
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Affiliation(s)
- Michael Bokros
- Department of Biochemistry and Molecular Biology, Miller School of Medicine, University of Miami, Miami, FL33136
- Sylvester Comprehensive Cancer Center, Miller School of Medicine, Cancer Epigenetics Program, University of Miami, Miami, FL33136
| | - Nathan C. Balukoff
- Department of Biochemistry and Molecular Biology, Miller School of Medicine, University of Miami, Miami, FL33136
- Sylvester Comprehensive Cancer Center, Miller School of Medicine, Cancer Epigenetics Program, University of Miami, Miami, FL33136
| | - Alex Grunfeld
- Department of Biochemistry and Molecular Biology, Miller School of Medicine, University of Miami, Miami, FL33136
- Sylvester Comprehensive Cancer Center, Miller School of Medicine, Cancer Epigenetics Program, University of Miami, Miami, FL33136
| | - Mathew Sebastiao
- Department of Chemistry, Université du Québec à Montréal, MontrealQCH3C 3P8, Canada
- Quebec Network for Research on Protein Function, Engineering, and Applications, PROTEO, Montreal, QCH3C 3P8, Canada
| | - Eléonore Beurel
- Department of Biochemistry and Molecular Biology, Miller School of Medicine, University of Miami, Miami, FL33136
- Department of Psychiatry and Behavioral Sciences, Miller School of Medicine, University of Miami, Miami, FL33136
| | - Steve Bourgault
- Department of Chemistry, Université du Québec à Montréal, MontrealQCH3C 3P8, Canada
- Quebec Network for Research on Protein Function, Engineering, and Applications, PROTEO, Montreal, QCH3C 3P8, Canada
| | - Stephen Lee
- Department of Biochemistry and Molecular Biology, Miller School of Medicine, University of Miami, Miami, FL33136
- Sylvester Comprehensive Cancer Center, Miller School of Medicine, Cancer Epigenetics Program, University of Miami, Miami, FL33136
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6
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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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7
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Miller MA, Medina S. Life at the interface: Engineering bio-nanomaterials through interfacial molecular self-assembly. WILEY INTERDISCIPLINARY REVIEWS. NANOMEDICINE AND NANOBIOTECHNOLOGY 2024; 16:e1966. [PMID: 38725255 PMCID: PMC11090466 DOI: 10.1002/wnan.1966] [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: 11/30/2023] [Revised: 04/18/2024] [Accepted: 04/20/2024] [Indexed: 05/15/2024]
Abstract
Interfacial self-assembly describes the directed organization of molecules and colloids at phase boundaries. Believed to be fundamental to the inception of primordial life, interfacial assembly is exploited by a myriad of eukaryotic and prokaryotic organisms to execute physiologic activities and maintain homeostasis. Inspired by these natural systems, chemists, engineers, and materials scientists have sought to harness the thermodynamic equilibria at phase boundaries to create multi-dimensional, highly ordered, and functional nanomaterials. Recent advances in our understanding of the biophysical principles guiding molecular assembly at gas-solid, gas-liquid, solid-liquid, and liquid-liquid interphases have enhanced the rational design of functional bio-nanomaterials, particularly in the fields of biosensing, bioimaging and biotherapy. Continued development of non-canonical building blocks, paired with deeper mechanistic insights into interphase self-assembly, holds promise to yield next generation interfacial bio-nanomaterials with unique, and perhaps yet unrealized, properties. This article is categorized under: Nanotechnology Approaches to Biology > Nanoscale Systems in Biology Therapeutic Approaches and Drug Discovery > Emerging Technologies.
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Affiliation(s)
- Michael A Miller
- Department of Biomedical Engineering, Pennsylvania State University, University Park, Pennsylvania, USA
| | - Scott Medina
- Department of Biomedical Engineering, Pennsylvania State University, University Park, Pennsylvania, USA
- Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, Pennsylvania, USA
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8
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Bagchi D, Maity A, Chakraborty A. Metal Ion-Induced Unusual Stability of the Metastable Vesicle-like Intermediates Evolving during the Self-Assembly of Phenylalanine: Prominent Role of Surface Charge Inversion. J Phys Chem Lett 2024; 15:4468-4476. [PMID: 38631022 DOI: 10.1021/acs.jpclett.4c00444] [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: 04/19/2024]
Abstract
The underlying mechanism and intermediate formation in the self-assembly of aromatic amino acids, peptides, and proteins remain elusive despite numerous reports. We, for the first time, report that one can stabilize the intermediates by tuning the metal ion-amino acid interaction. Microscopic and spectroscopic investigations of the self-assembly of carboxybenzyl (Z)-protected phenylalanine (ZF) reveal that the bivalent metal ions eventually lead to the formation of fibrillar networks similar to blank ZF whereas the trivalent ions develop vesicle-like intermediates that do not undergo fibrillation for a prolonged time. The time-lapse measurement of surface charge reveals that the surface charge of blank ZF and in the presence of bivalent metal ions changes from a negative value to zero, implying unstable intermediates leading to the fibril network. Strikingly, a prominent charge inversion from an initial negative value to a positive value in the presence of trivalent metal ions imparts unusual stability to the metastable intermediates.
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Affiliation(s)
- Debanjan Bagchi
- Indian Institute of Technology Indore, Department of Chemistry, Indore 453552, Madhya Pradesh, India
| | - Avijit Maity
- Indian Institute of Technology Indore, Department of Chemistry, Indore 453552, Madhya Pradesh, India
| | - Anjan Chakraborty
- Indian Institute of Technology Indore, Department of Chemistry, Indore 453552, Madhya Pradesh, India
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9
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Khorsand FR, Uversky VN. Liquid-liquid phase separation as triggering factor of fibril formation. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2024; 206:143-182. [PMID: 38811080 DOI: 10.1016/bs.pmbts.2024.03.006] [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: 05/31/2024]
Abstract
Liquid-liquid phase separation (LLPS) refers to the phenomenon, where a homogeneous solution spontaneously undergoes a transition into two or more immiscible phases. Through transient weak multivalent macromolecular interactions, a homogeneous solution can spontaneously separate into two phases: one rich in biomolecules and the other poor in biomolecules. Phase separation is believed to serve as the physicochemical foundation for the formation of membrane-less organelles (MLOs) and bio-molecular condensates within cells. Moreover, numerous biological processes depend on LLPS, such as transcription, immunological response, chromatin architecture, DNA damage response, stress granule formation, viral infection, etc. Abnormalities in phase separation can lead to diseases, such as cancer, neurodegeneration, and metabolic disorders. LLPS is regulated by various factors, such as concentration of molecules undergoing LLPS, salt concentration, pH, temperature, post-translational modifications, and molecular chaperones. Recent research on LLPS of biomolecules has progressed rapidly and led to the development of databases containing information pertaining to various aspects of the biomolecule separation analysis. However, more comprehensive research is still required to fully comprehend the specific molecular mechanisms and biological effects of LLPS.
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Affiliation(s)
| | - Vladimir N Uversky
- Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences, Institute for Biological Instrumentation, Pushchino, Moscow, Russia; Department of Molecular Medicine and USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL, United States.
