1
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Petersen I, Godec A, Ranjbarian F, Hofer A, Mirabello C, Hultqvist G. A charged tail on anti-α-Synuclein antibodies does not enhance their affinity to α-Synuclein fibrils. PLoS One 2024; 19:e0308521. [PMID: 39208301 PMCID: PMC11361660 DOI: 10.1371/journal.pone.0308521] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2024] [Accepted: 07/25/2024] [Indexed: 09/04/2024] Open
Abstract
The aggregation of α-Synuclein (αSyn) is strongly linked to neuronal death in Parkinson's disease and other synucleinopathies. The spreading of aggregated αSyn between neurons is at least partly dependent on electrostatic interactions between positively charged stretches on αSyn fibrils and the negatively charged heparan sulphate proteoglycans on the cell surface. To date there is still no therapeutic option available that could halt the progression of Parkinson's disease and one of the major limitations is likely the relatively low proportion of αSyn aggregates accessible to drugs in the extracellular space. Here, we investigated whether a negatively charged peptide tail fused to the αSyn aggregate-specific antibodies SynO2 and 9E4 could enhance the antibodies' avidity to αSyn aggregates in order to improve their potential therapeutic effect through inhibiting cell-to-cell spreading and enhancing the clearance of extracellular aggregates. We performed ELISAs to test the avidity to αSyn aggregates of both monovalent and bivalent antibody formats with and without the peptide tail. Our results show that the addition of the negatively charged peptide tail decreased the binding strength of both antibodies to αSyn aggregates at physiological salt conditions, which can likely be explained by intermolecular repulsions between the tail and the negatively charged C-terminus of αSyn. Additionally, the tail might interact with the paratopes of the SynO2 antibody abolishing its binding to αSyn aggregates. Conclusively, our peptide tail did not fulfil the required characteristics to improve the antibodies' binding to αSyn aggregates. Fine-tuning the design of the peptide tail to avoid its interaction with the antibodies' CDR and to better mimic relevant characteristics of heparan sulphates for αSyn aggregate binding may help overcome the limitations observed in this study.
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Affiliation(s)
- Inga Petersen
- Department of Pharmacy, Uppsala University, Uppsala, Sweden
| | - Ana Godec
- Department of Pharmacy, Uppsala University, Uppsala, Sweden
| | - Farahnaz Ranjbarian
- Department of Medical Biochemistry and Biophysics, Umeå University, Umeå, Sweden
| | - Anders Hofer
- Department of Medical Biochemistry and Biophysics, Umeå University, Umeå, Sweden
| | - Claudio Mirabello
- Department of Physics, Chemistry and Biology, National Bioinformatics Infrastructure Sweden, Science for Life Laboratory, Linköping University, Linköping, Sweden
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2
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Xu CK, Meisl G, Andrzejewska EA, Krainer G, Dear AJ, Castellana-Cruz M, Turi S, Edu IA, Vivacqua G, Jacquat RPB, Arter WE, Spillantini MG, Vendruscolo M, Linse S, Knowles TPJ. α-Synuclein oligomers form by secondary nucleation. Nat Commun 2024; 15:7083. [PMID: 39153989 PMCID: PMC11330488 DOI: 10.1038/s41467-024-50692-4] [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: 08/27/2023] [Accepted: 07/19/2024] [Indexed: 08/19/2024] Open
Abstract
Oligomeric species arising during the aggregation of α-synuclein are implicated as a major source of toxicity in Parkinson's disease, and thus a major potential drug target. However, both their mechanism of formation and role in aggregation are largely unresolved. Here we show that, at physiological pH and in the absence of lipid membranes, α-synuclein aggregates form by secondary nucleation, rather than simple primary nucleation, and that this process is enhanced by agitation. Moreover, using a combination of single molecule and bulk level techniques, we identify secondary nucleation on the surfaces of existing fibrils, rather than formation directly from monomers, as the dominant source of oligomers. Our results highlight secondary nucleation as not only the key source of oligomers, but also the main mechanism of aggregate formation, and show that these processes take place under conditions which recapitulate the neutral pH and ionic strength of the cytosol.
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Affiliation(s)
- Catherine K Xu
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK
- Max Planck Institute for the Science of Light, Erlangen, Germany
| | - Georg Meisl
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK
| | - Ewa A Andrzejewska
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK
| | - Georg Krainer
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK
- Institute of Molecular Biosciences (IMB), University of Graz, Graz, Austria
| | - Alexander J Dear
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK
- Biochemistry and Structural Biology, Lund University, Lund, Sweden
| | - Marta Castellana-Cruz
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK
| | - Soma Turi
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK
| | - Irina A Edu
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK
| | - Giorgio Vivacqua
- Integrated Research Center (PRAAB), Campus Biomedico University of Rome, Rome, Italy
- Department of Clinical Neurosciences, University of Cambridge, Cambridge, UK
| | - Raphaël P B Jacquat
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK
| | - William E Arter
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK
| | | | - Michele Vendruscolo
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK
| | - Sara Linse
- Biochemistry and Structural Biology, Lund University, Lund, Sweden
| | - Tuomas P J Knowles
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK.
- Cavendish Laboratory, University of Cambridge, Cambridge, UK.
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3
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Zampar S, Di Gregorio SE, Grimmer G, Watts JC, Ingelsson M. "Prion-like" seeding and propagation of oligomeric protein assemblies in neurodegenerative disorders. Front Neurosci 2024; 18:1436262. [PMID: 39161653 PMCID: PMC11330897 DOI: 10.3389/fnins.2024.1436262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2024] [Accepted: 07/17/2024] [Indexed: 08/21/2024] Open
Abstract
Intra- or extracellular aggregates of proteins are central pathogenic features in most neurodegenerative disorders. The accumulation of such proteins in diseased brains is believed to be the end-stage of a stepwise aggregation of misfolded monomers to insoluble cross-β fibrils via a series of differently sized soluble oligomers/protofibrils. Several studies have shown how α-synuclein, amyloid-β, tau and other amyloidogenic proteins can act as nucleating particles and thereby share properties with misfolded forms, or strains, of the prion protein. Although the roles of different protein assemblies in the respective aggregation cascades remain unclear, oligomers/protofibrils are considered key pathogenic species. Numerous observations have demonstrated their neurotoxic effects and a growing number of studies have indicated that they also possess seeding properties, enabling their propagation within cellular networks in the nervous system. The seeding behavior of oligomers differs between the proteins and is also affected by various factors, such as size, shape and epitope presentation. Here, we are providing an overview of the current state of knowledge with respect to the "prion-like" behavior of soluble oligomers for several of the amyloidogenic proteins involved in neurodegenerative diseases. In addition to providing new insight into pathogenic mechanisms, research in this field is leading to novel diagnostic and therapeutic opportunities for neurodegenerative diseases.
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Affiliation(s)
- Silvia Zampar
- Krembil Brain Institute, University Health Network, Toronto, ON, Canada
- Tanz Centre for Research in Neurodegenerative Diseases, University of Toronto, Toronto, ON, Canada
| | - Sonja E. Di Gregorio
- Krembil Brain Institute, University Health Network, Toronto, ON, Canada
- Tanz Centre for Research in Neurodegenerative Diseases, University of Toronto, Toronto, ON, Canada
| | - Gustavo Grimmer
- Krembil Brain Institute, University Health Network, Toronto, ON, Canada
- Tanz Centre for Research in Neurodegenerative Diseases, University of Toronto, Toronto, ON, Canada
| | - Joel C. Watts
- Tanz Centre for Research in Neurodegenerative Diseases, University of Toronto, Toronto, ON, Canada
- Department of Biochemistry, University of Toronto, Toronto, ON, Canada
| | - Martin Ingelsson
- Krembil Brain Institute, University Health Network, Toronto, ON, Canada
- Tanz Centre for Research in Neurodegenerative Diseases, University of Toronto, Toronto, ON, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
- Department of Medicine, University of Toronto, Toronto, ON, Canada
- Department of Public Health/Geriatrics, Rudbeck Laboratory, Uppsala University, Uppsala, Sweden
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4
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Halder B, Ghosh S, Khan T, Pal S, Das N, Sen P. Tracking heterogenous protein aggregation at nanoscale through fluorescence correlation spectroscopy. Photochem Photobiol 2024; 100:989-999. [PMID: 39032082 DOI: 10.1111/php.14004] [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: 02/21/2024] [Revised: 06/18/2024] [Accepted: 06/19/2024] [Indexed: 07/22/2024]
Abstract
Various biophysical techniques have been extensively employed to study protein aggregation due to its significance. Traditionally, these methods detect aggregation at micrometer length scales and micromolar concentrations. However, unlike in vitro, protein aggregation typically occurs at nanomolar concentrations in vivo. Here, using fluorescence correlation spectroscopy (FCS), we captured bromelain aggregation at concentrations as low as ~20 nM, surpassing the detection limit of traditional methods like thioflavin T fluorescence, scattering, and fluorescence microscopy by more than one order of magnitude. Moreover, using thioflavin T fluorescence-based FCS, we have detected larger aggregates at higher bromelain concentrations, which is undetectable in FCS otherwise. Importantly, our study reveals inherent heterogeneity in bromelain aggregation, inaccessible to ensemble-averaged techniques. The presented report may provide a platform for the characterization of premature aggregates at very low protein concentrations, which are thought to be functionally significant species in protein aggregation-induced diseases.
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Affiliation(s)
- Bisal Halder
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur, India
| | - Shreya Ghosh
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur, India
| | - Tanmoy Khan
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur, India
| | - Subhendu Pal
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur, India
| | - Nilimesh Das
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur, India
| | - Pratik Sen
- Department of Chemistry, Indian Institute of Technology Kanpur, Kanpur, India
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5
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Koroleva ON, Kuzmina NV, Dubrovin EV, Drutsa VL. Atomic force microscopy of spherical intermediates on the pathway to fibril formation of influenza A virus nuclear export protein. Microsc Res Tech 2024; 87:1131-1145. [PMID: 38270267 DOI: 10.1002/jemt.24499] [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: 08/25/2023] [Revised: 01/02/2024] [Accepted: 01/07/2024] [Indexed: 01/26/2024]
Abstract
The nuclear export protein of the influenza A virus (NEP) is involved in many important processes of the virus life cycle. This makes it an attractive target for the treatment of a disease caused by a virus. Previously it has been shown, that recombinant variants of NEP are highly prone to aggregation in solution under various conditions with the formation of amyloid-like aggregates. In the present work, the amyloid nature of NEP aggregates was evidenced by Congo red binding assays. Atomic force microscopy has shown that NEP can form two types of spherical nanoparticles, which provide an alternative pathway for the formation of amyloid-like fibrils. Type I of these "fibrillogenic" spheres, formed under physiological conditions, represents the micelle-like particles with height 10-60 nm, which can generate worm-like flexible fibrils with the diameter 2.5-4.0 nm, length 20-500 nm and the Young's modulus ~73 MPa. Type II spherical aggregates with size of about 400-1000 nm, formed at elevated temperatures, includes fractions of drop-like and vesicle-like particles, generating more rigid amyloid-like fibrils with height of ~8 nm, and length of up to 2 μm. The hypothetical mechanism of fibril formation via nanospherical structures was suggested. RESEARCH HIGHLIGHTS: AFM has revealed two types of the influenza A virus nuclear export protein spherical aggregates. They provide an alternative pathway for the formation of amyloid-like fibrils. The mechanism of fibril formation via spherical structures is suggested.
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Affiliation(s)
- Olga N Koroleva
- Faculty of Chemistry, Lomonosov Moscow State University, Moscow, Russian Federation
| | - Natalia V Kuzmina
- Frumkin Institute of Physical Chemistry and Electrochemistry, Russian Academy of Sciences, Moscow, Russian Federation
| | - Evgeniy V Dubrovin
- Faculty of Physics, Lomonosov Moscow State University, Moscow, Russian Federation
- National University of Science and Technology, MISIS, Moscow, Russian Federation
| | - Valeriy L Drutsa
- A.N.Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, Russian Federation
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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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Agha MM, Aziziyan F, Uversky VN. Each big journey starts with a first step: Importance of oligomerization. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2024; 206:111-141. [PMID: 38811079 DOI: 10.1016/bs.pmbts.2024.03.011] [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
Protein oligomers, widely found in nature, have significant physiological and pathological functions. They are classified into three groups based on their function and toxicity. Significant advancements are being achieved in the development of functional oligomers, with a focus on various applications and their engineering. The antimicrobial peptides oligomers play roles in death of bacterial and cancer cells. The predominant pathogenic species in neurodegenerative disorders, as shown by recent results, are amyloid oligomers, which are the main subject of this chapter. They are generated throughout the aggregation process, serving as both intermediates in the subsequent aggregation pathways and ultimate products. Some of them may possess potent cytotoxic properties and through diverse mechanisms cause cellular impairment, and ultimately, the death of cells and disease progression. Information regarding their structure, formation mechanism, and toxicity is limited due to their inherent instability and structural variability. This chapter aims to provide a concise overview of the current knowledge regarding amyloid oligomers.
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Affiliation(s)
- Mansoureh Mirza Agha
- Department of Biochemistry, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Fatemeh Aziziyan
- Department of Biochemistry, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - 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 Staes.
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8
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Stepanchuk AA, Stys PK. Spectral Fluorescence Pathology of Protein Misfolding Disorders. ACS Chem Neurosci 2024; 15:898-908. [PMID: 38407017 DOI: 10.1021/acschemneuro.3c00798] [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: 02/27/2024] Open
Abstract
Protein misfolding has been extensively studied in the context of neurodegenerative disorders and systemic amyloidoses. Due to misfolding and aggregation of proteins being highly heterogeneous and generating a variety of structures, a growing body of evidence illustrates numerous ways how the aggregates contribute to progression of diseases such as Alzheimer's disease, Parkinson's disease, and prion disorders. Different misfolded species of the same protein, commonly referred to as strains, appear to play a significant role in shaping the disease clinical phenotype and clinical progression. The distinct toxicity profiles of various misfolded proteins underscore their importance. Current diagnostics struggle to differentiate among these strains early in the disease course. This review explores the potential of spectral fluorescence approaches to illuminate the complexities of protein misfolding pathology and discusses the applications of advanced spectral methods in the detection and characterization of protein misfolding disorders. By examining spectrally variable probes, current data analysis approaches, and important considerations for the use of these techniques, this review aims to provide an overview of the progress made in this field and highlights directions for future research.
