1
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Sun Y, Jack K, Ercolani T, Sangar D, Hosszu L, Collinge J, Bieschke J. Direct Observation of Competing Prion Protein Fibril Populations with Distinct Structures and Kinetics. ACS NANO 2023; 17:6575-6588. [PMID: 36802500 PMCID: PMC10100569 DOI: 10.1021/acsnano.2c12009] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Accepted: 02/10/2023] [Indexed: 06/18/2023]
Abstract
In prion diseases, fibrillar assemblies of misfolded prion protein (PrP) self-propagate by incorporating PrP monomers. These assemblies can evolve to adapt to changing environments and hosts, but the mechanism of prion evolution is poorly understood. We show that PrP fibrils exist as a population of competing conformers, which are selectively amplified under different conditions and can "mutate" during elongation. Prion replication therefore possesses the steps necessary for molecular evolution analogous to the quasispecies concept of genetic organisms. We monitored structure and growth of single PrP fibrils by total internal reflection and transient amyloid binding super-resolution microscopy and detected at least two main fibril populations, which emerged from seemingly homogeneous PrP seeds. All PrP fibrils elongated in a preferred direction by an intermittent "stop-and-go" mechanism, but each population possessed distinct elongation mechanisms that incorporated either unfolded or partially folded monomers. Elongation of RML and ME7 prion rods likewise exhibited distinct kinetic features. The discovery of polymorphic fibril populations growing in competition, which were previously hidden in ensemble measurements, suggests that prions and other amyloid replicating by prion-like mechanisms may represent quasispecies of structural isomorphs that can evolve to adapt to new hosts and conceivably could evade therapeutic intervention.
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Affiliation(s)
- Yuanzi Sun
- MRC
Prion Unit at UCL/UCL Institute of Prion Diseases, University College London, London W1W 7FF, United Kingdom
| | - Kezia Jack
- MRC
Prion Unit at UCL/UCL Institute of Prion Diseases, University College London, London W1W 7FF, United Kingdom
| | - Tiziana Ercolani
- MRC
Prion Unit at UCL/UCL Institute of Prion Diseases, University College London, London W1W 7FF, United Kingdom
| | - Daljit Sangar
- MRC
Prion Unit at UCL/UCL Institute of Prion Diseases, University College London, London W1W 7FF, United Kingdom
| | - Laszlo Hosszu
- MRC
Prion Unit at UCL/UCL Institute of Prion Diseases, University College London, London W1W 7FF, United Kingdom
| | - John Collinge
- MRC
Prion Unit at UCL/UCL Institute of Prion Diseases, University College London, London W1W 7FF, United Kingdom
| | - Jan Bieschke
- MRC
Prion Unit at UCL/UCL Institute of Prion Diseases, University College London, London W1W 7FF, United Kingdom
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2
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Whitehead M, Yusoff S, Ahmad S, Schmidt L, Mayr M, Madine J, Middleton D, Shanahan CM. Vascular smooth muscle cell senescence accelerates medin aggregation via small extracellular vesicle secretion and extracellular matrix reorganization. Aging Cell 2023; 22:e13746. [PMID: 36433666 PMCID: PMC9924949 DOI: 10.1111/acel.13746] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 11/07/2022] [Accepted: 11/13/2022] [Indexed: 11/27/2022] Open
Abstract
Vascular amyloidosis, caused when peptide monomers aggregate into insoluble amyloid, is a prevalent age-associated pathology. Aortic medial amyloid (AMA) is the most common human amyloid and is composed of medin, a 50-amino acid peptide. Emerging evidence has implicated extracellular vesicles (EVs) as mediators of pathological amyloid accumulation in the extracellular matrix (ECM). To determine the mechanisms of AMA formation with age, we explored the impact of vascular smooth muscle cell (VSMC) senescence, EV secretion, and ECM remodeling on medin accumulation. Medin was detected in EVs secreted from primary VSMCs. Small, round medin aggregates colocalized with EV markers in decellularized ECM in vitro and medin was shown on the surface of EVs deposited in the ECM. Decreasing EV secretion with an inhibitor attenuated aggregation and deposition of medin in the ECM. Medin accumulation in the aortic wall of human subjects was strongly correlated with age and VSMC senescence increased EV secretion, increased EV medin loading and triggered deposition of fibril-like medin. Proteomic analysis showed VSMC senescence induced changes in EV cargo and ECM composition, which led to enhanced EV-ECM binding and accelerated medin aggregation. Abundance of the proteoglycan, HSPG2, was increased in the senescent ECM and colocalized with EVs and medin. Isolated EVs selectively bound to HSPG2 in the ECM and its knock-down decreased formation of fibril-like medin structures. These data identify VSMC-derived EVs and HSPG2 in the ECM as key mediators of medin accumulation, contributing to age-associated AMA development.