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10
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Arad E, Jelinek R. Catalytic physiological amyloids. Methods Enzymol 2024; 697:77-112. [PMID: 38816136 DOI: 10.1016/bs.mie.2024.01.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2024]
Abstract
Amyloid fibrils have been identified in many protein systems, mostly linked to progression and cytotoxicity in neurodegenerative diseases and other pathologies, but have also been observed in normal physiological systems. A growing body of work has shown that amyloid fibrils can catalyze chemical reactions. Most studies have focused on catalysis by de-novo synthetic amyloid-like peptides; however, recent studies reveal that physiological, native amyloids are catalytic as well. Here, we discuss methodologies and major experimental aspects pertaining to physiological catalytic amyloids. We highlight analyzes of kinetic parameters related to the catalytic activities of amyloid fibrils, structure-function considerations, characterization of the catalytic active sites, and deciphering of catalytic mechanisms.
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Affiliation(s)
- Elad Arad
- Ilse Katz Institute for Nanoscale Science and Technology and the Department of Chemistry, Ben Gurion University of the Negev, Beer Sheva, Israel; Department of Chemical Engineering, Columbia University in the City of New York, New York, NY, United States.
| | - Raz Jelinek
- Ilse Katz Institute for Nanoscale Science and Technology and the Department of Chemistry, Ben Gurion University of the Negev, Beer Sheva, Israel.
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11
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Rinauro DJ, Chiti F, Vendruscolo M, Limbocker R. Misfolded protein oligomers: mechanisms of formation, cytotoxic effects, and pharmacological approaches against protein misfolding diseases. Mol Neurodegener 2024; 19:20. [PMID: 38378578 PMCID: PMC10877934 DOI: 10.1186/s13024-023-00651-2] [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: 03/02/2023] [Accepted: 08/17/2023] [Indexed: 02/22/2024] Open
Abstract
The conversion of native peptides and proteins into amyloid aggregates is a hallmark of over 50 human disorders, including Alzheimer's and Parkinson's diseases. Increasing evidence implicates misfolded protein oligomers produced during the amyloid formation process as the primary cytotoxic agents in many of these devastating conditions. In this review, we analyze the processes by which oligomers are formed, their structures, physicochemical properties, population dynamics, and the mechanisms of their cytotoxicity. We then focus on drug discovery strategies that target the formation of oligomers and their ability to disrupt cell physiology and trigger degenerative processes.
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Affiliation(s)
- Dillon J Rinauro
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, CB2 1EW, UK
| | - Fabrizio Chiti
- Section of Biochemistry, Department of Experimental and Clinical Biomedical Sciences, University of Florence, 50134, Florence, Italy
| | - Michele Vendruscolo
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, CB2 1EW, UK.
| | - Ryan Limbocker
- Department of Chemistry and Life Science, United States Military Academy, West Point, NY, 10996, USA.
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12
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Wu X, Sun Y, Yu J, Miserez A. Tuning the viscoelastic properties of peptide coacervates by single amino acid mutations and salt kosmotropicity. Commun Chem 2024; 7:5. [PMID: 38177438 PMCID: PMC10766971 DOI: 10.1038/s42004-023-01094-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Accepted: 12/20/2023] [Indexed: 01/06/2024] Open
Abstract
Coacervation, or liquid-liquid phase separation (LLPS) of biomacromolecules, is increasingly recognized to play an important role both intracellularly and in the extracellular space. Central questions that remain to be addressed are the links between the material properties of coacervates (condensates) and both the primary and the secondary structures of their constitutive building blocks. Short LLPS-prone peptides, such as GY23 variants explored in this study, are ideal model systems to investigate these links because simple sequence modifications and the chemical environment strongly affect the viscoelastic properties of coacervates. Herein, a systematic investigation of the structure/property relationships of peptide coacervates was conducted using GY23 variants, combining biophysical characterization (plate rheology and surface force apparatus, SFA) with secondary structure investigations by infrared (IR) and circular dichroism (CD) spectroscopy. Mutating specific residues into either more hydrophobic or more hydrophilic residues strongly regulates the viscoelastic properties of GY23 coacervates. Furthermore, the ionic strength and kosmotropic characteristics (Hofmeister series) of the buffer in which LLPS is induced also significantly impact the properties of formed coacervates. Structural investigations by CD and IR indicate a direct correlation between variations in properties induced by endogenous (peptide sequence) or exogenous (ionic strength, kosmotropic characteristics, aging) factors and the β-sheet content within coacervates. These findings provide valuable insights to rationally design short peptide coacervates with programmable materials properties that are increasingly used in biomedical applications.
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Affiliation(s)
- Xi Wu
- Biological and Biomimetic Material Laboratory (BBML), Center for Sustainable Materials (SusMat), School of Materials Science and Engineering, Nanyang Technological University, Singapore, 637553, Singapore
| | - Yue Sun
- Biological and Biomimetic Material Laboratory (BBML), Center for Sustainable Materials (SusMat), School of Materials Science and Engineering, Nanyang Technological University, Singapore, 637553, Singapore
| | - Jing Yu
- School of Materials Science and Engineering, Nanyang Technological University, Singapore, 637553, Singapore.
- Institute for Digital Molecular Analytics and Science, Nanyang Technological University, Singapore, 637553, Singapore.
| | - Ali Miserez
- Biological and Biomimetic Material Laboratory (BBML), Center for Sustainable Materials (SusMat), School of Materials Science and Engineering, Nanyang Technological University, Singapore, 637553, Singapore.
- School of Biological Sciences, 60 Nanyang Drive, NTU, Singapore, 636921, Singapore.
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13
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Yamaguchi T, Chong SH, Yoshida N. Coexistence of two coacervate phases of polyglycine in water suggested by polymer reference interaction site model theory. J Chem Phys 2023; 159:245101. [PMID: 38131487 DOI: 10.1063/5.0185157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2023] [Accepted: 11/30/2023] [Indexed: 12/23/2023] Open
Abstract
Mixing Gibbs energy and phase equilibria of aqueous solutions of polyglycine were studied theoretically by means of polymer reference interaction site model integral equation theory combined with the Gibbs-Duhem method. In addition to the ordinary liquid-liquid phase separation between dilute and concentrated solutions, the theoretical calculation predicted the coexistence of two coacervate phases, namely, the lower- and higher-density coacervates. The relative thermodynamic stabilities of these two phases change with the polymerization degree of polyglycine. The higher-density coacervate phase was rapidly stabilized by increasing the polymer length, and the lower-density phase became metastable at large polymers. The hydrogen bonds between the peptide chains were strengthened, and water was thermodynamically destabilized in the higher-density coacervate. A possible relation with the formation of amyloid fibril within a liquid droplet is also discussed.