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Affiliation(s)
- Anastasiia A Stepanchuk
- Department of Clinical Neurosciences, Hotchkiss Brain Institute, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada
| | - Peter K Stys
- Department of Clinical Neurosciences, Hotchkiss Brain Institute, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada
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9
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Hivare P, Mujmer K, Swarup G, Gupta S, Bhatia D. Endocytic pathways of pathogenic protein aggregates in neurodegenerative diseases. Traffic 2023; 24:434-452. [PMID: 37392160 DOI: 10.1111/tra.12906] [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: 09/20/2022] [Revised: 05/14/2023] [Accepted: 06/11/2023] [Indexed: 07/03/2023]
Abstract
Endocytosis is the fundamental uptake process through which cells internalize extracellular materials and species. Neurodegenerative diseases (NDs) are characterized by a progressive accumulation of intrinsically disordered protein species, leading to neuronal death. Misfolding in many proteins leads to various NDs such as Alzheimer's disease (AD), Parkinson's disease (PD), Huntington's disease (HD), amyotrophic lateral sclerosis (ALS) and other disorders. Despite the significance of disordered protein species in neurodegeneration, their spread between cells and the cellular uptake of extracellular species is not entirely understood. This review discusses the major internalization mechanisms of the different conformer species of these proteins and their endocytic mechanisms. We briefly introduce the broad types of endocytic mechanisms found in cells and then summarize what is known about the endocytosis of monomeric, oligomeric and aggregated conformations of tau, Aβ, α-Syn, Huntingtin, Prions, SOD1, TDP-43 and other proteins associated with neurodegeneration. We also highlight the key players involved in internalizing these disordered proteins and the several techniques and approaches to identify their endocytic mechanisms. Finally, we discuss the obstacles involved in studying the endocytosis of these protein species and the need to develop better techniques to elucidate the uptake mechanisms of a particular disordered protein species.
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Affiliation(s)
- Pravin Hivare
- Biological Engineering Discipline, Indian Institute of Technology Gandhinagar, Palaj, Gujarat, India
| | - Kratika Mujmer
- Center for Brain and Cognitive Sciences, Indian Institute of Technology Gandhinagar, Palaj, Gujarat, India
| | - Gitanjali Swarup
- Biological Engineering Discipline, Indian Institute of Technology Gandhinagar, Palaj, Gujarat, India
| | - Sharad Gupta
- Biological Engineering Discipline, Indian Institute of Technology Gandhinagar, Palaj, Gujarat, India
- Center for Biomedical Engineering, Indian Institute of Technology Gandhinagar, Palaj, Gujarat, India
| | - Dhiraj Bhatia
- Biological Engineering Discipline, Indian Institute of Technology Gandhinagar, Palaj, Gujarat, India
- Center for Biomedical Engineering, Indian Institute of Technology Gandhinagar, Palaj, Gujarat, India
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10
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Mahapatra S, Sarbahi A, Punia N, Joshi A, Avni A, Walimbe A, Mukhopadhyay S. ATP modulates self-perpetuating conformational conversion generating structurally distinct yeast prion amyloids that limit autocatalytic amplification. J Biol Chem 2023; 299:104654. [PMID: 36990219 PMCID: PMC10149227 DOI: 10.1016/j.jbc.2023.104654] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 03/07/2023] [Accepted: 03/21/2023] [Indexed: 03/30/2023] Open
Abstract
Prion-like self-perpetuating conformational conversion of proteins into amyloid aggregates is associated with both transmissible neurodegenerative diseases and non-Mendelian inheritance. The cellular energy currency ATP is known to indirectly regulate the formation, dissolution, or transmission of amyloid-like aggregates by providing energy to the molecular chaperones that maintain protein homeostasis. In this work, we demonstrate that ATP molecules, independent of any chaperones, modulate the formation and dissolution of amyloids from a yeast prion domain (NM domain of Saccharomyces cerevisiae Sup35) and restricts autocatalytic amplification by controlling the amount of fragmentable and seeding-competent aggregates. ATP, at (high) physiological concentrations in the presence of Mg2+, kinetically accelerates NM aggregation. Interestingly, ATP also promotes phase-separation-mediated aggregation of a human protein harboring a yeast prion-like domain. We also show that ATP disaggregates preformed NM fibrils in a dose-independent manner. Our results indicate that ATP-mediated disaggregation, unlike the disaggregation by the disaggregase Hsp104, yields no oligomers that are considered one of the critical species for amyloid transmission. Furthermore, high concentrations of ATP delimited the number of seeds by giving rise to compact, ATP-bound NM fibrils that exhibited nominal fragmentation by either free ATP or Hsp104 disaggregase to generate lower molecular weight amyloids. Additionally, (low) pathologically relevant ATP concentrations restricted autocatalytic amplification by forming structurally distinct amyloids which are found seeding-inefficient due to their reduced β-content. Our results provide key mechanistic underpinnings of concentration-dependent chemical chaperoning by ATP against prion-like transmissions of amyloids.
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Affiliation(s)
- Sayanta Mahapatra
- 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.
| | - Anusha Sarbahi
- 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
| | - Neha Punia
- 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
| | - Ashish Joshi
- 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
| | - Anamika Avni
- Centre for Protein Science, Design and Engineering, 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
| | - Anuja Walimbe
- 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
| | - 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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11
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Ajmal MR. Protein Misfolding and Aggregation in Proteinopathies: Causes, Mechanism and Cellular Response. Diseases 2023; 11:30. [PMID: 36810544 PMCID: PMC9944956 DOI: 10.3390/diseases11010030] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Revised: 02/02/2023] [Accepted: 02/05/2023] [Indexed: 02/11/2023] Open
Abstract
Proteins are central to life functions. Alterations in the structure of proteins are reflected in their function. Misfolded proteins and their aggregates present a significant risk to the cell. Cells have a diverse but integrated network of protection mechanisms. Streams of misfolded proteins that cells are continuously exposed to must be continually monitored by an elaborated network of molecular chaperones and protein degradation factors to control and contain protein misfolding problems. Aggregation inhibition properties of small molecules such as polyphenols are important as they possess other beneficial properties such as antioxidative, anti-inflammatory, and pro-autophagic properties and help neuroprotection. A candidate with such desired features is important for any possible treatment development for protein aggregation diseases. There is a need to study the protein misfolding phenomenon so that we can treat some of the worst kinds of human ailments related to protein misfolding and aggregation.
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Affiliation(s)
- Mohammad Rehan Ajmal
- Physical Biochemistry Research Laboratory, Biochemistry Department, Faculty of Science, University of Tabuk, Tabuk 71491, Saudi Arabia
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12
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Tsoi PS, Quan MD, Ferreon JC, Ferreon ACM. Aggregation of Disordered Proteins Associated with Neurodegeneration. Int J Mol Sci 2023; 24:3380. [PMID: 36834792 PMCID: PMC9966039 DOI: 10.3390/ijms24043380] [Citation(s) in RCA: 23] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2023] [Revised: 02/02/2023] [Accepted: 02/06/2023] [Indexed: 02/10/2023] Open
Abstract
Cellular deposition of protein aggregates, one of the hallmarks of neurodegeneration, disrupts cellular functions and leads to neuronal death. Mutations, posttranslational modifications, and truncations are common molecular underpinnings in the formation of aberrant protein conformations that seed aggregation. The major proteins involved in neurodegeneration include amyloid beta (Aβ) and tau in Alzheimer's disease, α-synuclein in Parkinson's disease, and TAR DNA-binding protein (TDP-43) in amyotrophic lateral sclerosis (ALS). These proteins are described as intrinsically disordered and possess enhanced ability to partition into biomolecular condensates. In this review, we discuss the role of protein misfolding and aggregation in neurodegenerative diseases, specifically highlighting implications of changes to the primary/secondary (mutations, posttranslational modifications, and truncations) and the quaternary/supramolecular (oligomerization and condensation) structural landscapes for the four aforementioned proteins. Understanding these aggregation mechanisms provides insights into neurodegenerative diseases and their common underlying molecular pathology.
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Affiliation(s)
| | | | - Josephine C. Ferreon
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Allan Chris M. Ferreon
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, Houston, TX 77030, USA
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13
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Housmans JAJ, Wu G, Schymkowitz J, Rousseau F. A guide to studying protein aggregation. FEBS J 2023; 290:554-583. [PMID: 34862849 DOI: 10.1111/febs.16312] [Citation(s) in RCA: 56] [Impact Index Per Article: 56.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Revised: 11/18/2021] [Accepted: 12/03/2021] [Indexed: 02/04/2023]
Abstract
Disrupted protein folding or decreased protein stability can lead to the accumulation of (partially) un- or misfolded proteins, which ultimately cause the formation of protein aggregates. Much of the interest in protein aggregation is associated with its involvement in a wide range of human diseases and the challenges it poses for large-scale biopharmaceutical manufacturing and formulation of therapeutic proteins and peptides. On the other hand, protein aggregates can also be functional, as observed in nature, which triggered its use in the development of biomaterials or therapeutics as well as for the improvement of food characteristics. Thus, unmasking the various steps involved in protein aggregation is critical to obtain a better understanding of the underlying mechanism of amyloid formation. This knowledge will allow a more tailored development of diagnostic methods and treatments for amyloid-associated diseases, as well as applications in the fields of new (bio)materials, food technology and therapeutics. However, the complex and dynamic nature of the aggregation process makes the study of protein aggregation challenging. To provide guidance on how to analyse protein aggregation, in this review we summarize the most commonly investigated aspects of protein aggregation with some popular corresponding methods.
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Affiliation(s)
- Joëlle A J Housmans
- Switch Laboratory, VIB Center for Brain and Disease Research, Leuven, Belgium.,Switch Laboratory, Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium
| | - Guiqin Wu
- Switch Laboratory, VIB Center for Brain and Disease Research, Leuven, Belgium.,Switch Laboratory, Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium
| | - Joost Schymkowitz
- Switch Laboratory, VIB Center for Brain and Disease Research, Leuven, Belgium.,Switch Laboratory, Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium
| | - Frederic Rousseau
- Switch Laboratory, VIB Center for Brain and Disease Research, Leuven, Belgium.,Switch Laboratory, Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium
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14
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Li Z, Wu H, Ji Y, Shi Z, Liu S, Bao X, Shan P, Hu D, Li M. Toward Reagent-Free Discrimination of Alzheimer's Disease Using Blood Plasma Spectral Digital Biomarkers and Machine Learning. J Alzheimers Dis 2023; 95:1175-1188. [PMID: 37661884 DOI: 10.3233/jad-230248] [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: 09/05/2023]
Abstract
BACKGROUND Alzheimer's disease (AD) is the most prevalent neurodegenerative disease. The detection of early-stage AD is particularly desirable because it would allow early intervention. However, a minimally invasive, low-cost, and accurate discrimination or diagnostic method for AD is especially difficult in the earliest stage of AD. OBJECTIVE The aim of this research is to discover blood plasma spectral digital biomarkers of AD, develop a novel intelligent method for the discrimination of AD and accelerate the translation of Fourier transform infrared (FTIR) spectral-based disease discrimination methods from the laboratory to clinical practice. METHODS Since vibration spectroscopy can provide the structure and chemical composition information of biological samples at the molecular level, we investigated the potential of FTIR spectral biomarkers of blood plasma to differentiate between AD patients and healthy controls. Combined with machine learning technology, we designed a hierarchical discrimination system that provides reagent-free and accurate AD discrimination based on blood plasma spectral digital biomarkers of AD. RESULTS Accurate segregation between AD patients and healthy controls was achieved with 89.3% sensitivity and 85.7% specificity for early-stage AD patients, 92.8% sensitivity and 87.5% specificity for middle-stage AD patients, and 100% sensitivity and 100% specificity for late-stage AD patients. CONCLUSIONS Our results show that blood plasma spectral digital biomarkers hold great promise as discrimination markers of AD, indicating the potential for the development of an inexpensive, reagent-free, and less laborious clinical test. As a result, our research outcome will accelerate the clinical application of spectral digital biomarkers and machine learning.
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Affiliation(s)
- Zhigang Li
- College of Information Science and Engineering, Northeastern University, Shenyang, China
- Hebei Key Laboratory of Micro-Nano Precision Optical Sensing and Measurement Technology, Qinhuangdao, China
| | - Hao Wu
- Department of Neurology, Tianjin Huanhu Hospital, Tianjin, China
- Tianjin Key Laboratory of Cerebral Vascular and Neurodegenerative Diseases, Tianjin Dementia Institute, Tianjin, China
| | - Yong Ji
- Department of Neurology, Tianjin Huanhu Hospital, Tianjin, China
- Tianjin Key Laboratory of Cerebral Vascular and Neurodegenerative Diseases, Tianjin Dementia Institute, Tianjin, China
| | - Zhihong Shi
- Department of Neurology, Tianjin Huanhu Hospital, Tianjin, China
- Tianjin Key Laboratory of Cerebral Vascular and Neurodegenerative Diseases, Tianjin Dementia Institute, Tianjin, China
| | - Shuai Liu
- Department of Neurology, Tianjin Huanhu Hospital, Tianjin, China
- Tianjin Key Laboratory of Cerebral Vascular and Neurodegenerative Diseases, Tianjin Dementia Institute, Tianjin, China
| | - Xinran Bao
- First Hospital of Qinhuangdao, Qinhuangdao, China
| | - Peng Shan
- College of Information Science and Engineering, Northeastern University, Shenyang, China
- Hebei Key Laboratory of Micro-Nano Precision Optical Sensing and Measurement Technology, Qinhuangdao, China
| | - Dean Hu
- College of Information Science and Engineering, Northeastern University, Shenyang, China
- Hebei Key Laboratory of Micro-Nano Precision Optical Sensing and Measurement Technology, Qinhuangdao, China
| | - Meimei Li
- College of Information Science and Engineering, Northeastern University, Shenyang, China
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15
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Dasari AKR, Lim KH. CD and Solid-State NMR Studies of Low-Order Oligomers of Transthyretin. Methods Mol Biol 2023; 2551:311-320. [PMID: 36310212 DOI: 10.1007/978-1-0716-2597-2_21] [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: 06/16/2023]
Abstract
Characterization of oligomeric intermediate states populated at an early stage of misfolding and aggregation is essential to understanding molecular mechanism of pathogenic protein aggregation. Growing evidence also suggests that oligomeric species are more toxic than mature fibrillar counterparts. Here, we describe procedures for isolating oligomeric species of an aggregation-prone protein, transthyretin, associated with protein misfolding disorders, including cardiomyopathy and polyneuropathy. We also describe methods for structural studies of the oligomeric species using circular dichroism and solid-state NMR spectroscopy. These methods can be applied to structural characterization of oligomeric intermediates of other aggregation-prone proteins.
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Affiliation(s)
- Anvesh K R Dasari
- Department of Chemistry, East Carolina University, Greenville, NC, USA
| | - Kwang Hun Lim
- Department of Chemistry, East Carolina University, Greenville, NC, USA.
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16
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Kim JR. Oligomerization by co-assembly of β-amyloid and α-synuclein. Front Mol Biosci 2023; 10:1153839. [PMID: 37021111 PMCID: PMC10067735 DOI: 10.3389/fmolb.2023.1153839] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2023] [Accepted: 03/07/2023] [Indexed: 04/07/2023] Open
Abstract
Aberrant self-assembly of an intrinsically disordered protein is a pathological hallmark of protein misfolding diseases, such as Alzheimer's and Parkinson's diseases (AD and PD, respectively). In AD, the 40-42 amino acid-long extracellular peptide, β-amyloid (Aβ), self-assembles into oligomers, which eventually aggregate into fibrils. A similar self-association of the 140 amino acid-long intracellular protein, α-synuclein (αS), is responsible for the onset of PD pathology. While Aβ and αS are primarily extracellular and intracellular polypeptides, respectively, there is evidence of their colocalization and pathological overlaps of AD and PD. This evidence has raised the likelihood of synergistic, toxic protein-protein interactions between Aβ and αS. This mini review summarizes the findings of studies on Aβ-αS interactions related to enhanced oligomerization via co-assembly, aiming to provide a better understanding of the complex biology behind AD and PD and common pathological mechanisms among the major neurodegenerative diseases.
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17
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Wu K, Sun W, Li D, Diao J, Xiu P. Inhibition of Amyloid Nucleation by Steric Hindrance. J Phys Chem B 2022; 126:10045-10054. [PMID: 36417323 DOI: 10.1021/acs.jpcb.2c06330] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Despite recent experiments and simulations suggesting that small-molecule inhibitors and some post-translational modifications (e.g., glycosylation and ubiquitination) can suppress the pathogenic aggregation of proteins due to steric hindrance, the effect of steric hindrance on amyloid formation has not been systematically studied. Based on Monte Carlo simulations using a coarse-grained model for amyloidogenic proteins and a hard sphere acting as steric hindrance, we investigated how steric hindrance on proteins could affect amyloid formation, particularly two steps of primary nucleation, namely, oligomerization and conformational conversion into a β-sheet-enriched nucleus. We found that steric spheres played an inhibitory role in oligomerization with the effect proportional to the sphere radius RS, which we attributed to the decline in the nonspecific attractions between proteins. During the second step, small steric spheres facilitated the conformational conversion of proteins while large ones suppressed the conversion. The overall steric effect on amyloid nucleation was inhibitory regardless of RS. As RS increased, oligomeric assemblies changed from amorphous into sheet-like, structurally ordered species, reminiscent of the structure of amyloid fibrils. The oligomers with large RS were off-pathway with their ordered structures induced by the competition between steric hindrance and nonspecific attractions of soluble proteins. Interestingly, the equimolar mixture of proteins with and without steric hindrance amplified the sterically inhibitory effect by increasing the energy barrier of protein's conformational conversion. The physical mechanisms and biological implications of the above results are discussed. Our findings improve the current understanding of how nature regulates protein aggregation and amyloid formation by steric hindrance.
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Affiliation(s)
- Kai Wu
- Department of Engineering Mechanics, Zhejiang University, Hangzhou 310027, People's Republic of China.,School of Physical Sciences, University of Chinese Academy of Sciences, Beijing 100049, China.,Wenzhou Institute, University of Chinese Academy of Sciences, Wenzhou 325001, China.,Department of Cancer Biology, University of Cincinnati College of Medicine, Cincinnati, Ohio 45267, United States of America
| | - Wuxuepeng Sun
- Department of Engineering Mechanics, Zhejiang University, Hangzhou 310027, People's Republic of China
| | - Dechang Li
- Department of Engineering Mechanics, Zhejiang University, Hangzhou 310027, People's Republic of China
| | - Jiajie Diao
- Department of Cancer Biology, University of Cincinnati College of Medicine, Cincinnati, Ohio 45267, United States of America
| | - Peng Xiu
- Department of Engineering Mechanics, Zhejiang University, Hangzhou 310027, People's Republic of China
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18
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Rhomboid protease RHBDL4 promotes retrotranslocation of aggregation-prone proteins for degradation. Cell Rep 2022; 40:111175. [PMID: 35947953 PMCID: PMC9437926 DOI: 10.1016/j.celrep.2022.111175] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 06/02/2022] [Accepted: 07/18/2022] [Indexed: 11/22/2022] Open
Abstract
Protein degradation is fundamentally important to ensure cell homeostasis. In the endoplasmic reticulum (ER), the ER-associated degradation (ERAD) pathway targets incorrectly folded and unassembled proteins for turnover by the cytoplasmic proteasome. Previously, we showed that the rhomboid protease RHBDL4, together with p97, mediates membrane protein degradation. However, whether RHBDL4 acts in concert with additional ERAD components is unclear, and its full substrate spectrum remains to be defined. Here, we show that, in addition to membrane proteins, RHBDL4 cleaves aggregation-prone luminal ERAD substrates. Since mutations of the RHBDL4 rhomboid domain led to stabilization of substrates at the cytoplasmic side, we hypothesize that, analogous to the homolog ERAD factor derlin, RHBDL4 is directly involved in substrate retrotranslocation. RHBDL4's interaction with the erlin ERAD complex and reciprocal interaction of rhomboid substrates with erlins suggest that RHBDL4 and erlins form a complex that clips substrates and thereby rescues aggregation-prone peptides in the ER from aggregation.
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19
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Mahapatra S, Sarbahi A, Madhu P, Swasthi HM, Sharma A, Singh P, Mukhopadhyay S. Sub-stoichiometric Hsp104 regulates the genesis and persistence of self-replicable amyloid seeds of Sup35 prion domain. J Biol Chem 2022; 298:102143. [PMID: 35714774 PMCID: PMC9304785 DOI: 10.1016/j.jbc.2022.102143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Revised: 06/01/2022] [Accepted: 06/07/2022] [Indexed: 11/21/2022] Open
Abstract
Prion-like self-perpetuating conformational conversion of proteins is involved in both transmissible neurodegenerative diseases in mammals and non-Mendelian inheritance in yeast. The transmissibility of amyloid-like aggregates is dependent on the stoichiometry of chaperones such as heat shock proteins (Hsps), including disaggregases. To provide the mechanistic underpinnings of the formation and persistence of prefibrillar amyloid seeds, we investigated the role of substoichiometric Hsp104 on the in vitro amyloid aggregation of the prion domain (NM-domain) of Saccharomyces cerevisiae Sup35. At low substoichiometric concentrations, we show Hsp104 exhibits a dual role: it considerably accelerates the formation of prefibrillar species by shortening the lag phase but also prolongs their persistence by introducing unusual kinetic halts and delaying their conversion into mature amyloid fibers. Additionally, Hsp104-modulated amyloid species displayed a better seeding capability compared to NM-only amyloids. Using biochemical and biophysical tools coupled with site-specific dynamic readouts, we characterized the distinct structural and dynamical signatures of these amyloids. We reveal that Hsp104-remodeled amyloidogenic species are compositionally diverse in prefibrillar aggregates and are packed in a more ordered fashion compared to NM-only amyloids. Finally, we show these Hsp104-remodeled, conformationally distinct NM aggregates display an enhanced autocatalytic self-templating ability that might be crucial for phenotypic outcomes. Taken together, our results demonstrate that substoichiometric Hsp104 promotes compositional diversity and conformational modulations during amyloid formation, yielding effective prefibrillar seeds that are capable of driving prion-like Sup35 propagation. Our findings underscore the key functional and pathological roles of substoichiometric chaperones in prion-like propagation.
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Affiliation(s)
- Sayanta Mahapatra
- Centre for Protein Science, Design and Engineering; Department of Biological Sciences
| | - Anusha Sarbahi
- Centre for Protein Science, Design and Engineering; Department of Biological Sciences
| | - Priyanka Madhu
- Centre for Protein Science, Design and Engineering; Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Punjab, India
| | - Hema M Swasthi
- Centre for Protein Science, Design and Engineering; Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Punjab, India
| | - Abhishek Sharma
- CSIR-Institute of Microbial Technology (IMTECH), Chandigarh, India
| | - Priyanka Singh
- CSIR-Institute of Microbial Technology (IMTECH), Chandigarh, India
| | - Samrat Mukhopadhyay
- Centre for Protein Science, Design and Engineering; Department of Biological Sciences; Department of Chemical Sciences, Indian Institute of Science Education and Research (IISER) Mohali, Punjab, India.
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20
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Gao L, Xie X, Liu P, Jin J. High-avidity binding drives nucleation of amyloidogenic transthyretin monomer. JCI Insight 2022; 7:150131. [PMID: 35393947 PMCID: PMC9057628 DOI: 10.1172/jci.insight.150131] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Accepted: 02/23/2022] [Indexed: 11/17/2022] Open
Abstract
Amyloidosis involves stepwise growth of fibrils assembled from soluble precursors. Transthyretin (TTR) naturally folds into a stable tetramer, whereas conditions and mutations that foster aberrant monomer formations facilitate TTR oligomeric aggregation and subsequent fibril extension. We investigated the early assembly of oligomers by WT TTR compared with its V30M and V122I variants. We monitored time-dependent redistribution among monomer, dimer, tetramer, and oligomer contents in the presence and absence of multimeric TTR seeds. The seeds were artificially constructed recombinant multimers that contained 20–40 TTR subunits via engineered biotin-streptavidin (SA) interactions. As expected, these multimer seeds rapidly nucleated TTR monomers into larger complexes, while having less effect on dimers and tetramers. In vivo, SA-induced multimers formed TTR-like deposits in the heart and the kidney following i.v. injection in mice. While all 3 variants prominently deposited glomerulus in the kidney, only V30M resulted in extensive deposition in the heart. The cardiac TTR deposits varied in size and shape and were localized in the intermyofibrillar space along the capillaries. These results are consistent with the notion of monomeric TTR engaging in high-avidity interactions with tissue amyloids. Our multimeric induction approach provides a model for studying the initiation of TTR deposition in the heart.
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Affiliation(s)
- Li Gao
- Feinberg Cardiovascular and Renal Research Institute, Northwestern University, Feinberg School of Medicine, Chicago, Illinois, USA.,Department of Cardiology, and
| | - Xinfang Xie
- Feinberg Cardiovascular and Renal Research Institute, Northwestern University, Feinberg School of Medicine, Chicago, Illinois, USA.,Department of Nephrology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Pan Liu
- Feinberg Cardiovascular and Renal Research Institute, Northwestern University, Feinberg School of Medicine, Chicago, Illinois, USA
| | - Jing Jin
- Feinberg Cardiovascular and Renal Research Institute, Northwestern University, Feinberg School of Medicine, Chicago, Illinois, USA
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21
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Mee Hayes E, Sirvio L, Ye Y. A Potential Mechanism for Targeting Aggregates With Proteasomes and Disaggregases in Liquid Droplets. Front Aging Neurosci 2022; 14:854380. [PMID: 35517053 PMCID: PMC9062979 DOI: 10.3389/fnagi.2022.854380] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Accepted: 02/18/2022] [Indexed: 01/26/2023] Open
Abstract
Insoluble protein deposits are hallmarks of neurodegenerative disorders and common forms of dementia. The aberrant aggregation of misfolded proteins involves a complex cascade of events that occur over time, from the cellular to the clinical phase of neurodegeneration. Declining neuronal health through increased cell stress and loss of protein homeostasis (proteostasis) functions correlate with the accumulation of aggregates. On the cellular level, increasing evidence supports that misfolded proteins may undergo liquid-liquid phase separation (LLPS), which is emerging as an important process to drive protein aggregation. Studying, the reverse process of aggregate disassembly and degradation has only recently gained momentum, following reports of enzymes with distinct aggregate-disassembly activities. In this review, we will discuss how the ubiquitin-proteasome system and disaggregation machineries such as VCP/p97 and HSP70 system may disassemble and/or degrade protein aggregates. In addition to their canonically associated functions, these enzymes appear to share a common feature: reversibly assembling into liquid droplets in an LLPS-driven manner. We review the role of LLPS in enhancing the disassembly of aggregates through locally increasing the concentration of these enzymes and their co-proteins together within droplet structures. We propose that such activity may be achieved through the concerted actions of disaggregase machineries, the ubiquitin-proteasome system and their co-proteins, all of which are condensed within transient aggregate-associated droplets (TAADs), ultimately resulting in aggregate clearance. We further speculate that sustained engagement of these enzymatic activities within TAADs will be detrimental to normal cellular functions, where these activities are required. The possibility of facilitating endogenous disaggregation and degradation activities within TAADs potentially represents a novel target for therapeutic intervention to restore protein homeostasis at the early stages of neurodegeneration.