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Affiliation(s)
- Tsuyoshi Yamaguchi
- Graduate School of Engineering, Nagoya University, Chikusa, Nagoya 464-8603, Japan
| | - Song-Ho Chong
- Global Center for Natural Resources Sciences, Faculty of Life Sciences, Kumamoto University, Oe-honmachi 5-1, Chuo-ku, Kumamoto 862-0973, Japan
| | - Norio Yoshida
- Graduate School of Informatics, Nagoya University, Chikusa, Nagoya 464-8601, Japan
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14
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Ramírez de Mingo D, López-García P, Vaquero ME, Hervás R, Laurents DV, Carrión-Vázquez M. Phase separation modulates the functional amyloid assembly of human CPEB3. Prog Neurobiol 2023; 231:102540. [PMID: 37898314 DOI: 10.1016/j.pneurobio.2023.102540] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 09/15/2023] [Accepted: 10/21/2023] [Indexed: 10/30/2023]
Abstract
How functional amyloids are regulated to restrict their activity is poorly understood. The cytoplasmic polyadenylation element-binding protein 3 (CPEB3) is an RNA-binding protein that adopts an amyloid state key for memory persistence. Its monomer represses the translation of synaptic target mRNAs while phase separated, whereas its aggregated state acts as a translational activator. Here, we have explored the sequence-driven molecular determinants behind the functional aggregation of human CPEB3 (hCPEB3). We found that the intrinsically disordered region (IDR) of hCPEB3 encodes both an amyloidogenic and a phase separation domain, separated by a poly-A-rich region. The hCPEB3 amyloid core is composed by a hydrophobic region instead of the Q-rich stretch found in the Drosophila orthologue. The hCPEB3 phase separation domain relies on hydrophobic interactions with ionic strength dependence, and its droplet ageing process leads to a liquid-to-solid transition with the formation of a non-fibril-based hydrogel surrounded by starburst droplets. Furthermore, we demonstrate the differential behavior of the protein depending on its environment. Under physiological-like conditions, hCPEB3 can establish additional electrostatic interactions with ions, increasing the stability of its liquid droplets and driving a condensation-based amyloid pathway.
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Affiliation(s)
| | - Paula López-García
- Instituto Cajal, CSIC, Avenida Doctor Arce 37, Madrid 28002, Spain; PhD Program in Neuroscience, Universidad Autónoma de Madrid-Cajal Institute, Madrid 28029, Spain
| | | | - Rubén Hervás
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region of China
| | - Douglas V Laurents
- Instituto de Química Física "Blas Cabrera", CSIC, C/ Serrano 119, Madrid 28006, Spain
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15
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Kang WB, Bao L, Zhang K, Guo J, Zhu BC, Tang QY, Ren WT, Zhu G. Multi-scale molecular simulation of random peptide phase separation and its extended-to-compact structure transition driven by hydrophobic interactions. SOFT MATTER 2023; 19:7944-7954. [PMID: 37815389 DOI: 10.1039/d3sm00633f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/11/2023]
Abstract
Intrinsically disordered proteins (IDPs) often undergo liquid-liquid phase separation (LLPS) and form membraneless organelles or protein condensates. One of the core problems is how do electrostatic repulsion and hydrophobic interactions in peptides regulate the phase separation process? To answer this question, this study uses random peptides composed of positively charged arginine (Arg, R) and hydrophobic isoleucine (Ile, I) as the model systems, and conduct large-scale simulations using all atom and coarse-grained model multi-scale simulation methods. In this article, we investigate the phase separation of different sequences using a coarse-grained model. It is found that the stronger the electrostatic repulsion in the system, the more extended the single-chain structure, and the more likely the system forms a low-density homogeneous phase. In contrast, the stronger the hydrophobic effect of the system, the more compact the single-chain structure, the easier phase separation, and the higher the critical temperature of phase separation. Overall, by taking the random polypeptides composed of two types of amino acid residues as model systems, this study discusses the relationship between the protein sequence and phase behaviour, and provides theoretical insights into the interactions within or between proteins. It is expected to provide essential physical information for the sequence design of functional IDPs, as well as data to support the diagnosis and treatment of the LLPS-associated diseases.
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Affiliation(s)
- Wen Bin Kang
- School of Public Health, Hubei University of Medicine, Shiyan 442000, China.
| | - Lei Bao
- School of Public Health, Hubei University of Medicine, Shiyan 442000, China.
| | - Kai Zhang
- School of Physics, Nanjing University, Nanjing 210093, China
| | - Jia Guo
- School of Public Health, Hubei University of Medicine, Shiyan 442000, China.
| | - Ben Chao Zhu
- School of Public Health, Hubei University of Medicine, Shiyan 442000, China.
| | - Qian-Yuan Tang
- Department of Physics, Hong Kong Baptist University, Kowloon, Hong Kong SAR, China
| | - Wei Tong Ren
- Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou, China
| | - Gen Zhu
- School of Public Health, Hubei University of Medicine, Shiyan 442000, China.
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16
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Ferreira PA. Nucleocytoplasmic transport at the crossroads of proteostasis, neurodegeneration and neuroprotection. FEBS Lett 2023; 597:2567-2589. [PMID: 37597509 DOI: 10.1002/1873-3468.14722] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 08/04/2023] [Accepted: 08/05/2023] [Indexed: 08/21/2023]
Abstract
Nucleocytoplasmic transport comprises the multistep assembly, transport, and disassembly of protein and RNA cargoes entering and exiting nuclear pores. Accruing evidence supports that impairments to nucleocytoplasmic transport are a hallmark of neurodegenerative diseases. These impairments cause dysregulations in nucleocytoplasmic partitioning and proteostasis of nuclear transport receptors and client substrates that promote intracellular deposits - another hallmark of neurodegeneration. Disturbances in liquid-liquid phase separation (LLPS) between dense and dilute phases of biomolecules implicated in nucleocytoplasmic transport promote micrometer-scale coacervates, leading to proteinaceous aggregates. This Review provides historical and emerging principles of LLPS at the interface of nucleocytoplasmic transport, proteostasis, aging and noxious insults, whose dysregulations promote intracellular aggregates. E3 SUMO-protein ligase Ranbp2 constitutes the cytoplasmic filaments of nuclear pores, where it acts as a molecular hub for rate-limiting steps of nucleocytoplasmic transport. A vignette is provided on the roles of Ranbp2 in nucleocytoplasmic transport and at the intersection of proteostasis in the survival of photoreceptor and motor neurons under homeostatic and pathophysiological environments. Current unmet clinical needs are highlighted, including therapeutics aiming to manipulate aggregation-dissolution models of purported neurotoxicity in neurodegeneration.
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Affiliation(s)
- Paulo A Ferreira
- Department of Ophthalmology, Department of Pathology, Duke University Medical Center, NC, Durham, USA
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17
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Hou K, Liu T, Li J, Xian M, Sun L, Wei J. Liquid-liquid phase separation regulates alpha-synuclein aggregate and mitophagy in Parkinson's disease. Front Neurosci 2023; 17:1250532. [PMID: 37781241 PMCID: PMC10536155 DOI: 10.3389/fnins.2023.1250532] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 08/29/2023] [Indexed: 10/03/2023] Open
Abstract
Parkinson's disease (PD) is the second most common neurodegenerative disease in the world, and alpha-synuclein (α-syn) abnormal aggregate and mitochondrial dysfunction play a crucial role in its pathological development. Recent studies have revealed that proteins can form condensates through liquid-liquid phase separation (LLPS), and LLPS has been found to be widely present in α-syn aberrant aggregate and mitophagy-related protein physiological processes. This review summarizes the occurrence of α-syn LLPS and its influencing factors, introduces the production and transformation of the related protein LLPS during PINK1-Parkin-mediated mitophagy, hoping to provide new ideas and methods for the study of PD pathology.