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Affiliation(s)
- Emma Mee Hayes
- Division of Neuroscience, Department of Brain Sciences, Imperial College London, London, United Kingdom
- UK Dementia Research Institute at Imperial College London, London, United Kingdom
| | - Liina Sirvio
- Division of Neuroscience, Department of Brain Sciences, Imperial College London, London, United Kingdom
- UK Dementia Research Institute at Imperial College London, London, United Kingdom
| | - Yu Ye
- Division of Neuroscience, Department of Brain Sciences, Imperial College London, London, United Kingdom
- UK Dementia Research Institute at Imperial College London, London, United Kingdom
- *Correspondence: Yu Ye,
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22
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Chau E, Kim JR. α-synuclein-assisted oligomerization of β-amyloid (1-42). Arch Biochem Biophys 2022; 717:109120. [PMID: 35041853 PMCID: PMC8818042 DOI: 10.1016/j.abb.2022.109120] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 12/24/2021] [Accepted: 01/12/2022] [Indexed: 11/02/2022]
Abstract
Alzheimer's disease (AD) and Parkinson's disease (PD) are the two most common neurodegenerative disorders, characterized by aggregation of amyloid polypeptides, β-amyloid (Aβ) and α-synuclein (αS), respectively. Aβ and αS follow similar aggregation pathways, starting from monomers, to soluble toxic oligomeric assemblies, and to insoluble fibrils. Various studies have suggested overlaps in the pathologies of AD and PD, and have shown Aβ-αS interactions. Unfortunately, whether these protein-protein interactions lead to self- and co-assembly of Aβ and αS into oligomers - a potentially toxic synergistic mechanism - is poorly understood. Among the various Aβ isoforms, interactions of Aβ containing 42 amino acids (Aβ (1-42), referred to as Aβ42) with αS are of most direct relevance due to the high aggregation propensity and the strong toxic effect of this Aβ isoform. In this study, we carefully determined molecular consequences of interactions between Aβ42 and αS in their respective monomeric, oligomeric, and fibrillar forms using a comprehensive set of experimental tools. We show that the three αS conformers, namely, monomers, oligomers and fibrils interfered with fibrillization of Aβ42. Specifically, αS monomers and oligomers promoted oligomerization and stabilization of soluble Aβ42, possibly via direct binding or co-assembly, while αS fibrils hindered soluble Aβ42 species from converting into insoluble aggregates by the formation of large oligomers. We also provide evidence that the interactions with αS were mediated by various parts of Aβ42, depending on Aβ42 and αS conformers. Furthermore, we compared similarities and dissimilarities between Aβ42-αS and Aβ40-αS interactions. Overall, the present study provides a comprehensive depiction of the molecular interplay between Aβ42 and αS, providing insight into its synergistic toxic mechanism.
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Affiliation(s)
- Edward Chau
- Department of Chemical and Biomolecular Engineering, New York University, 6 MetroTech Center, Brooklyn, NY, 11201, USA
| | - Jin Ryoun Kim
- Department of Chemical and Biomolecular Engineering, New York University, 6 MetroTech Center, Brooklyn, NY, 11201, USA.
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23
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Hjalte J, Hossain S, Hugerth A, Sjögren H, Wahlgren M, Larsson P, Lundberg D. Aggregation Behavior of Structurally Similar Therapeutic Peptides Investigated by 1H NMR and All-Atom Molecular Dynamics Simulations. Mol Pharm 2022; 19:904-917. [PMID: 35104408 PMCID: PMC8905580 DOI: 10.1021/acs.molpharmaceut.1c00883] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 01/20/2022] [Accepted: 01/20/2022] [Indexed: 11/30/2022]
Abstract
Understanding of peptide aggregation propensity is an important aspect in pharmaceutical development of peptide drugs. In this work, methodologies based on all-atom molecular dynamics (AA-MD) simulations and 1H NMR (in neat H2O) were evaluated as tools for identification and investigation of peptide aggregation. A series of structurally similar, pharmaceutically relevant peptides with known differences in aggregation behavior (D-Phe6-GnRH, ozarelix, cetrorelix, and degarelix) were investigated. The 1H NMR methodology was used to systematically investigate variations in aggregation with peptide concentration and time. Results show that 1H NMR can be used to detect the presence of coexisting classes of aggregates and the inclusion or exclusion of counterions in peptide aggregates. Interestingly, results suggest that the acetate counterions are included in aggregates of ozarelix and cetrorelix but not in aggregates of degarelix. The peptides investigated in AA-MD simulations (D-Phe6-GnRH, ozarelix, and cetrorelix) showed the same rank order of aggregation propensity as in the NMR experiments. The AA-MD simulations also provided molecular-level insights into aggregation dynamics, aggregation pathways, and the influence of different structural elements on peptide aggregation propensity and intermolecular interactions within the aggregates. Taken together, the findings from this study illustrate that 1H NMR and AA-MD simulations can be useful, complementary tools in early evaluation of aggregation propensity and formulation development for peptide drugs.
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Affiliation(s)
- Johanna Hjalte
- Food
Technology, Engineering and Nutrition, Lund
University, Box 124, 221 00 Lund, Sweden
| | - Shakhawath Hossain
- Department
of Pharmacy, Drug Delivery, Uppsala University, Box 580, 751 23 Uppsala, Sweden
| | - Andreas Hugerth
- Ferring
Pharmaceuticals A/S, Amager Strandvej 405, 2770 Kastrup, Denmark
| | - Helen Sjögren
- Ferring
Pharmaceuticals A/S, Amager Strandvej 405, 2770 Kastrup, Denmark
| | - Marie Wahlgren
- Food
Technology, Engineering and Nutrition, Lund
University, Box 124, 221 00 Lund, Sweden
| | - Per Larsson
- Department
of Pharmacy, Drug Delivery, Uppsala University, Box 580, 751 23 Uppsala, Sweden
| | - Dan Lundberg
- CR
Competence AB, Center for Chemistry and Chemical Engineering, Box 124, 221 00 Lund, Sweden
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24
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Leite DM, Seifi M, Ruiz-Perez L, Nguemo F, Plomann M, Swinny JD, Battaglia G. Syndapin-2 mediated transcytosis of amyloid-ß across the blood-brain barrier. Brain Commun 2022; 4:fcac039. [PMID: 35233527 PMCID: PMC8882007 DOI: 10.1093/braincomms/fcac039] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2021] [Revised: 10/31/2021] [Accepted: 02/15/2022] [Indexed: 11/14/2022] Open
Abstract
A deficient transport of amyloid-β across the blood–brain barrier, and its diminished clearance from the brain, contribute to neurodegenerative and vascular pathologies, such as Alzheimer’s disease and cerebral amyloid angiopathy, respectively. At the blood–brain barrier, amyloid-β efflux transport is associated with the low-density lipoprotein receptor-related protein 1. However, the precise mechanisms governing amyloid-β transport across the blood–brain barrier, in health and disease, remain to be fully understood. Recent evidence indicates that the low-density lipoprotein receptor-related protein 1 transcytosis occurs through a tubulation-mediated mechanism stabilized by syndapin-2. Here, we show that syndapin-2 is associated with amyloid-β clearance via low-density lipoprotein receptor-related protein 1 across the blood–brain barrier. We further demonstrate that risk factors for Alzheimer’s disease, amyloid-β expression and ageing, are associated with a decline in the native expression of syndapin-2 within the brain endothelium. Our data reveals that syndapin-2-mediated pathway, and its balance with the endosomal sorting, are important for amyloid-β clearance proposing a measure to evaluate Alzheimer’s disease and ageing, as well as a target for counteracting amyloid-β build-up. Moreover, we provide evidence for the impact of the avidity of amyloid-β assemblies in their trafficking across the brain endothelium and in low-density lipoprotein receptor-related protein 1 expression levels, which may affect the overall clearance of amyloid-β across the blood–brain barrier.
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Affiliation(s)
- Diana M. Leite
- Department of Chemistry, University College London, London, United Kingdom
- Institute for the Physics of Living Systems, University College London, London, United Kingdom
| | - Mohsen Seifi
- Leicester School of Pharmacy, Faculty of Health and Life Sciences, De Montfort University, Leicester, United Kingdom
| | - Lorena Ruiz-Perez
- Department of Chemistry, University College London, London, United Kingdom
- Institute for the Physics of Living Systems, University College London, London, United Kingdom
| | - Filomain Nguemo
- Institute for Neurophysiology, Faculty of Medicine, University of Cologne, Cologne, Germany
| | - Markus Plomann
- Institute of Biochemistry, Faculty of Medicine, University of Cologne, Cologne, Germany
| | - Jerome D. Swinny
- School of Pharmacy and Biomedical Sciences, University of Portsmouth, United Kingdom
| | - Giuseppe Battaglia
- Department of Chemistry, University College London, London, United Kingdom
- Institute for the Physics of Living Systems, University College London, London, United Kingdom
- Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute for Science and Technology (BIST), Barcelona, Spain
- Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, Spain
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25
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Han Q, Brown SJ, Drummond CJ, Greaves TL. Protein aggregation and crystallization with ionic liquids: Insights into the influence of solvent properties. J Colloid Interface Sci 2022; 608:1173-1190. [PMID: 34735853 DOI: 10.1016/j.jcis.2021.10.087] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 10/13/2021] [Accepted: 10/15/2021] [Indexed: 12/13/2022]
Abstract
Ionic liquids (ILs) have been used in solvents for proteins in many applications, including biotechnology, pharmaceutics, and medicine due to their tunable physicochemical and biological properties. Protein aggregation is often undesirable, and predominantly occurs during bioprocesses, while the aggregation process can be reversible or irreversible and the aggregates formed can be native/non-native and soluble/insoluble. Recent studies have clearly identified key properties of ILs and IL-water mixtures related to protein performance, suggesting the use of the tailorable properties of ILs to inhibit protein aggregation, to promote protein crystallization, and to control protein aggregation pathways. This review discusses the critical properties of IL and IL-water mixtures and presents the latest understanding of the protein aggregation pathways and the development of IL systems that affect or control the protein aggregation process. Through this feature article, we hope to inspire further advances in understanding and new approaches to controlling protein behavior to optimize bioprocesses.
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Affiliation(s)
- Qi Han
- School of Science, STEM College, RMIT University, 124 La Trobe Street, Melbourne, VIC 3000, Australia
| | - Stuart J Brown
- School of Science, STEM College, RMIT University, 124 La Trobe Street, Melbourne, VIC 3000, Australia
| | - Calum J Drummond
- School of Science, STEM College, RMIT University, 124 La Trobe Street, Melbourne, VIC 3000, Australia
| | - Tamar L Greaves
- School of Science, STEM College, RMIT University, 124 La Trobe Street, Melbourne, VIC 3000, Australia.
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26
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Zhou X, Fennema Galparsoro D, Østergaard Madsen A, Vetri V, van de Weert M, Mørck Nielsen H, Foderà V. Polysorbate 80 controls Morphology, structure and stability of human insulin Amyloid-Like spherulites. J Colloid Interface Sci 2022; 606:1928-1939. [PMID: 34695760 DOI: 10.1016/j.jcis.2021.09.132] [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: 06/26/2021] [Revised: 09/09/2021] [Accepted: 09/21/2021] [Indexed: 01/09/2023]
Abstract
Amyloid protein aggregates are not only associated with neurodegenerative diseases and may also occur as unwanted by-products in protein-based therapeutics. Surfactants are often employed to stabilize protein formulations and reduce the risk of aggregation. However, surfactants alter protein-protein interactions and may thus modulate the physicochemical characteristics of any aggregates formed. Human insulin aggregation was induced at low pH in the presence of varying concentrations of the surfactant polysorbate 80. Various spectroscopic and imaging methods were used to study the aggregation kinetics, as well as structure and morphology of the formed aggregates. Molecular dynamics simulations were employed to investigate the initial interaction between the surfactant and insulin. Addition of polysorbate 80 slowed down, but did not prevent, aggregation of insulin. Amyloid spherulites formed under all conditions, with a higher content of intermolecular beta-sheets in the presence of the surfactant above its critical micelle concentration. In addition, a denser packing was observed, leading to a more stable aggregate. Molecular dynamics simulations suggested a tendency for insulin to form dimers in the presence of the surfactant, indicating a change in protein-protein interactions. It is thus shown that surfactants not only alter aggregation kinetics, but also affect physicochemical properties of any aggregates formed.
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Affiliation(s)
- Xin Zhou
- Drug Delivery and Biophysics of Biopharmaceuticals, Department of Pharmacy, University of Copenhagen, Universitetsparken 2, Copenhagen 2100, Denmark
| | - Dirk Fennema Galparsoro
- Dipartimento di Fisica e Chimica, Università di Palermo, Viale delle Scienze, Ed. 18, Palermo 90128, Italy
| | - Anders Østergaard Madsen
- Manufacturing and Materials, Department of Pharmacy, University of Copenhagen, Universitetsparken 2, Copenhagen 2100, Denmark
| | - Valeria Vetri
- Dipartimento di Fisica e Chimica, Università di Palermo, Viale delle Scienze, Ed. 18, Palermo 90128, Italy.
| | - Marco van de Weert
- Drug Delivery and Biophysics of Biopharmaceuticals, Department of Pharmacy, University of Copenhagen, Universitetsparken 2, Copenhagen 2100, Denmark
| | - Hanne Mørck Nielsen
- Drug Delivery and Biophysics of Biopharmaceuticals, Department of Pharmacy, University of Copenhagen, Universitetsparken 2, Copenhagen 2100, Denmark
| | - Vito Foderà
- Drug Delivery and Biophysics of Biopharmaceuticals, Department of Pharmacy, University of Copenhagen, Universitetsparken 2, Copenhagen 2100, Denmark.
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27
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TAT-RHIM: a more complex issue than expected. Biochem J 2022; 479:259-272. [PMID: 35015082 PMCID: PMC8883498 DOI: 10.1042/bcj20210677] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 01/10/2022] [Accepted: 01/11/2022] [Indexed: 11/17/2022]
Abstract
Murine cytomegalovirus protein M45 contains a RIP homotypic interaction motif (RHIM) that is sufficient to confer protection of infected cells against necroptotic cell death. Mechanistically, the N-terminal region of M45 drives rapid self-assembly into homo-oligomeric amyloid fibrils, and interacts with the endogenous RHIM domains of receptor-interacting protein kinases (RIPK) 1, RIPK3, Z-DNA binding protein 1, and TIR domain-containing adaptor-inducing interferon-β. Remarkably, all four mammalian proteins harbouring such a RHIM domain are key components of inflammatory signalling and regulated cell death processes. Immunogenic cell death by regulated necrosis causes extensive tissue damage in a wide range of diseases, including ischemia reperfusion injury, myocardial infarction, sepsis, stroke and organ transplantation. To harness the cell death suppression properties of M45 protein in a therapeutically usable manner, we developed a synthetic peptide encompassing only the RHIM domain of M45. To trigger delivery of RHIM into target cells, we fused the transactivator protein transduction domain of human immunodeficiency virus 1 to the N-terminus of the peptide. The fused peptide could efficiently penetrate eukaryotic cells, but unexpectedly it killed all tested cancer cell lines and primary cells irrespective of species without further stimulus through a necrosis-like cell death. Typical inhibitors of different forms of regulated cell death cannot impede this process, which appears to involve a direct disruption of biomembranes. Nevertheless, our finding has potential clinical relevance; reliable induction of a necrotic form of cell death distinct from all known forms of regulated cell death may offer a novel therapeutic approach to combat resistant tumour cells.
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28
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Arghavani P, Pirhaghi M, Moosavi-Movahedi F, Mamashli F, Hosseini E, Moosavi-Movahedi AA. Amyloid management by chaperones: The mystery underlying protein oligomers’ dual functions. Curr Res Struct Biol 2022; 4:356-364. [DOI: 10.1016/j.crstbi.2022.11.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Revised: 11/24/2022] [Accepted: 11/25/2022] [Indexed: 12/12/2022] Open
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King KM, Sharp AK, Davidson DS, Brown AM, Lemkul JA. Impact of Electronic Polarization on Preformed, β-Strand Rich Homogenous and Heterogeneous Amyloid Oligomers. JOURNAL OF COMPUTATIONAL BIOPHYSICS AND CHEMISTRY 2021; 21:449-460. [PMID: 35756548 DOI: 10.1142/s2737416521420059] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Amyloids are a subset of intrinsically disordered proteins (IDPs) that self-assemble into cross-[Formula: see text] oligomers and fibrils. The structural plasticity of amyloids leads to sampling of metastable, low-molecular-weight oligomers that contribute to cytotoxicity. Of interest are amyloid-[Formula: see text] (A[Formula: see text] and islet amyloid polypeptide (IAPP), which are involved in the pathology of Alzheimer’s disease and Type 2 diabetes mellitus, respectively. In addition to forming homogenous oligomers and fibrils, these species have been found to cross-aggregate in heterogeneous structures. Biophysical properties, including electronic effects, that are unique or conserved between homogenous and heterogeneous amyloids oligomers are thus far unexplored. Here, we simulated homogenous and heterogeneous amyloid oligomers of A[Formula: see text] and IAPP[Formula: see text] fragments using the Drude oscillator model to investigate the impact of electronic polarization on the structural morphology and stability of preformed hexamers. Upon simulation of preformed, [Formula: see text]-strand rich oligomers with Drude, structural rearrangement occurred causing some loss of [Formula: see text]-strand structure in favor of random coil content for all oligomers. Homogenous A[Formula: see text] was the most stable system, deriving stability from low polarization in hydrophobic residues and through salt bridge formation. Changes in polarization were observed primarily for A[Formula: see text] residues in heterogeneous cross-amyloid systems, displaying a decrease in charged residue dipole moments and an increase in hydrophobic sidechain dipole moments. This work is the first study utilizing the Drude-2019 force field with amyloid oligomers, providing insight into the impact of electronic effects on oligomer structure and highlighting the importance of different microenvironments on amyloid oligomer stability.
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Affiliation(s)
- Kelsie M. King
- Program in Genetics, Bioinformatics, and Computational Biology, Virginia Tech, 340 West Campus Dr, Blacksburg, VA 24061, USA
| | - Amanda K. Sharp
- Program in Genetics, Bioinformatics, and Computational Biology, Virginia Tech, 340 West Campus Dr, Blacksburg, VA 24061, USA
| | - Darcy S. Davidson
- Department of Biochemistry, Virginia Tech, 340 West Campus, Dr Blacksburg, VA 24061, USA
| | - Anne M. Brown
- Program in Genetics, Bioinformatics, and Computational Biology, Virginia Tech, 340 West Campus Dr, Blacksburg, VA 24061, USA
- Department of Biochemistry, Virginia Tech, 340 West Campus, Dr Blacksburg, VA 24061, USA
- University Libraries, Virginia Tech, 560 Drillfield, Dr Blacksburg, VA 24061, USA
| | - Justin A. Lemkul
- Department of Biochemistry, Virginia Tech, 340 West Campus, Dr Blacksburg, VA 24061, USA
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30
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Dey A, Vishvakarma V, Das A, Kallianpur M, Dey S, Joseph R, Maiti S. Single Molecule Measurements of the Accessibility of Molecular Surfaces. Front Mol Biosci 2021; 8:745313. [PMID: 34926574 PMCID: PMC8672140 DOI: 10.3389/fmolb.2021.745313] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Accepted: 11/03/2021] [Indexed: 11/13/2022] Open
Abstract
An important measure of the conformation of protein molecules is the degree of surface exposure of its specific segments. However, this is hard to measure at the level of individual molecules. Here, we combine single molecule photobleaching (smPB, which resolves individual photobleaching steps of single molecules) and fluorescence quenching techniques to measure the accessibility of individual fluorescently labeled protein molecules to quencher molecules in solution. A quencher can reduce the time a fluorophore spends in the excited state, increasing its photostability under continuous irradiation. Consequently, the photo-bleaching step length would increase, providing a measure for the accessibility of the fluorophore to the solvent. We demonstrate the method by measuring the bleaching step-length increase in a lipid, and also in a lipid-anchored peptide (both labelled with rhodamine-B and attached to supported lipid bilayers). The fluorophores in both molecules are expected to be solvent-exposed. They show a near two-fold increase in the step length upon incubation with 5 mM tryptophan (a quencher of rhodamine-B), validating our approach. A population distribution plot of step lengths before and after addition of tryptophan show that the increase is not always homogenous. Indeed there are different species present with differential levels of exposure. We then apply this technique to determine the solvent exposure of membrane-attached N-terminus labelled amylin (h-IAPP, an amyloid associated with Type II diabetes) whose interaction with lipid bilayers is poorly understood. hIAPP shows a much smaller increase of the step length, signifying a lower level of solvent exposure of its N-terminus. Analysis of results from individual molecules and step length distribution reveal that there are at least two different conformers of amylin in the lipid bilayer. Our results show that our method (“Q-SLIP”, Quenching-induced Step Length increase in Photobleaching) provides a simple route to probe the conformational states of membrane proteins at a single molecule level.
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Affiliation(s)
- Arpan Dey
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Mumbai, India
| | - Vicky Vishvakarma
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Mumbai, India
| | - Anirban Das
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Mumbai, India
| | - Mamata Kallianpur
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Mumbai, India
| | - Simli Dey
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Mumbai, India
| | - Roshni Joseph
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Mumbai, India
| | - Sudipta Maiti
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Mumbai, India
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31
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Niyangoda C, Barton J, Bushra N, Karunarathne K, Strauss G, Fakhre F, Koria P, Muschol M. Origin, toxicity and characteristics of two amyloid oligomer polymorphs. RSC Chem Biol 2021; 2:1631-1642. [PMID: 34977578 PMCID: PMC8637835 DOI: 10.1039/d1cb00081k] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Accepted: 08/18/2021] [Indexed: 11/25/2022] Open
Abstract
There is compelling evidence that small oligomeric aggregates, emerging during the assembly of amyloid fibrils and plaques, are important molecular pathogens in many amyloid diseases. While significant progress has been made in revealing the mechanisms underlying fibril growth, understanding how amyloid oligomers fit into the fibril assembly process, and how they contribute to the pathogenesis of amyloid diseases, has remained elusive. Commonly, amyloid oligomers are considered to be metastable, early-stage precursors to fibril formation that are either on- or off-pathway from fibril growth. In addition, amyloid oligomers have been reported to colocalize with late-stage fibrils and plaques. Whether these early and late-stage oligomer species are identical or distinct, and whether both are relevant to pathogenesis remains unclear. Here we report on the formation of two distinct oligomer species of lysozyme, formed either during the early or late-stages of in vitro fibril growth. We further observe that the pH change from in vitro growth conditions to cell media used for toxicity studies induced distinct mesoscopic precipitates, two of which resemble either diffuse or neuritic plaques seen in Alzheimer's histology. Our biophysical characterization indicates that both oligomer species share morphological and tinctorial features considered characteristic for amyloid oligomers. At the same time, their sizes, morphologies, their immunostaining, detailed tinctorial profiles and, most prominently, their biological activity are clearly distinct from each other. Probing the conditions promoting the formation of these two distinct oligomer species suggests distinct roles of charge interactions, hydrophobicity and monomer flexibility in directing oligomer assembly.
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Affiliation(s)
| | - Jeremy Barton
- Dept. of Physics, University of South Florida Tampa FL 33620 USA
| | - Nabila Bushra
- Dept. of Physics, University of South Florida Tampa FL 33620 USA
| | | | - Graham Strauss
- Dept. of Chemical and Biomedical Engineering, University of South Florida Tampa FL 33620 USA
| | - Fadia Fakhre
- Dept. of Physics, University of South Florida Tampa FL 33620 USA
| | - Piyush Koria
- Dept. of Chemical and Biomedical Engineering, University of South Florida Tampa FL 33620 USA
| | - Martin Muschol
- Dept. of Physics, University of South Florida Tampa FL 33620 USA
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32
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Saffari B, Amininasab M. Crocin Inhibits the Fibrillation of Human α-synuclein and Disassembles Mature Fibrils: Experimental Findings and Mechanistic Insights from Molecular Dynamics Simulation. ACS Chem Neurosci 2021; 12:4037-4057. [PMID: 34636232 DOI: 10.1021/acschemneuro.1c00379] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
The aggregation of human alpha-synuclein (hαS) is pivotally implicated in the development of most types of synucleinopathies. Molecules that can inhibit or reverse the aggregation process of amyloidogenic proteins have potential therapeutic value. The anti-aggregating activity of multiple carotenoid compounds has been reported over the past decades against a growing list of amyloidogenic polypeptides. Here, we aimed to determine whether crocin, the main carotenoid glycoside component of saffron, would inhibit hαS aggregation or could disassemble its preformed fibrils. By employing a series of biochemical and biophysical techniques, crocin was exhibited to inhibit hαS fibrillation in a dose-dependent fashion by stabilizing very early aggregation intermediates in off-pathway non-toxic conformations with little β-sheet content. We also observed that crocin at high concentrations could efficiently destabilize mature fibrils and disassemble them into seeding-incompetent intermediates by altering their β-sheet conformation and reshaping their structure. Our atomistic molecular dynamics (MD) simulations demonstrated that crocin molecules bind to both the non amyloid-β component (NAC) region and C-terminal domain of hαS. These interactions could thereby stabilize the autoinhibitory conformation of the protein and prevent it from adopting aggregation-prone structures. MD simulations further suggested that ligand molecules prefer to reside longitudinally along the fibril axis onto the edges of the inter-protofilament interface where they establish hydrogen and hydrophobic bonds with steric zipper stabilizing residues. These interactions turned out to destabilize hαS fibrils by altering the interstrand twist angles, increasing the rigidity of the fibril core, and elevating its radius of gyration. Our findings suggest the potential pharmaceutical implication of crocin in synucleinopathies.