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Affiliation(s)
- Kaiying Hou
- School of Life Sciences, Henan University, Kaifeng, China
| | - Tingting Liu
- School of Life Sciences, Henan University, Kaifeng, China
| | - Jingwen Li
- School of Life Sciences, Henan University, Kaifeng, China
| | - Meiyan Xian
- School of Life Sciences, Henan University, Kaifeng, China
| | - Lin Sun
- College of Chemistry and Molecular Sciences, Henan University, Kaifeng, China
| | - Jianshe Wei
- School of Life Sciences, Henan University, Kaifeng, China
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18
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Szała-Mendyk B, Phan TM, Mohanty P, Mittal J. Challenges in studying the liquid-to-solid phase transitions of proteins using computer simulations. Curr Opin Chem Biol 2023; 75:102333. [PMID: 37267850 PMCID: PMC10527940 DOI: 10.1016/j.cbpa.2023.102333] [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: 03/01/2023] [Revised: 04/24/2023] [Accepted: 04/30/2023] [Indexed: 06/04/2023]
Abstract
"Membraneless organelles," also referred to as biomolecular condensates, perform a variety of cellular functions and their dysregulation is implicated in cancer and neurodegeneration. In the last two decades, liquid-liquid phase separation (LLPS) of intrinsically disordered and multidomain proteins has emerged as a plausible mechanism underlying the formation of various biomolecular condensates. Further, the occurrence of liquid-to-solid transitions within liquid-like condensates may give rise to amyloid structures, implying a biophysical link between phase separation and protein aggregation. Despite significant advances, uncovering the microscopic details of liquid-to-solid phase transitions using experiments remains a considerable challenge and presents an exciting opportunity for the development of computational models which provide valuable, complementary insights into the underlying phenomenon. In this review, we first highlight recent biophysical studies which provide new insights into the molecular mechanisms underlying liquid-to-solid (fibril) phase transitions of folded, disordered and multi-domain proteins. Next, we summarize the range of computational models used to study protein aggregation and phase separation. Finally, we discuss recent computational approaches which attempt to capture the underlying physics of liquid-to-solid transitions along with their merits and shortcomings.
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Affiliation(s)
- Beata Szała-Mendyk
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, TAMU 3127, College Station, 77843, Texas, United States.
| | - Tien Minh Phan
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, TAMU 3127, College Station, 77843, Texas, United States.
| | - Priyesh Mohanty
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, TAMU 3127, College Station, 77843, Texas, United States.
| | - Jeetain Mittal
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, TAMU 3127, College Station, 77843, Texas, United States; Department of Chemistry, Texas A&M University, TAMU 3255, College Station, 77843, Texas, United States; Interdisciplinary Graduate Program in Genetics and Genomics, Texas A&M University, TAMU 3255, College Station, 77843, Texas, United States.
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19
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Zhang Z, Huang G, Song Z, Gatch AJ, Ding F. Amyloid Aggregation and Liquid-Liquid Phase Separation from the Perspective of Phase Transitions. J Phys Chem B 2023; 127:6241-6250. [PMID: 37414583 PMCID: PMC10404378 DOI: 10.1021/acs.jpcb.3c01426] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/08/2023]
Abstract
Amyloid aggregation describes the aberrant self-assembly of peptides into ordered fibrils characterized by cross-β spine cores and is associated with many neurodegenerative diseases and Type 2 diabetes. Oligomers, populated during the early stage of aggregation, are found to be more cytotoxic than mature fibrils. Recently, many amyloidogenic peptides have been reported to undergo liquid-liquid phase separation (LLPS)─a biological process important for the compartmentalization of biomolecules in living cells─prior to fibril formation. Understanding the relationship between LLPS and amyloid aggregation, especially the formation of oligomers, is essential for uncovering disease mechanisms and mitigating amyloid toxicity. In this Perspective, available theories and models of amyloid aggregation and LLPS are first briefly reviewed. By drawing analogies to gas, liquid, and solid phases in thermodynamics, a phase diagram of protein monomer, droplet, and fibril states separated by coexistence lines can be inferred. Due to the high free energy barrier of fibrillization kinetically delaying the formation of fibril seeds out of the droplets, a "hidden" monomer-droplet coexistence line extends into the fibril phase. Amyloid aggregation can then be described as the equilibration process from the initial "out-of-equilibrium" state of a homogeneous solution of monomers to the final equilibrium state of stable amyloid fibrils coexisting with monomers and/or droplets via the formation of metastable or stable droplets as the intermediates. The relationship between droplets and oligomers is also discussed. We suggest that the droplet formation of LLPS should be considered in future studies of amyloid aggregation, which may help to better understand the aggregation process and develop therapeutic strategies to mitigate amyloid toxicity.
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Affiliation(s)
- Zhenzhen Zhang
- Department of Physics and Astronomy, Clemson University, Clemson, SC 29634, United States
| | - Gangtong Huang
- Department of Physics and Astronomy, Clemson University, Clemson, SC 29634, United States
| | - Zhiyuan Song
- Department of Physics and Astronomy, Clemson University, Clemson, SC 29634, United States
| | - Adam J. Gatch
- Department of Physics and Astronomy, Clemson University, Clemson, SC 29634, United States
- Department of Genetics and Biochemistry, Clemson University, Clemson, SC 29634, United States
| | - Feng Ding
- Department of Physics and Astronomy, Clemson University, Clemson, SC 29634, United States
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20
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Moreira GG, Gomes CM. Tau liquid-liquid phase separation is modulated by the Ca 2+ -switched chaperone activity of the S100B protein. J Neurochem 2023; 166:76-86. [PMID: 36621842 DOI: 10.1111/jnc.15756] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2022] [Revised: 12/03/2022] [Accepted: 12/19/2022] [Indexed: 01/10/2023]
Abstract
Aggregation of the microtubule-associated protein tau is implicated in several neurodegenerative tauopathies including Alzheimer's disease (AD). Recent studies evidenced tau liquid-liquid phase separation (LLPS) into droplets as an early event in tau pathogenesis with the potential to enhance aggregation. Tauopathies like AD are accompanied by sustained neuroinflammation and the release of alarmins at early stages of inflammatory responses encompass protective functions. The Ca2+ -binding S100B protein is an alarmin augmented in AD that was recently implicated as a proteostasis regulator acting as a chaperone-type protein, inhibiting aggregation and toxicity through interactions of amyloidogenic clients with a regulatory surface exposed upon Ca2+ -binding. Here we expand the regulatory functions of S100B over protein condensation phenomena by reporting its Ca2+ -dependent activity as a modulator of tau LLPS induced by crowding agents (PEG) and metal ions (Zn2+ ). We observe that apo S100B has a negligible effect on PEG-induced tau demixing but that Ca2+ -bound S100B prevents demixing, resulting in a shift of the phase diagram boundary to higher crowding concentrations. Also, while incubation with apo S100B does not compromise tau LLPS, addition of Ca2+ results in a sharp decrease in turbidity, indicating that interactions with S100B-Ca2+ promote transition of tau to the mixed phase. Further, electrophoretic analysis and FLIM-FRET studies revealed that S100B incorporates into tau liquid droplets, suggesting an important stabilizing and chaperoning role contributing to minimize toxic tau aggregates. Resorting to Alexa488-labeled tau we observed that S100B-Ca2+ reduces the formation of tau fluorescent droplets, without compromising liquid-like behavior and droplet fusion events. The Zn2+ -binding properties of S100B also contribute to regulate Zn2+ -promoted tau LLPS as droplets are decreased by Zn2+ buffering by S100B, in addition to the Ca2+ -triggered interactions with tau. Altogether this work uncovers the versatility of S100B as a proteostasis regulator acting on protein condensation phenomena of relevance across the neurodegeneration continuum.