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Affiliation(s)
- Babak Saffari
- Department of Cell and Molecular Biology, School of Biology, College of Science, University of Tehran, Tehran 14155-6455, Iran
| | - Mehriar Amininasab
- Department of Cell and Molecular Biology, School of Biology, College of Science, University of Tehran, Tehran 14155-6455, Iran
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33
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Kalsoom U, Alazmi M, Farrukh HSUB, Chung KHK, Alshammari N, Kakinen A, Chotana GA, Javed I, Davis TP, Saleem RSZ. Structure Dependent Differential Modulation of Aβ Fibrillization by Selenadiazole-Based Inhibitors. ACS Chem Neurosci 2021; 12:3806-3817. [PMID: 34595924 DOI: 10.1021/acschemneuro.1c00478] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Misfolding and fibrillar aggregation of Aβ is a characteristic hallmark of Alzheimer's disease and primarily participates in neurodegenerative pathologies. There has been no breakthrough made in the therapeutic regime of Alzheimer's disease while the pharmacological interventions against Aβ are designed to sequester and clear Aβ burden from the neurological tissues. Based on the physiological relevance of Aβ, therapeutic approaches are required to inhibit and stabilize Aβ fibrillization, instead of cleaning it from the neurological system. In this context, we have designed a selenadiazole-based library of compounds against the fibrillization paradigm of Aβ. Compounds that completely inhibited the Aβ fibrillization appeared to stabilize Aβ at the monomeric stage as indicated by ThT assay, CD spectrophotometry, and TEM imaging. Partial inhibitors elongated the nucleation phase and allowed limited fibrillization of Aβ into smaller fragments with slightly higher β-sheets contents, while noninhibitors did not interfere in Aβ aggregation and resulted in mature fibrils with fibrillization kinetics similar to Aβ control. Molecular docking revealed the different binding positions of the compounds for three classes. Complete inhibitors alleviated Aβ toxicity to SH-SY5Y neuroblastoma cells and permeated across the blood-brain barrier in zebrafish larvae. The amino acid residues from Aβ peptide that interacted with the compounds from all three classes were overlapping and majorly lying in the amyloidogenic regions. However, compounds that stabilize Aβ monomers displayed higher association constants (Ka) and lower dissociation constants (Kd) in comparison to partial and noninhibitors, as corroborated by ITC. These results support further structure activity-based preclinical development of these selenadiazole compounds for potential anti-Alzheimer's therapy.
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Affiliation(s)
- Umme Kalsoom
- Department of Chemistry and Chemical Engineering, Syed Babar Ali School of Science and Engineering, Lahore University of Management Sciences, Lahore 54792, Pakistan
| | - Meshari Alazmi
- Department of Information and Computer Science, College of Computer Science and Engineering, University of Ha’il, P.O. Box 2440, Ha’il 81411, Saudi Arabia
| | - Hafiz Syed Usama Bin Farrukh
- Department of Chemistry and Chemical Engineering, Syed Babar Ali School of Science and Engineering, Lahore University of Management Sciences, Lahore 54792, Pakistan
| | - Ka Hang Karen Chung
- Australian Institute for Bioengineering and Nanotechnology, University of Queensland, Brisbane, Queensland 4072, Australia
| | - Nawaf Alshammari
- Department of Biology, College of Sciences, University of Ha’il, P.O. Box 2440, Ha’il 81411, Saudi Arabia
| | - Aleksandr Kakinen
- Australian Institute for Bioengineering and Nanotechnology, University of Queensland, Brisbane, Queensland 4072, Australia
| | - Ghayoor Abbas Chotana
- Department of Chemistry and Chemical Engineering, Syed Babar Ali School of Science and Engineering, Lahore University of Management Sciences, Lahore 54792, Pakistan
| | - Ibrahim Javed
- Australian Institute for Bioengineering and Nanotechnology, University of Queensland, Brisbane, Queensland 4072, Australia
| | - Thomas Paul Davis
- Australian Institute for Bioengineering and Nanotechnology, University of Queensland, Brisbane, Queensland 4072, Australia
| | - Rahman Shah Zaib Saleem
- Department of Chemistry and Chemical Engineering, Syed Babar Ali School of Science and Engineering, Lahore University of Management Sciences, Lahore 54792, Pakistan
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Tikader B, Maji SK, Kar S. A generic approach to decipher the mechanistic pathway of heterogeneous protein aggregation kinetics. Chem Sci 2021; 12:13530-13545. [PMID: 34777773 PMCID: PMC8528017 DOI: 10.1039/d1sc03190b] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Accepted: 09/01/2021] [Indexed: 12/31/2022] Open
Abstract
Amyloid formation is a generic property of many protein/polypeptide chains. A broad spectrum of proteins, despite having diversity in the inherent precursor sequence and heterogeneity present in the mechanism of aggregation produces a common cross β-spine structure that is often associated with several human diseases. However, a general modeling framework to interpret amyloid formation remains elusive. Herein, we propose a data-driven mathematical modeling approach that elucidates the most probable interaction network for the aggregation of a group of proteins (α-synuclein, Aβ42, Myb, and TTR proteins) by considering an ensemble set of network models, which include most of the mechanistic complexities and heterogeneities related to amyloidogenesis. The best-fitting model efficiently quantifies various timescales involved in the process of amyloidogenesis and explains the mechanistic basis of the monomer concentration dependency of amyloid-forming kinetics. Moreover, the present model reconciles several mutant studies and inhibitor experiments for the respective proteins, making experimentally feasible non-intuitive predictions, and provides further insights about how to fine-tune the various microscopic events related to amyloid formation kinetics. This might have an application to formulate better therapeutic measures in the future to counter unwanted amyloidogenesis. Importantly, the theoretical method used here is quite general and can be extended for any amyloid-forming protein.
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Affiliation(s)
| | - Samir K Maji
- Department of Biosciences and Bioengineering, IIT Bombay Powai Mumbai - 400076 India
| | - Sandip Kar
- Department of Chemistry, IIT Bombay Powai Mumbai - 400076 India
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35
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Lin LE, Miao K, Qian C, Wei L. High spatial-resolution imaging of label-free in vivo protein aggregates by VISTA. Analyst 2021; 146:4135-4145. [PMID: 33949430 PMCID: PMC8238904 DOI: 10.1039/d1an00060h] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Amyloid aggregation, formed by aberrant proteins, is a pathological hallmark for neurodegenerative diseases, including Alzheimer's disease and Huntington's disease. High-resolution holistic mapping of the fine structures from these aggregates should facilitate our understanding of their pathological roles. Here, we achieved label-free high-resolution imaging of the polyQ and the amyloid-beta (Aβ) aggregates in cells and tissues utilizing a sample-expansion stimulated Raman strategy. We further focused on characterizing the Aβ plaques in 5XFAD mouse brain tissues. 3D volumetric imaging enabled visualization of the whole plaques, resolving both the fine protein filaments and the surrounding components. Coupling our expanded label-free Raman imaging with machine learning, we obtained specific segmentation of aggregate cores, peripheral filaments together with cell nuclei and blood vessels by pre-trained convolutional neural network models. Combining with 2-channel fluorescence imaging, we achieved a 6-color holistic view of the same sample. This ability for precise and multiplex high-resolution imaging of the protein aggregates and their micro-environment without the requirement of labeling would open new biomedical applications.
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Affiliation(s)
- Li-En Lin
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, USA.
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36
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Sahoo BR, Panda PK, Liang W, Tang WJ, Ahuja R, Ramamoorthy A. Degradation of Alzheimer's Amyloid-β by a Catalytically Inactive Insulin-Degrading Enzyme. J Mol Biol 2021; 433:166993. [PMID: 33865867 PMCID: PMC8169600 DOI: 10.1016/j.jmb.2021.166993] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2020] [Revised: 03/24/2021] [Accepted: 04/06/2021] [Indexed: 02/06/2023]
Abstract
It is known that insulin-degrading-enzyme (IDE) plays a crucial role in the clearance of Alzheimer's amyloid-β (Aβ). The cysteine-free IDE mutant (cf-E111Q-IDE) is catalytically inactive against insulin, but its effect on Aβ degradation is unknown that would help in the allosteric modulation of the enzyme activity. Herein, the degradation of Aβ(1-40) by cf-E111Q-IDE via a non-chaperone mechanism is demonstrated by NMR and LC-MS, and the aggregation of fragmented peptides is characterized using fluorescence and electron microscopy. cf-E111Q-IDE presented a reduced effect on the aggregation kinetics of Aβ(1-40) when compared with the wild-type IDE. Whereas LC-MS and diffusion ordered NMR spectroscopy revealed the generation of Aβ fragments by both wild-type and cf-E111Q-IDE. The aggregation propensities and the difference in the morphological phenotype of the full-length Aβ(1-40) and its fragments are explained using multi-microseconds molecular dynamics simulations. Notably, our results reveal that zinc binding to Aβ(1-40) inactivates cf-E111Q-IDE's catalytic function, whereas zinc removal restores its function as evidenced from high-speed AFM, electron microscopy, chromatography, and NMR results. These findings emphasize the catalytic role of cf-E111Q-IDE on Aβ degradation and urge the development of zinc chelators as an alternative therapeutic strategy that switches on/off IDE's function.
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Affiliation(s)
- Bikash R Sahoo
- Biophysics, Department of Chemistry, Macromolecular Engineering and Science, and Biomedical Engineering, University of Michigan, Ann Arbor, MI 48109, USA
| | - Pritam Kumar Panda
- Condensed Matter Theory Group, Materials Theory Division, Department of Physics and Astronomy, Uppsala University, Box 516, SE-75120 Uppsala, Sweden
| | - Wenguang Liang
- Ben-May Department for Cancer Research, The University of Chicago, Chicago, IL 60637, USA
| | - Wei-Jen Tang
- Ben-May Department for Cancer Research, The University of Chicago, Chicago, IL 60637, USA
| | - Rajeev Ahuja
- Condensed Matter Theory Group, Materials Theory Division, Department of Physics and Astronomy, Uppsala University, Box 516, SE-75120 Uppsala, Sweden; Applied Materials Physics, Department of Materials Science and Engineering, Royal Institute of Technology (KTH) SE-10044 Stockholm, Sweden
| | - Ayyalusamy Ramamoorthy
- Biophysics, Department of Chemistry, Macromolecular Engineering and Science, and Biomedical Engineering, University of Michigan, Ann Arbor, MI 48109, USA.
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37
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Mohammadi F, Takalloo Z, Rahmani H, Nasiri Khalili MA, Khajeh K, Riazi G, H Sajedi R. Interplay of isoform 1N4R tau protein and amyloid-β peptide fragment 25-35 in reducing and non-reducing conditions. J Biochem 2021; 169:119-134. [PMID: 32857841 DOI: 10.1093/jb/mvaa101] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Accepted: 08/14/2020] [Indexed: 11/13/2022] Open
Abstract
Amyloid-β (Aβ) peptide and tau protein are two hallmark proteins in Alzheimer's disease (AD); however, the parameters, which mediate the abnormal aggregation of Aβ and tau, have not been fully discovered. Here, we have provided an optimum method to purify tau protein isoform 1N4R by using nickel-nitrilotriacetic acid agarose chromatography under denaturing condition. The biochemical and biophysical properties of the purified protein were further characterized using in vitro tau filament assembly, tubulin polymerization assay, circular dichroism (CD) spectroscopy and atomic force microscopy. Afterwards, we investigated the effect of tau protein on aggregation of Aβ (25-35) peptide using microscopic imaging and cell viability assay. Incubation of tau at physiologic and supra-physiologic concentrations with Aβ25-35 for 40 days under reducing and non-reducing conditions revealed formation of two types of aggregates with distinct morphologies and dimensions. In non-reducing condition, the co-incubated sample showed granular aggregates, while in reducing condition, they formed annular protofibrils. Results from cell viability assay revealed the increased cell viability for the co-incubated sample. Therefore, the disassembling action shown by tau protein on Aβ25-35 suggests the possibility that tau may have a protective role in preventing Aβ peptide from acquiring the cytotoxic, aggregated form against oxidative stress damages.
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Affiliation(s)
- Fatemeh Mohammadi
- Department of Biochemistry, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Jalal AleAhmad Highway, P.O.Box: 14115-111, Iran
| | - Zeinab Takalloo
- Department of Biochemistry, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Jalal AleAhmad Highway, P.O.Box: 14115-111, Iran
| | - Hossein Rahmani
- Department of Biochemistry, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Jalal AleAhmad Highway, P.O.Box: 14115-111, Iran
| | - Mohammad Ali Nasiri Khalili
- Department of Bioscience and Biotechnology, Malek Ashtar University of Technology, Tehran, Lavizan, Babaei Highway, P.O.Box: 15875-1774, Iran
| | - Khosro Khajeh
- Department of Biochemistry, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Jalal AleAhmad Highway, P.O.Box: 14115-111, Iran
| | - Gholamhossein Riazi
- Institute of Biochemistry and Biophysics (IBB), University of Tehran, Tehran, Enghelab Square, Postal Code: 1417466191, Iran
| | - Reza H Sajedi
- Department of Biochemistry, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Jalal AleAhmad Highway, P.O.Box: 14115-111, Iran
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Palazzi L, Fongaro B, Leri M, Acquasaliente L, Stefani M, Bucciantini M, Polverino de Laureto P. Structural Features and Toxicity of α-Synuclein Oligomers Grown in the Presence of DOPAC. Int J Mol Sci 2021; 22:ijms22116008. [PMID: 34199427 PMCID: PMC8199589 DOI: 10.3390/ijms22116008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Revised: 05/30/2021] [Accepted: 05/30/2021] [Indexed: 12/20/2022] Open
Abstract
The interplay between α-synuclein and dopamine derivatives is associated with oxidative stress-dependent neurodegeneration in Parkinson’s disease (PD). The formation in the dopaminergic neurons of intraneuronal inclusions containing aggregates of α-synuclein is a typical hallmark of PD. Even though the biochemical events underlying the aberrant aggregation of α-synuclein are not completely understood, strong evidence correlates this process with the levels of dopamine metabolites. In vitro, 3,4-dihydroxyphenylacetaldehyde (DOPAL) and the other two metabolites, 3,4-dihydroxyphenylacetic acid (DOPAC) and 3,4-dihydroxyphenylethanol (DOPET), share the property to inhibit the growth of mature amyloid fibrils of α-synuclein. Although this effect occurs with the formation of differently toxic products, the molecular basis of this inhibition is still unclear. Here, we provide information on the effect of DOPAC on the aggregation properties of α-synuclein and its ability to interact with membranes. DOPAC inhibits α-synuclein aggregation, stabilizing monomer and inducing the formation of dimers and trimers. DOPAC-induced oligomers did not undergo conformational transition in the presence of membranes, and penetrated the cell, where they triggered autophagic processes. Cellular assays showed that DOPAC reduced cytotoxicity and ROS production induced by α-synuclein aggregates. Our findings show that the early radicals resulting from DOPAC autoxidation produced covalent modifications of the protein, which were not by themselves a primary cause of either fibrillation or membrane binding inhibition. These findings are discussed in the light of the potential mechanism of DOPAC protection against the toxicity of α-synuclein aggregates to better understand protein and catecholamine biology and to eventually suggest a scaffold that can help in the design of candidate molecules able to interfere in α-synuclein aggregation.