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Affiliation(s)
- Guilherme G Moreira
- BioISI-Instituto de Biosistemas e Ciências Integrativas, Faculdade de Ciências, Universidade de Lisboa, Lisbon, Portugal
- Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade de Lisboa, Lisbon, Portugal
| | - Cláudio M Gomes
- BioISI-Instituto de Biosistemas e Ciências Integrativas, Faculdade de Ciências, Universidade de Lisboa, Lisbon, Portugal
- Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade de Lisboa, Lisbon, Portugal
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21
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Huang Y, Wang J, Wang N, Li X, Ji X, Yang J, Zhou L, Wang T, Huang X, Hao H. Molecular mechanism of liquid–liquid phase separation in preparation process of crystalline materials. Chem Eng Sci 2022. [DOI: 10.1016/j.ces.2022.118005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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22
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Xing Y, Andrikopoulos N, Zhang Z, Sun Y, Ke PC, Ding F. Modulating Nanodroplet Formation En Route to Fibrillization of Amyloid Peptides with Designed Flanking Sequences. Biomacromolecules 2022; 23:4179-4191. [PMID: 36137260 PMCID: PMC9618360 DOI: 10.1021/acs.biomac.2c00642] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Soluble oligomers populating early amyloid aggregation can be regarded as nanodroplets of liquid-liquid phase separation (LLPS). Amyloid peptides typically contain hydrophobic aggregation-prone regions connected by hydrophilic linkers and flanking sequences, and such a sequence hydropathy pattern drives the formation of supramolecular structures in the nanodroplets and modulates subsequent fibrillization. Here, we studied LLPS and fibrillization of coarse-grained amyloid peptides with increasing flanking sequences. Nanodroplets assumed lamellar, cylindrical micellar, and spherical micellar structures with increasing peptide hydrophilic/hydrophobic ratios, and such morphologies governed subsequent fibrillization processes. Adding glycine-serine repeats as flanking sequences to Aβ16-22, the amyloidogenic core of amyloid-β, our computational predictions of morphological transitions were corroborated experimentally. The uncovered inter-relationships between the peptide sequence pattern, oligomer/nanodroplet morphology, and fibrillization pathway, kinetics, and structure may contribute to our understanding of pathogenic amyloidosis in aging, facilitate future efforts ameliorating amyloidosis through peptide engineering, and aid in the design of novel amyloid-based functional nanobiomaterials and nanocomposites.
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Affiliation(s)
- Yanting Xing
- Department of Physics and Astronomy, Clemson University, Clemson, SC 29634, United States
| | - Nicholas Andrikopoulos
- Drug Delivery, Disposition and Dynamics, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC 3052, Australia
| | - Zhenzhen Zhang
- Department of Physics and Astronomy, Clemson University, Clemson, SC 29634, United States
| | - Yunxiang Sun
- Department of Physics and Astronomy, Clemson University, Clemson, SC 29634, United States
- Department of Physics, Ningbo University, Ningbo 315211, China
| | - Pu Chun Ke
- Drug Delivery, Disposition and Dynamics, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC 3052, Australia
- Nanomedicine Center, The GBA National Institute for Nanotechnology Innovation, 136 Kaiyuan Avenue, Guangzhou, 510700, China
| | - Feng Ding
- Department of Physics and Astronomy, Clemson University, Clemson, SC 29634, United States
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23
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Liquid–Liquid Phase Separation of Biomacromolecules and Its Roles in Metabolic Diseases. Cells 2022; 11:cells11193023. [PMID: 36230986 PMCID: PMC9562192 DOI: 10.3390/cells11193023] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2022] [Revised: 08/24/2022] [Accepted: 09/24/2022] [Indexed: 11/30/2022] Open
Abstract
Liquid–liquid phase separation (LLPS) compartmentalizes and concentrates biomacromolecules into liquid-like condensates, which underlies membraneless organelles (MLOs) formation in eukaryotic cells. With increasing evidence of the LLPS concept and methods, this phenomenon as a novel principle accounts for explaining the precise spatial and temporal regulation of cellular functions. Moreover, the phenomenon that LLPS tends to concentrate proteins is often accompanied by several abnormal signals for human diseases. It is reported that multiple metabolic diseases are strongly associated with the deposition of insoluble proteinaceous aggregating termed amyloids. At present, recent studies have observed the roles of LLPS in several metabolic diseases, including type 2 diabetes mellitus (T2DM), Alzheimer’s disease (AD), and metabolic bone diseases (MBDs). This review aims to expound on the current concept and methods of LLPS and summarize its vital roles in T2DM, AD, and MBDs, uncover novel mechanisms of these metabolic diseases, and thus provide powerful potential therapeutic strategies and targets for ameliorating these metabolic diseases.
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24
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Xu B, Chen J, Liu Y. Curcumin Interacts with α-Synuclein Condensates To Inhibit Amyloid Aggregation under Phase Separation. ACS OMEGA 2022; 7:30281-30290. [PMID: 36061735 PMCID: PMC9434619 DOI: 10.1021/acsomega.2c03534] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Accepted: 08/03/2022] [Indexed: 05/27/2023]
Abstract
The amyloid aggregation of α-synuclein (α-Syn) is highly associated with Parkinson's disease (PD). Discovering α-Syn amyloid inhibitors is one of the strategies for PD therapies. Recent studies suggested that α-Syn undergoes phase separation to accelerate amyloid aggregation. Molecules modulating α-Syn phase separation or transition have the potential to regulate amyloid aggregation. Here, we discovered that curcumin, a small natural molecule, interacts with α-Syn during phase separation. Our study showed that curcumin neither affects the formation of α-Syn condensates nor influences the initial morphology of α-Syn condensates. However, curcumin decreases the fluidity of α-Syn inside the condensates and efficiently inhibits α-Syn from turning into an amyloid. It also inhibits the amyloid aggregations of PD disease-related α-Syn E46K and H50Q mutants under phase separation. Furthermore, curcumin can destabilize preformed α-Syn amyloid aggregates in the condensates. Together, our findings demonstrate that curcumin regulates α-Syn amyloid formation during protein phase separation and reveal that α-Syn amyloid aggregation under phase separation can be modulated by small molecules.