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Affiliation(s)
- Luana Palazzi
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova, 35131 Padova, Italy; (L.P.); (B.F.); (L.A.)
| | - Benedetta Fongaro
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova, 35131 Padova, Italy; (L.P.); (B.F.); (L.A.)
| | - Manuela Leri
- Department of Biomedical, Experimental and Clinical Sciences, University of Firenze, 50134 Firenze, Italy; (M.L.); (M.S.); (M.B.)
| | - Laura Acquasaliente
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova, 35131 Padova, Italy; (L.P.); (B.F.); (L.A.)
| | - Massimo Stefani
- Department of Biomedical, Experimental and Clinical Sciences, University of Firenze, 50134 Firenze, Italy; (M.L.); (M.S.); (M.B.)
| | - Monica Bucciantini
- Department of Biomedical, Experimental and Clinical Sciences, University of Firenze, 50134 Firenze, Italy; (M.L.); (M.S.); (M.B.)
| | - Patrizia Polverino de Laureto
- Department of Pharmaceutical and Pharmacological Sciences, University of Padova, 35131 Padova, Italy; (L.P.); (B.F.); (L.A.)
- Correspondence:
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Misra P, Ramirez-Alvarado M. Early events in light chain aggregation at physiological pH reveal new insights on assembly, stability, and aggregate dissociation. Amyloid 2021; 28:113-124. [PMID: 33533277 PMCID: PMC8848840 DOI: 10.1080/13506129.2021.1877129] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
Early events in immunoglobulin light chain (AL) amyloid formation are especially important as some early intermediates formed during the aggregation reaction are cytotoxic and play a critical role in the initiation of amyloid assembly. We investigated the early events in in vitro aggregation of cardiac amyloidosis AL proteins at pH 7.4. In this study we make distinctions between general aggregation and amyloid formation. Aggregation is defined by the disappearance of monomers and the detection of sedimentable intermediates we call non-fibrillar macromolecular (NFM) intermediates by transmission electron microscopy (TEM). Amyloid formation is defined by the disappearance of monomers, Thioflavin T fluorescence enhancement, and the presence of fibrils by TEM. All proteins aggregated at very similar rates via the formation of NFM intermediates. The condensed NFM intermediates were composed of non-native monomers. Amyloid formation and amyloid yield was variable among the different proteins. During the stationary phase, all proteins demonstrated different degrees of dissociation. These dissociated species could play a key role in the already complex pathophysiology of AL amyloidosis. The degree of dissociation is inversely proportional to the amyloid yield. Our results highlight the importance and physiological consequences of intermediates/fibril dissociation in AL amyloidosis.
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Affiliation(s)
- Pinaki Misra
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, USA
| | - Marina Ramirez-Alvarado
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, USA.,Department of Immunology, Mayo Clinic, Rochester, MN, USA
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Shin EJ, Park JW. Nanoaggregates Derived from Amyloid-beta and Alpha-synuclein Characterized by Sequential Quadruple Force Mapping. NANO LETTERS 2021; 21:3789-3797. [PMID: 33845574 DOI: 10.1021/acs.nanolett.1c00058] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Overlapping of Alzheimer's disease and Parkinson's disease is associated with the formation of hetero-oligomers derived from amyloid-beta and alpha-synuclein. However, the structural identity of the hetero-oligomer has yet to be elucidated, particularly at high resolution. Here, with atomic force microscopy, the surface structure of hetero-oligomer was examined with four AFM tips tethering one of the selected antibodies recognizing N-terminus or C-terminus of each peptide. All aggregates were found to be hetero-oligomers, and probability of recognizing the termini is higher than that for the homo-oligomers, suggesting that the termini of the former have a greater tendency to be located at the surface or the termini have more freedom to be recognized, probably through loose packing. The methodology in this study provides us with a new approach to elucidate the structure of such aggregates at the single-molecule level, allowing the exploration of other intrinsically disordered proteins frequently found in nature.
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Affiliation(s)
- Eun Ji Shin
- Department of Chemistry, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang 37673, Republic of Korea
| | - Joon Won Park
- Department of Chemistry, Pohang University of Science and Technology, 77 Cheongam-Ro, Nam-Gu, Pohang 37673, Republic of Korea
- Institute of Convergence Science, Yonsei University, 50 Yonsei-ro, Seodaemun-gu, Seoul, 03722, Republic of Korea
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Abstract
Protein aggregation and amyloid formation are pathogenic events underlying the development of an increasingly large number of human diseases named “proteinopathies”. Abnormal accumulation in affected tissues of amyloid β (Aβ) peptide, islet amyloid polypeptide (IAPP), and the prion protein, to mention a few, are involved in the occurrence of Alzheimer’s (AD), type 2 diabetes mellitus (T2DM) and prion diseases, respectively. Many reports suggest that the toxic properties of amyloid aggregates are correlated with their ability to damage cell membranes. However, the molecular mechanisms causing toxic amyloid/membrane interactions are still far to be completely elucidated. This review aims at describing the mutual relationships linking abnormal protein conformational transition and self-assembly into amyloid aggregates with membrane damage. A cross-correlated analysis of all these closely intertwined factors is thought to provide valuable insights for a comprehensive molecular description of amyloid diseases and, in turn, the design of effective therapies.
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Smeralda W, Since M, Cardin J, Corvaisier S, Lecomte S, Cullin C, Malzert-Fréon A. β-Amyloid peptide interactions with biomimetic membranes: A multiparametric characterization. Int J Biol Macromol 2021; 181:769-777. [PMID: 33811932 DOI: 10.1016/j.ijbiomac.2021.03.107] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Revised: 02/14/2021] [Accepted: 03/19/2021] [Indexed: 10/21/2022]
Abstract
Alzheimer's disease is the most common form of senile dementia in the world, and amyloid β peptide1-42 (Aβ1-42) is one of its two principal biological hallmarks. While interactome concept was getting forward the scientific community, we proposed that the study of the molecular interactions of amyloid β peptide with the biological membranes will allow to highlight underlying mechanisms responsive of AD. We have developed two simple liposomal formulations (phosphatidylcholine, cholesterol, phosphatidylglycerol) mimicking neuronal cell membrane (composition, charge, curvature radius). Interactions with Aβ1-42 and mutant oG37C, a stable oligomeric form of the peptide, were characterized according to a simple multiparametric procedure based on ThT fluorescence, liposome leakage assay, ATR-FTIR spectroscopy. Kinetic aggregation, membrane damage and peptide conformation provided our first methodologic bases to develop an original model to describe interactions of Aβ peptide and lipids.
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Affiliation(s)
| | - Marc Since
- Normandie Univ, UNICAEN, CERMN, 14000 Caen, France.
| | - Julien Cardin
- NIMPH Team, CIMAP CNRS UMR 6252, EnsiCaen-UNICAEN-CEA, 14050 Caen, France.
| | | | - Sophie Lecomte
- CBMN, CNRS UMR 5248, Univ. Bordeaux, 33600 Pessac, France.
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Wang Y, Guo Z, Tan T, Ji Y, Hu J, Zhang Y. The effects of nanobubbles on the assembly of glucagon amyloid fibrils. SOFT MATTER 2021; 17:3486-3493. [PMID: 33657201 DOI: 10.1039/d0sm02279a] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Some recent studies have shown that the surface and interface play an important role in the assembly and aggregation of amyloid proteins. However, it is unclear how the gas-liquid interface affects the protein assembly at the nanometer scale although the presence of gas-liquid interfaces is very common in in vitro experiments. Nanobubbles have a large specific surface area, which provides a stage for interactions with various proteins and peptides on the nanometer scale. In this work, nanobubbles produced in solution were employed for studying the effects of the gas-liquid interface on the assembly of glucagon proteins. Atomic force microscopy (AFM) studies showed that nanobubble-treated glucagon solution formed fibrils with an apparent height of 4.02 ± 0.71 nm, in contrast to the fibrils formed with a height of 2.14 ± 0.53 nm in the control. Transmission electron microscopy (TEM) results also showed that nanobubbles promoted the assembly of glucagon to form more fibrils. Thioflavin T (ThT) fluorescence and Fourier transform infrared (FTIR) analyses indicated that the nanobubbles induced the change of the glucagon conformation to a β-sheet structure. A mechanism that explains how nanobubbles affect the assembly of glucagon amyloid fibrils was proposed based on the above-mentioned experimental results. Given the fact that there are a considerable amount of nanobubbles existing in protein solutions, our results indicate that nanobubbles should be considered for fully understanding the protein aggregation events in vitro.
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Affiliation(s)
- Yujiao Wang
- Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
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Wells C, Brennan S, Keon M, Ooi L. The role of amyloid oligomers in neurodegenerative pathologies. Int J Biol Macromol 2021; 181:582-604. [PMID: 33766600 DOI: 10.1016/j.ijbiomac.2021.03.113] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Revised: 02/18/2021] [Accepted: 03/19/2021] [Indexed: 11/25/2022]
Abstract
Many neurodegenerative diseases are rooted in the activities of amyloid-like proteins which possess conformations that spread to healthy proteins. These include Alzheimer's disease (AD), Parkinson's disease (PD), Huntington's disease (HD) and amyotrophic lateral sclerosis (ALS). While their clinical manifestations vary, their protein-level mechanisms are remarkably similar. Aberrant monomeric proteins undergo conformational shifts, facilitating aggregation and formation of solid fibrils. However, there is growing evidence that intermediate oligomeric stages are key drivers of neuronal toxicity. Analysis of protein dynamics is complicated by the fact that nucleation and growth of amyloid-like proteins is not a linear pathway. Feedback within this pathway results in exponential acceleration of aggregation, but activities exerted by oligomers and fibrils can alter cellular interactions and the cellular environment as a whole. The resulting cascade of effects likely contributes to the late onset and accelerating progression of amyloid-like protein disorders and the widespread effects they have on the body. In this review we explore the amyloid-like proteins associated with AD, PD, HD and ALS, as well as the common mechanisms of amyloid-like protein nucleation and aggregation. From this, we identify core elements of pathological progression which have been targeted for therapies, and which may become future therapeutic targets.
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Affiliation(s)
- Cameron Wells
- GenieUs Genomics, Sydney, NSW 2010, Australia; University of New South Wales, Sydney, NSW 2052, Australia
| | | | - Matt Keon
- GenieUs Genomics, Sydney, NSW 2010, Australia
| | - Lezanne Ooi
- Illawarra Health and Medical Research Institute, Wollongong, NSW 2522, Australia; School of Chemistry and Molecular Bioscience, and Molecular Horizons, University of Wollongong, Wollongong, NSW 2522, Australia; GenieUs Genomics, Sydney, NSW 2010, Australia
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Wu M, Dorosh L, Schmitt-Ulms G, Wille H, Stepanova M. Aggregation of Aβ40/42 chains in the presence of cyclic neuropeptides investigated by molecular dynamics simulations. PLoS Comput Biol 2021; 17:e1008771. [PMID: 33711010 PMCID: PMC7990313 DOI: 10.1371/journal.pcbi.1008771] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2020] [Revised: 03/24/2021] [Accepted: 02/04/2021] [Indexed: 11/18/2022] Open
Abstract
Alzheimer’s disease is associated with the formation of toxic aggregates of amyloid beta (Aβ) peptides. Despite tremendous efforts, our understanding of the molecular mechanisms of aggregation, as well as cofactors that might influence it, remains incomplete. The small cyclic neuropeptide somatostatin-14 (SST14) was recently found to be the most selectively enriched protein in human frontal lobe extracts that binds Aβ42 aggregates. Furthermore, SST14’s presence was also found to promote the formation of toxic Aβ42 oligomers in vitro. In order to elucidate how SST14 influences the onset of Aβ oligomerization, we performed all-atom molecular dynamics simulations of model mixtures of Aβ42 or Aβ40 peptides with SST14 molecules and analyzed the structure and dynamics of early-stage aggregates. For comparison we also analyzed the aggregation of Aβ42 in the presence of arginine vasopressin (AVP), a different cyclic neuropeptide. We observed the formation of self-assembled aggregates containing the Aβ chains and small cyclic peptides in all mixtures of Aβ42–SST14, Aβ42–AVP, and Aβ40–SST14. The Aβ42–SST14 mixtures were found to develop compact, dynamically stable, but small aggregates with the highest exposure of hydrophobic residues to the solvent. Differences in the morphology and dynamics of aggregates that comprise SST14 or AVP appear to reflect distinct (1) regions of the Aβ chains they interact with; (2) propensities to engage in hydrogen bonds with Aβ peptides; and (3) solvent exposures of hydrophilic and hydrophobic groups. The presence of SST14 was found to impede aggregation in the Aβ42–SST14 system despite a high hydrophobicity, producing a stronger “sticky surface” effect in the aggregates at the onset of Aβ42–SST14 oligomerization. Improper folding of proteins causes disorders known as protein misfolding diseases. Under normal conditions most proteins adopt particular folds, which allow them functioning properly. However, for reasons that are not yet fully understood, proteins may misfold and aggregate, forming deposits known as amyloid fibrils, which accumulate in the brain or other tissues. This process affects functioning of the nervous system, gradually causing loss of cognitive abilities. Alzheimer’s disease is one of the most common diseases from this group. A better understanding of the aggregation of peptides implicated in Alzheimer’s disease, known as amyloid beta (Aβ) peptides, may facilitate the development of treatments that ameliorate or prevent the disease. We use detailed molecular dynamics simulations to investigate the influence of somatostatin-14 (SST14), a cyclic neuropeptide that might be involved in the amyloidogenic aggregation of Aβ, on molecular processes occurring at the onset of Aβ aggregation. Results of these simulations explain how the presence of SST14 might alter pathways of aggregation of Aβ, shedding light upon the possible role of extrinsic factors in the aggregation at a molecular level.