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25
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Arad E, Jelinek R. Catalytic amyloids. TRENDS IN CHEMISTRY 2022. [DOI: 10.1016/j.trechm.2022.07.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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26
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Sulatskaya AI, Stepanenko OV, Sulatsky MI, Mikhailova EV, Kuznetsova IM, Turoverov KK, Stepanenko OV. sfGFP throws light on the early stages of β-barrel amyloidogenesis. Int J Biol Macromol 2022; 215:224-234. [PMID: 35718155 DOI: 10.1016/j.ijbiomac.2022.06.108] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Revised: 06/01/2022] [Accepted: 06/13/2022] [Indexed: 11/26/2022]
Abstract
The accumulation of β-sheet-rich protein aggregates, amyloid fibrils, accompanies severe pathologies (Alzheimer's, Parkinson's diseases, ALS, etc.). The high amyloidogenicity of proteins with a native β-barrel structure, and the amyloidogenic peptides ability to form a universal cylindrin-like oligomeric state were proven. The mechanisms for the proteins' transformation from this state to a fibrillar one are still not fully understood. We defined the structural rearrangements of the amyloidogenic β-barrel superfolder GFP (sfGFP) prior to fibrillogenesis using its tryptophan and chromophore fluorescence. We characterized the early intermediate "native-like" state preserving the integrity of the sfGFP β-barrel scaffold despite the partial distortion of the three β-strands closing it. The interaction between the "melted" regions of the protein leads to the assembly of high molecular weight complexes, which are not dynamic structures but are less stable and less cytotoxic than mature amyloids. Additional contacts of sfGFP monomers facilitate the global reorganization of its structure and stabilization of the second intermediate state in which the β-barrel opens and some of the native α-helices and disordered regions refold into non-native β-strands, which, along with native β-strands, form an amyloid fiber. Reported sfGFP structural transformations may occur during the fibrillogenesis of other β-barrel proteins, and the identified intermediate states are likely universal. Thus sfGFP can be used as a sensing platform to develop therapeutic agents inhibiting amyloidogenesis through interaction with protein intermediates and destroying low-stable aggregates formed at the early stages of fibrillogenesis.
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Affiliation(s)
- Anna I Sulatskaya
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, 4 Tikhoretsky Avenue, 194064 St. Petersburg, Russia
| | - Olga V Stepanenko
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, 4 Tikhoretsky Avenue, 194064 St. Petersburg, Russia
| | - Maksim I Sulatsky
- Laboratory of Cell Morphology, Institute of Cytology, Russian Academy of Sciences, 4 Tikhoretsky Avenue, 194064 St. Petersburg, Russia
| | - Ekaterina V Mikhailova
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, 4 Tikhoretsky Avenue, 194064 St. Petersburg, Russia
| | - Irina M Kuznetsova
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, 4 Tikhoretsky Avenue, 194064 St. Petersburg, Russia
| | - Konstantin K Turoverov
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, 4 Tikhoretsky Avenue, 194064 St. Petersburg, Russia.
| | - Olesya V Stepanenko
- Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, 4 Tikhoretsky Avenue, 194064 St. Petersburg, Russia
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27
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Lao Z, Dong X, Liu X, Li F, Chen Y, Tang Y, Wei G. Insights into the Atomistic Mechanisms of Phosphorylation in Disrupting Liquid-Liquid Phase Separation and Aggregation of the FUS Low-Complexity Domain. J Chem Inf Model 2022; 62:3227-3238. [PMID: 35709363 DOI: 10.1021/acs.jcim.2c00414] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Fused in sarcoma (FUS), a nuclear RNA binding protein, can not only undergo liquid-liquid phase separation (LLPS) to form dynamic biomolecular condensates but also aggregate into solid amyloid fibrils which are associated with the pathology of amyotrophic lateral sclerosis and frontotemporal lobar degeneration diseases. Phosphorylation in the FUS low-complexity domain (FUS-LC) inhibits FUS LLPS and aggregation. However, it remains largely elusive what are the underlying atomistic mechanisms of this inhibitory effect and whether phosphorylation can disrupt preformed FUS fibrils, reversing the FUS gel/solid phase toward the liquid phase. Herein, we systematically investigate the impacts of phosphorylation on the conformational ensemble of the FUS37-97 monomer and dimer and the structure of the FUS37-97 fibril by performing extensive all-atom molecular dynamics simulations. Our simulations reveal three key findings: (1) phosphorylation shifts the conformations of FUS37-97 from the β-rich, fibril-competent state toward a helix-rich, fibril-incompetent state; (2) phosphorylation significantly weakens protein-protein interactions and enhances protein-water interactions, which disfavor FUS-LC LLPS as well as aggregation and facilitate the dissolution of the preformed FUS-LC fibril; and (3) the FUS37-97 peptide displays a high β-strand probability in the region spanning residues 52-67, and phosphorylation at S54 and S61 residues located in this region is crucial for the disruption of LLPS and aggregation of FUS-LC. This study may pave the way for ameliorating phase-separation-related pathologies via site-specific phosphorylation.
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Affiliation(s)
- Zenghui Lao
- Department of Physics, State Key Laboratory of Surface Physics, Key Laboratory for Computational Physical Sciences (Ministry of Education), Fudan University, Shanghai 200433, People's Republic of China
| | - Xuewei Dong
- Department of Physics, State Key Laboratory of Surface Physics, Key Laboratory for Computational Physical Sciences (Ministry of Education), Fudan University, Shanghai 200433, People's Republic of China
| | - Xianshi Liu
- Department of Physics, State Key Laboratory of Surface Physics, Key Laboratory for Computational Physical Sciences (Ministry of Education), Fudan University, Shanghai 200433, People's Republic of China
| | - Fangying Li
- Department of Physics, State Key Laboratory of Surface Physics, Key Laboratory for Computational Physical Sciences (Ministry of Education), Fudan University, Shanghai 200433, People's Republic of China
| | - Yujie Chen
- Department of Physics, State Key Laboratory of Surface Physics, Key Laboratory for Computational Physical Sciences (Ministry of Education), Fudan University, Shanghai 200433, People's Republic of China
| | - Yiming Tang
- Department of Physics, State Key Laboratory of Surface Physics, Key Laboratory for Computational Physical Sciences (Ministry of Education), Fudan University, Shanghai 200433, People's Republic of China
| | - Guanghong Wei
- Department of Physics, State Key Laboratory of Surface Physics, Key Laboratory for Computational Physical Sciences (Ministry of Education), Fudan University, Shanghai 200433, People's Republic of China
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28
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Tang X, Han W. Multiscale Exploration of Concentration-Dependent Amyloid-β(16-21) Amyloid Nucleation. J Phys Chem Lett 2022; 13:5009-5016. [PMID: 35649244 DOI: 10.1021/acs.jpclett.2c00685] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Atomic descriptions of peptide aggregation nucleation remain lacking due to the difficulty of exploring complex configurational spaces on long time scales. To elucidate this process, we develop a multiscale approach combining a metadynamics-based method with cluster statistical mechanics to derive concentration-dependent free energy surfaces of nucleation at near-atomic resolution. A kinetic transition network of nucleation is then constructed and employed to systematically explore nucleation pathways and kinetics through stochastic simulations. This approach is applied to describe Aβ16-21 amyloid nucleation, revealing a two-step mechanism involving disordered aggregates at millimolar concentration, and an unexpected mechanism at submillimolar concentrations that exhibits kinetics reminiscent of classical nucleation but atypical pathways involving growing clusters with structured cores wrapped by disordered surface. When this atypical mechanism is operative, critical nucleus size can be reflected by the nucleation reaction order. Collectively, our approach paves the way for a more quantitative and detailed understanding of peptide aggregation nucleation.
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Affiliation(s)
- Xuan Tang
- State Key Laboratory of Chemical Oncogenomics, Guangdong Provincial Key Laboratory of Chemical Genomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, 518055, China
| | - Wei Han
- State Key Laboratory of Chemical Oncogenomics, Guangdong Provincial Key Laboratory of Chemical Genomics, School of Chemical Biology and Biotechnology, Peking University Shenzhen Graduate School, Shenzhen, 518055, China
- Institute of Chemical Biology, Shenzhen Bay Laboratory, Shenzhen, 518132, China
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29
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Huang S, Mo X, Wang J, Ye X, Yu H, Liu Y. α-Synuclein phase separation and amyloid aggregation are modulated by C-terminal truncations. FEBS Lett 2022; 596:1388-1400. [PMID: 35485974 DOI: 10.1002/1873-3468.14361] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2022] [Revised: 04/10/2022] [Accepted: 04/16/2022] [Indexed: 11/11/2022]
Abstract
The aggregation of α-synuclein (α-Syn) is a key pathological hallmark of Parkinson's disease (PD). α-Syn undergoes liquid-liquid phase separation (LLPS) to drive amyloid aggregation. How the LLPS of α-Syn is regulated remains largely unknown. Here, we discovered that the C-terminal region modulates α-Syn phase separation through electrostatic interactions. The wild-type (WT) and PD disease-related truncated α-Syn can co-exist in the condensates. The truncated α-Syn could dramatically promote WT α-Syn phase separation. Further studies demonstrated that the truncated α-Syn accelerated WT α-Syn turning to amyloid aggregates by modulation of phase separation. Together, our findings disclose the role of the C-terminal domain in the LLPS of α-Syn and pave the path for understanding the mechanism of truncated α-Syn in PD pathology.
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Affiliation(s)
- Shuai Huang
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China
| | - Xiaoli Mo
- Biology Department, Clark University, Worcester, Massachusetts, 01610, USA
| | - Jieyi Wang
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China
| | - Xinyi Ye
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China
| | - Haijia Yu
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China
| | - Yinghui Liu
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China
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30
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Deleanu M, Deschaume O, Cipelletti L, Hernandez JF, Bartic C, Cottet H, Chamieh J. Taylor Dispersion Analysis and Atomic Force Microscopy Provide a Quantitative Insight into the Aggregation Kinetics of Aβ (1-40)/Aβ (1-42) Amyloid Peptide Mixtures. ACS Chem Neurosci 2022; 13:786-795. [PMID: 35201761 DOI: 10.1021/acschemneuro.1c00784] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Aggregation of amyloid β peptides is known to be one of the main processes responsible for Alzheimer's disease. The resulting dementia is believed to be due in part to the formation of potentially toxic oligomers. However, the study of such intermediates and the understanding of how they form are very challenging because they are heterogeneous and transient in nature. Unfortunately, few techniques can quantify, in real time, the proportion and the size of the different soluble species during the aggregation process. In a previous work (Deleanu et al. Anal. Chem. 2021, 93, 6523-6533), we showed the potential of Taylor dispersion analysis (TDA) in amyloid speciation during the aggregation process of Aβ (1-40) and Aβ (1-42). The current work aims at exploring in detail the aggregation of amyloid Aβ (1-40):Aβ (1-42) peptide mixtures with different proportions of each peptide (1:0, 3:1, 1:1, 1:3, and 0:1) using TDA and atomic force microscopy (AFM). TDA allowed for monitoring the kinetics of the amyloid assembly and quantifying the transient intermediates. Complementarily, AFM allowed the formation of insoluble fibrils to be visualized. Together, the two techniques enabled us to study the influence of the peptide ratios on the kinetics and the formation of potentially toxic oligomeric species.
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Affiliation(s)
- Mihai Deleanu
- IBMM, Univ Montpellier, CNRS, ENSCM, 34095 Montpellier, France
| | - Olivier Deschaume
- Department of Physics and Astronomy, Soft-Matter Physics and Biophysics Section, KU Leuven, Celestijnenlaan 200D, Box 2416, 3001 Heverlee, Belgium
| | - Luca Cipelletti
- L2C, Université Montpellier, 34095 Montpellier, France
- Institut Universitaire de France (IUF), Paris, France
| | | | - Carmen Bartic
- Department of Physics and Astronomy, Soft-Matter Physics and Biophysics Section, KU Leuven, Celestijnenlaan 200D, Box 2416, 3001 Heverlee, Belgium
| | - Hervé Cottet
- IBMM, Univ Montpellier, CNRS, ENSCM, 34095 Montpellier, France
| | - Joseph Chamieh
- IBMM, Univ Montpellier, CNRS, ENSCM, 34095 Montpellier, France
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31
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Huang S, Xu B, Liu Y. Calcium promotes α-synuclein liquid-liquid phase separation to accelerate amyloid aggregation. Biochem Biophys Res Commun 2022; 603:13-20. [PMID: 35276458 DOI: 10.1016/j.bbrc.2022.02.097] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Accepted: 02/23/2022] [Indexed: 12/26/2022]
Abstract
α-Synuclein (α-Syn) is an aggregation-prone protein whose accumulation in Lewy bodies leads to neurodegenerative diseases like Parkinson's disease (PD). Calcium plays a critical role in neurons, and calcium dysregulation is one of the risk factors of PD. It is known that Ca2+ interacts with α-Syn and affects its assembly. However, how Ca2+ regulates α-Syn aggregation remains unclear. Here, we reported that Ca2+ accelerates α-Syn amyloid aggregation through the modulation of protein phase separation. We observed that Ca2+ promotes the formation of α-Syn liquid droplets but does not change the protein fluidity inside the droplets. Further studies showed Ca2+-involved α-Syn droplets are still able to fuse. A metal chelator eliminated Ca2+-induced enlargement of α-Syn droplets, suggesting the influence of Ca2+ on α-Syn assembly could be reversed at the stage of liquid-liquid phase separation (LLPS). Interestingly, our data showed Ca2+ still promoted α-Syn phase separation in the presence of the lipid membranes. In addition, Ca2+/α-syn droplets could efficiently recruit lipid vesicles to the surface of these condensates. Our findings demonstrate that Ca2+ facilitates α-Syn phase separation to accelerate amyloid aggregation and pave the path for understanding the implications of Ca2+ in α-Syn accumulation and PD.
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Affiliation(s)
- Shuai Huang
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China
| | - Bingkuan Xu
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China
| | - Yinghui Liu
- Jiangsu Key Laboratory for Molecular and Medical Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China.
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32
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Zhang Y, Liu Y, Zhao W, Sun Y. Hydroxylated single-walled carbon nanotube inhibits β2m 21-31 fibrillization and disrupts pre-formed proto-fibrils. Int J Biol Macromol 2021; 193:1-7. [PMID: 34687758 DOI: 10.1016/j.ijbiomac.2021.10.103] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Revised: 10/11/2021] [Accepted: 10/14/2021] [Indexed: 11/17/2022]
Abstract
Pathological aggregation of amyloid polypeptides is associated with numerous degenerative diseases. Preventing aggregation and clearing amyloid deposits are considered as promising strategies against amyloidosis. With the capacity of crossing the blood-brain barrier and good biocompatibility, the hydroxylated single-walled carbon nanotube (SWCNT-OH) has been shown with excellent anti-amyloid properties. Here, we systematically studied the SWCNT-OH effects on the fibrillization of the β2m21-31 peptides utilizing all-atom discrete molecular dynamics (DMD) simulation. Our results demonstrated the isolated β2m21-31 peptides first nucleated into unstructured oligomers followed by coil-to-sheet conformational conversions in oligomers with at least six peptides. The elongation and lateral surfaces of the preformed β-sheet could catalyze the other unstructured monomers and small oligomers converted into β-sheet formations via dock-lock fibril growth and secondary nucleation processes. Eventually, the β2m21-31 peptides would self-assemble into well-ordered cross-β structures. Regardless of isolated monomers or well-defined cross-β assemblies, the β2m21-31 would attach on the surfaces of SWCNT-OH adopting unstructured formations indicating the SWCNT-OH not only inhibited the fibrillization of β2m21-31 but also destroyed pre-formed proto-fibrils. Overall, our study displays a complete picture of the fibrillization mechanism of β2m21-31 and the amyloid inhibitory mechanism of SWCNT-OH, offering new insight into the de-novo design of anti-amyloid inhibitors.