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Affiliation(s)
- Min Wu
- Department of Electrical and Computer Engineering, University of Alberta, Edmonton, Canada
| | - Lyudmyla Dorosh
- Department of Electrical and Computer Engineering, University of Alberta, Edmonton, Canada
| | - Gerold Schmitt-Ulms
- Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada
| | - Holger Wille
- Department of Biochemistry, University of Alberta, Edmonton, Canada
- Centre for Prions and Protein Folding Diseases, Edmonton, Canada
- Neuroscience and Mental Health Institute, University of Alberta, Edmonton, Canada
| | - Maria Stepanova
- Department of Electrical and Computer Engineering, University of Alberta, Edmonton, Canada
- * E-mail:
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Caruana M, Camilleri A, Farrugia MY, Ghio S, Jakubíčková M, Cauchi RJ, Vassallo N. Extract from the Marine Seaweed Padina pavonica Protects Mitochondrial Biomembranes from Damage by Amyloidogenic Peptides. Molecules 2021; 26:1444. [PMID: 33799979 PMCID: PMC7962105 DOI: 10.3390/molecules26051444] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 03/02/2021] [Accepted: 03/04/2021] [Indexed: 11/30/2022] Open
Abstract
The identification of compounds which protect the double-membrane of mitochondrial organelles from disruption by toxic confomers of amyloid proteins may offer a therapeutic strategy to combat human neurodegenerative diseases. Here, we exploited an extract from the marine brown seaweed Padina pavonica (PPE) as a vital source of natural bioactive compounds to protect mitochondrial membranes against insult by oligomeric aggregates of the amyloidogenic proteins amyloid-β (Aβ), α-synuclein (α-syn) and tau, which are currently considered to be major targets for drug discovery in Alzheimer's disease (AD) and Parkinson's disease (PD). We show that PPE manifested a significant inhibitory effect against swelling of isolated mitochondria exposed to the amyloid oligomers, and attenuated the release of cytochrome c from the mitochondria. Using cardiolipin-enriched synthetic lipid membranes, we also show that dye leakage from fluorophore-loaded vesicles and formation of channel-like pores in planar bilayer membranes are largely prevented by incubating the oligomeric aggregates with PPE. Lastly, we demonstrate that PPE curtails the ability of Aβ42 and α-syn monomers to self-assemble into larger β-aggregate structures, as well as potently disrupts their respective amyloid fibrils. In conclusion, the mito-protective and anti-aggregator biological activities of Padina pavonica extract may be of therapeutic value in neurodegenerative proteinopathies, such as AD and PD.
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Affiliation(s)
- Mario Caruana
- Department of Physiology and Biochemistry, Faculty of Medicine and Surgery, University of Malta, 2023 Msida, Malta; (M.C.); (A.C.); (M.Y.F.); (S.G.); (M.J.); (R.J.C.)
- Centre for Molecular Medicine and Biobanking, Biomedical Sciences Building, University of Malta, 2023 Msida, Malta
| | - Angelique Camilleri
- Department of Physiology and Biochemistry, Faculty of Medicine and Surgery, University of Malta, 2023 Msida, Malta; (M.C.); (A.C.); (M.Y.F.); (S.G.); (M.J.); (R.J.C.)
- Centre for Molecular Medicine and Biobanking, Biomedical Sciences Building, University of Malta, 2023 Msida, Malta
| | - Maria Ylenia Farrugia
- Department of Physiology and Biochemistry, Faculty of Medicine and Surgery, University of Malta, 2023 Msida, Malta; (M.C.); (A.C.); (M.Y.F.); (S.G.); (M.J.); (R.J.C.)
- Centre for Molecular Medicine and Biobanking, Biomedical Sciences Building, University of Malta, 2023 Msida, Malta
| | - Stephanie Ghio
- Department of Physiology and Biochemistry, Faculty of Medicine and Surgery, University of Malta, 2023 Msida, Malta; (M.C.); (A.C.); (M.Y.F.); (S.G.); (M.J.); (R.J.C.)
- Centre for Molecular Medicine and Biobanking, Biomedical Sciences Building, University of Malta, 2023 Msida, Malta
| | - Michaela Jakubíčková
- Department of Physiology and Biochemistry, Faculty of Medicine and Surgery, University of Malta, 2023 Msida, Malta; (M.C.); (A.C.); (M.Y.F.); (S.G.); (M.J.); (R.J.C.)
- Department of Experimental Biology, Faculty of Science, Masaryk University, 60300 Brno, Czech Republic
| | - Ruben J. Cauchi
- Department of Physiology and Biochemistry, Faculty of Medicine and Surgery, University of Malta, 2023 Msida, Malta; (M.C.); (A.C.); (M.Y.F.); (S.G.); (M.J.); (R.J.C.)
- Centre for Molecular Medicine and Biobanking, Biomedical Sciences Building, University of Malta, 2023 Msida, Malta
| | - Neville Vassallo
- Department of Physiology and Biochemistry, Faculty of Medicine and Surgery, University of Malta, 2023 Msida, Malta; (M.C.); (A.C.); (M.Y.F.); (S.G.); (M.J.); (R.J.C.)
- Centre for Molecular Medicine and Biobanking, Biomedical Sciences Building, University of Malta, 2023 Msida, Malta
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García-Viñuales S, Sciacca MFM, Lanza V, Santoro AM, Grasso G, Tundo GR, Sbardella D, Coletta M, Grasso G, La Rosa C, Milardi D. The interplay between lipid and Aβ amyloid homeostasis in Alzheimer's Disease: risk factors and therapeutic opportunities. Chem Phys Lipids 2021; 236:105072. [PMID: 33675779 DOI: 10.1016/j.chemphyslip.2021.105072] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Revised: 02/15/2021] [Accepted: 03/01/2021] [Indexed: 12/19/2022]
Abstract
Alzheimer's Diseases (AD) is characterized by the accumulation of amyloid deposits of Aβ peptide in the brain. Besides genetic background, the presence of other diseases and an unhealthy lifestyle are known risk factors for AD development. Albeit accumulating clinical evidence suggests that an impaired lipid metabolism is related to Aβ deposition, mechanistic insights on the link between amyloid fibril formation/clearance and aberrant lipid interactions are still unavailable. Recently, many studies have described the key role played by membrane bound Aβ assemblies in neurotoxicity. Moreover, it has been suggested that a derangement of the ubiquitin proteasome pathway and autophagy is significantly correlated with toxic Aβ aggregation and dysregulation of lipid levels. Thus, studies focusing on the role played by lipids in Aβ aggregation and proteostasis could represent a promising area of investigation for the design of valuable treatments. In this review we examine current knowledge concerning the effects of lipids in Aβ aggregation and degradation processes, focusing on the therapeutic opportunities that a comprehensive understanding of all biophysical, biochemical, and biological processes involved may disclose.
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Affiliation(s)
| | - Michele F M Sciacca
- Consiglio Nazionale delle Ricerche, Istituto di Cristallografia, Catania, Italy
| | - Valeria Lanza
- Consiglio Nazionale delle Ricerche, Istituto di Cristallografia, Catania, Italy
| | - Anna Maria Santoro
- Consiglio Nazionale delle Ricerche, Istituto di Cristallografia, Catania, Italy
| | - Giulia Grasso
- Consiglio Nazionale delle Ricerche, Istituto di Cristallografia, Catania, Italy
| | - Grazia R Tundo
- Department of Clinical Sciences and Translational Medicine, University of Rome Tor Vergata, Rome, Italy
| | | | - Massimiliano Coletta
- Department of Clinical Sciences and Translational Medicine, University of Rome Tor Vergata, Rome, Italy
| | - Giuseppe Grasso
- Department of Chemistry, University of Catania, Catania, Italy
| | - Carmelo La Rosa
- Department of Chemistry, University of Catania, Catania, Italy
| | - Danilo Milardi
- Consiglio Nazionale delle Ricerche, Istituto di Cristallografia, Catania, Italy.
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Alberti S, Hyman AA. Biomolecular condensates at the nexus of cellular stress, protein aggregation disease and ageing. Nat Rev Mol Cell Biol 2021; 22:196-213. [PMID: 33510441 DOI: 10.1038/s41580-020-00326-6] [Citation(s) in RCA: 485] [Impact Index Per Article: 161.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/16/2020] [Indexed: 12/14/2022]
Abstract
Biomolecular condensates are membraneless intracellular assemblies that often form via liquid-liquid phase separation and have the ability to concentrate biopolymers. Research over the past 10 years has revealed that condensates play fundamental roles in cellular organization and physiology, and our understanding of the molecular principles, components and forces underlying their formation has substantially increased. Condensate assembly is tightly regulated in the intracellular environment, and failure to control condensate properties, formation and dissolution can lead to protein misfolding and aggregation, which are often the cause of ageing-associated diseases. In this Review, we describe the mechanisms and regulation of condensate assembly and dissolution, highlight recent advances in understanding the role of biomolecular condensates in ageing and disease, and discuss how cellular stress, ageing-related loss of homeostasis and a decline in protein quality control may contribute to the formation of aberrant, disease-causing condensates. Our improved understanding of condensate pathology provides a promising path for the treatment of protein aggregation diseases.
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Affiliation(s)
- Simon Alberti
- Technische Universität Dresden, Biotechnology Center (BIOTEC) and Center for Molecular and Cellular Engineering (CMCB), Dresden, Germany.
| | - Anthony A Hyman
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany.
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Cawood EE, Karamanos TK, Wilson AJ, Radford SE. Visualizing and trapping transient oligomers in amyloid assembly pathways. Biophys Chem 2021; 268:106505. [PMID: 33220582 PMCID: PMC8188297 DOI: 10.1016/j.bpc.2020.106505] [Citation(s) in RCA: 81] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2020] [Revised: 10/29/2020] [Accepted: 11/01/2020] [Indexed: 12/31/2022]
Abstract
Oligomers which form during amyloid fibril assembly are considered to be key contributors towards amyloid disease. However, understanding how such intermediates form, their structure, and mechanisms of toxicity presents significant challenges due to their transient and heterogeneous nature. Here, we discuss two different strategies for addressing these challenges: use of (1) methods capable of detecting lowly-populated species within complex mixtures, such as NMR, single particle methods (including fluorescence and force spectroscopy), and mass spectrometry; and (2) chemical and biological tools to bias the amyloid energy landscape towards specific oligomeric states. While the former methods are well suited to following the kinetics of amyloid assembly and obtaining low-resolution structural information, the latter are capable of producing oligomer samples for high-resolution structural studies and inferring structure-toxicity relationships. Together, these different approaches should enable a clearer picture to be gained of the nature and role of oligomeric intermediates in amyloid formation and disease.
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Affiliation(s)
- Emma E Cawood
- Astbury Centre for Structural Molecular Biology, School of Chemistry, University of Leeds, LS2 9JT, UK; Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, University of Leeds, LS2 9JT, UK
| | - Theodoros K Karamanos
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, University of Leeds, LS2 9JT, UK; Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Andrew J Wilson
- Astbury Centre for Structural Molecular Biology, School of Chemistry, University of Leeds, LS2 9JT, UK.
| | - Sheena E Radford
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, University of Leeds, LS2 9JT, UK.
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Cicalese S, Okuno K, Eguchi S. Detection of Protein Aggregation and Proteotoxicity Induced by Angiotensin II in Vascular Smooth Muscle Cells. J Cardiovasc Pharmacol 2021; 77:43-48. [PMID: 33079831 DOI: 10.1097/fjc.0000000000000934] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Accepted: 10/06/2020] [Indexed: 12/26/2022]
Abstract
ABSTRACT Disruption of protein quality control occurs with aging and cardiovascular pathologies including arterial stiffness and hypertension. Angiotensin II (Ang II) is believed to induce endoplasmic reticulum stress in vascular smooth muscle cells (VSMCs), thus contributing to vascular remodeling and dysfunction. However, whether Ang II increases formation of protein aggregates and mediates proteotoxicity in VSMCs remain obscure. Accordingly, this study aimed to establish a quantitative method of protein aggregate detection induced by Ang II and to investigate their potential involvement in inflammatory and senescence responses. Proteostat staining showed increased aggregate numbers per cell on Ang II exposure. Immunoblot analysis further showed an increase in preamyloid oligomer presence in a detergent insoluble protein fraction purified from VSMCs stimulated with Ang II. Moreover, these responses were attenuated by treatment with chemical chaperone, 4-phenylbutyrate. 4-phenylbutyrate further blocked Ang II-induced senescence associated β-galactosidase activity and THP-1 monocyte adhesion in VSMCs. These data suggest that Ang II induces proteotoxicity in VSMCs which likely contributes to aging and inflammation in the vasculature.
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MESH Headings
- Angiotensin II/toxicity
- Animals
- Cell Adhesion/drug effects
- Cellular Senescence/drug effects
- Endoplasmic Reticulum Stress/drug effects
- Humans
- Male
- Monocytes/drug effects
- Monocytes/metabolism
- Muscle, Smooth, Vascular/drug effects
- Muscle, Smooth, Vascular/metabolism
- Muscle, Smooth, Vascular/pathology
- Myocytes, Smooth Muscle/drug effects
- Myocytes, Smooth Muscle/metabolism
- Myocytes, Smooth Muscle/pathology
- Protein Aggregates
- Protein Aggregation, Pathological
- Rats, Sprague-Dawley
- THP-1 Cells
- Rats
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Affiliation(s)
- Stephanie Cicalese
- Department of Physiology, Cardiovascular Research Center, Lewis Katz School of Medicine, Temple University, Philadelphia, PA
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