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Affiliation(s)
- Yu Zhang
- School of Physical Science and Technology, Ningbo University, Ningbo 315211, China
| | - Yuying Liu
- School of Physical Science and Technology, Ningbo University, Ningbo 315211, China
| | - Wenhui Zhao
- School of Physical Science and Technology, Ningbo University, Ningbo 315211, China
| | - Yunxiang Sun
- School of Physical Science and Technology, Ningbo University, Ningbo 315211, China.
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33
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Manganese promotes α-synuclein amyloid aggregation through the induction of protein phase transition. J Biol Chem 2021; 298:101469. [PMID: 34871547 PMCID: PMC8717548 DOI: 10.1016/j.jbc.2021.101469] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Revised: 11/24/2021] [Accepted: 11/25/2021] [Indexed: 01/31/2023] Open
Abstract
α-Synuclein (α-Syn) is the major protein component of Lewy bodies, a key pathological feature of Parkinson’s disease (PD). The manganese ion Mn2+ has been identified as an environmental risk factor of PD. However, it remains unclear how Mn2+ regulates α-Syn aggregation. Here, we discovered that Mn2+accelerates α-Syn amyloid aggregation through the regulation of protein phase separation. We found that Mn2+ not only promotes α-Syn liquid-to-solid phase transition but also directly induces soluble α-Syn monomers to form solid-like condensates. Interestingly, the lipid membrane is integrated into condensates during Mn2+-induced α-Syn phase transition; however, the preformed Mn2+/α-syn condensates can only recruit lipids to the surface of condensates. In addition, this phase transition can largely facilitate α-Syn amyloid aggregation. Although the Mn2+-induced condensates do not fuse, our results demonstrated that they could recruit soluble α-Syn monomers into the existing condensates. Furthermore, we observed that a manganese chelator reverses Mn2+-induced α-Syn aggregation during the phase transition stage. However, after maturation, α-Syn aggregation becomes irreversible. These findings demonstrate that Mn2+ facilitates α-Syn phase transition to accelerate the formation of α-Syn aggregates and provide new insights for targeting α-Syn phase separation in PD treatment.
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34
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Dec R, Puławski W, Dzwolak W. Selective and stoichiometric incorporation of ATP by self-assembling amyloid fibrils. J Mater Chem B 2021; 9:8626-8630. [PMID: 34622264 DOI: 10.1039/d1tb01976g] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
ATP acts as a biological hydrotrope preventing protein aggregation. Here, we report a novel chimeric peptide, ACC1-13K8, with an unusual capacity to bind and incorporate ATP while self-assembling into amyloid fibrils. The amino acid sequence combines a highly amyloidogenic segment of insulin's A-chain (ACC1-13) and octalysine (K8). Fibrillization requires binding 2 ATP molecules per ACC1-13K8 monomer and is not triggered by adenosine di- and monophosphates (ADP, AMP). Infrared and CD spectra and AFM-based morphological analysis reveal tight and orderly entrapment of ATP within superstructural hybrid peptide-ATP fibrils. The incorporation of ATP is an emergent property of ACC1-13K8 not observed for ACC1-13 and K8 segments separately. We demonstrate how new functionalities (e.g. ATP storage) emerge from synergistic coupling of amyloidogenic segments with non-amyloidogenic peptide ligands, and suggest that ATP's role in protein misfolding is more nuanced than previously assumed.
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Affiliation(s)
- Robert Dec
- Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, 1 Pasteur Street, 02-093 Warsaw, Poland. .,Institute of High Pressure Physics, Polish Academy of Sciences, 29/37 Sokołowska Street, 01-142 Warsaw, Poland
| | - Wojciech Puławski
- Institute of High Pressure Physics, Polish Academy of Sciences, 29/37 Sokołowska Street, 01-142 Warsaw, Poland.,Bioinformatics Laboratory, Mossakowski Medical Research Institute, Polish Academy of Sciences, 5 Pawinskiego Street, 02-106 Warsaw, Poland
| | - Wojciech Dzwolak
- Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, 1 Pasteur Street, 02-093 Warsaw, Poland. .,Institute of High Pressure Physics, Polish Academy of Sciences, 29/37 Sokołowska Street, 01-142 Warsaw, Poland
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35
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Nakasone Y, Terazima M. A Time-Resolved Diffusion Technique for Detection of the Conformational Changes and Molecular Assembly/Disassembly Processes of Biomolecules. Front Genet 2021; 12:691010. [PMID: 34276791 PMCID: PMC8278059 DOI: 10.3389/fgene.2021.691010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Accepted: 05/31/2021] [Indexed: 12/20/2022] Open
Abstract
Biological liquid-liquid phase separation (LLPS) is driven by dynamic and multivalent interactions, which involves conformational changes and intermolecular assembly/disassembly processes of various biomolecules. To understand the molecular mechanisms of LLPS, kinetic measurements of the intra- and intermolecular reactions are essential. In this review, a time-resolved diffusion technique which has a potential to detect molecular events associated with LLPS is presented. This technique can detect changes in protein conformation and intermolecular interaction (oligomer formation, protein-DNA interaction, and protein-lipid interaction) in time domain, which are difficult to obtain by other methods. After the principle and methods for signal analyses are described in detail, studies on photoreactive molecules (intermolecular interaction between light sensor proteins and its target DNA) and a non-photoreactive molecule (binding and folding reaction of α-synuclein upon mixing with SDS micelle) are presented as typical examples of applications of this unique technique.
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Affiliation(s)
- Yusuke Nakasone
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto, Japan
| | - Masahide Terazima
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto, Japan
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36
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Nilsson D, Irbäck A. Finite-size shifts in simulated protein droplet phase diagrams. J Chem Phys 2021; 154:235101. [PMID: 34241264 DOI: 10.1063/5.0052813] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Computer simulation can provide valuable insight into the forces driving biomolecular liquid-liquid phase separation. However, the simulated systems have a limited size, which makes it important to minimize and control finite-size effects. Here, using a phenomenological free-energy ansatz, we investigate how the single-phase densities observed in a canonical system under coexistence conditions depend on the system size and the total density. We compare the theoretical expectations with results from Monte Carlo simulations based on a simple hydrophobic/polar protein model. We consider both cubic systems with spherical droplets and elongated systems with slab-like droplets. The results presented suggest that the slab simulation method greatly facilitates the estimation of the coexistence densities in the large-system limit.
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Affiliation(s)
- Daniel Nilsson
- Computational Biology and Biological Physics, Department of Astronomy and Theoretical Physics, Lund University, Sölvegatan 14A, SE-223 62 Lund, Sweden
| | - Anders Irbäck
- Computational Biology and Biological Physics, Department of Astronomy and Theoretical Physics, Lund University, Sölvegatan 14A, SE-223 62 Lund, Sweden
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