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Affiliation(s)
- Meredith Whitehead
- School of Cardiovascular and Metabolic Medicine & SciencesKing's College LondonLondonUK
| | - Syabira Yusoff
- School of Cardiovascular and Metabolic Medicine & SciencesKing's College LondonLondonUK
| | - Sadia Ahmad
- School of Cardiovascular and Metabolic Medicine & SciencesKing's College LondonLondonUK
| | - Lukas Schmidt
- School of Cardiovascular and Metabolic Medicine & SciencesKing's College LondonLondonUK
| | - Manuel Mayr
- School of Cardiovascular and Metabolic Medicine & SciencesKing's College LondonLondonUK
| | - Jillian Madine
- Institute of Systems, Molecular and Integrative BiologyUniversity of LiverpoolLondonUK
| | | | - Catherine M. Shanahan
- School of Cardiovascular and Metabolic Medicine & SciencesKing's College LondonLondonUK
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3
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Lemarre P, Pujo-Menjouet L, Sindi SS. Generalizing a mathematical model of prion aggregation allows strain coexistence and co-stability by including a novel misfolded species. J Math Biol 2018; 78:465-495. [PMID: 30116882 PMCID: PMC6399074 DOI: 10.1007/s00285-018-1280-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2017] [Revised: 02/20/2018] [Indexed: 11/29/2022]
Abstract
Prions are proteins capable of adopting misfolded conformations and transmitting these conformations to other normally folded proteins. Prions are most commonly known for causing fatal neurodegenerative diseases in mammals but are also associated with several harmless phenotypes in yeast. A distinct feature of prion propagation is the existence of different phenotypical variants, called strains. It is widely accepted that these strains correspond to different conformational states of the protein, but the mechanisms driving their interactions remain poorly understood. This study uses mathematical modeling to provide insight into this problem. We show that the classical model of prion dynamics allows at most one conformational strain to stably propagate. In order to conform to biological observations of strain coexistence and co-stability, we develop an extension of the classical model by introducing a novel prion species consistent with biological studies. Qualitative analysis of this model reveals a new variety of behavior. Indeed, it allows for stable coexistence of different strains in a wide parameter range, and it also introduces intricate initial condition dependency. These new behaviors are consistent with experimental observations of prions in both mammals and yeast. As such, our model provides a valuable tool for investigating the underlying mechanisms of prion propagation and the link between prion strains and strain specific phenotypes. The consideration of a novel prion species brings a change in perspective on prion biology and we use our model to generate hypotheses about prion infectivity.
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Affiliation(s)
- Paul Lemarre
- School of Natural Sciences, University of California, Merced, 5200 North Lake Road, Merced, CA, 95343, USA
| | - Laurent Pujo-Menjouet
- Institut Camille Jordan, Université de Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5208, 43 blvd. du 11 novembre 1918, 69622, Villeurbanne cedex, France.,Team Dracula, INRIA, 69603, Villeurbanne cedex, France
| | - Suzanne S Sindi
- Applied Mathematics School of Natural Sciences, University of California, Merced, 5200 North Lake Road, Merced, CA, 95343, USA.
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4
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Davies HA, Lee CF, Miller L, Liu LN, Madine J. Insights into the Origin of Distinct Medin Fibril Morphologies Induced by Incubation Conditions and Seeding. Int J Mol Sci 2018; 19:ijms19051357. [PMID: 29751581 PMCID: PMC5983645 DOI: 10.3390/ijms19051357] [Citation(s) in RCA: 4] [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: 03/07/2018] [Revised: 04/25/2018] [Accepted: 05/01/2018] [Indexed: 12/16/2022] Open
Abstract
Incubation conditions are an important factor to consider when studying protein aggregation in vitro. Here, we employed biophysical methods and atomic force microscopy to show that agitation dramatically alters the morphology of medin, an amyloid protein deposited in the aorta. Agitation reduces the lag time for fibrillation by ~18-fold, suggesting that the rate of fibril formation plays a key role in directing the protein packing arrangement within fibrils. Utilising preformed sonicated fibrils as seeds, we probed the role of seeding on medin fibrillation and revealed three distinct fibril morphologies, with biophysical modelling explaining the salient features of experimental observations. We showed that nucleation pathways to distinct fibril morphologies may be switched on and off depending on the properties of the seeding fibrils and growth conditions. These findings may impact on the development of amyloid-based biomaterials and enhance understanding of seeding as a pathological mechanism.
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Affiliation(s)
- Hannah A Davies
- Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK.
| | - Chiu Fan Lee
- Department of Bioengineering, Imperial College London, London SW7 2AZ, UK.
| | - Leanne Miller
- Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK.
- Department of Physics, University of Liverpool, Liverpool L69 7ZE, UK.
| | - Lu-Ning Liu
- Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK.
| | - Jillian Madine
- Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, UK.
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5
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Dean DN, Rana P, Campbell RP, Ghosh P, Rangachari V. Propagation of an Aβ Dodecamer Strain Involves a Three-Step Mechanism and a Key Intermediate. Biophys J 2018; 114:539-549. [PMID: 29414699 PMCID: PMC5985009 DOI: 10.1016/j.bpj.2017.11.3778] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2017] [Revised: 11/27/2017] [Accepted: 11/28/2017] [Indexed: 11/18/2022] Open
Abstract
Proteinaceous deposits composed of fibrillar amyloid-β (Aβ) are the primary neuropathological hallmarks in Alzheimer disease (AD) brains. The nucleation-dependent aggregation of Aβ is a stochastic process with frequently observed heterogeneity in aggregate size, structure, and conformation that manifests in fibril polymorphism. Emerging evidence indicates that polymorphic variations in Aβ fibrils contribute to phenotypic diversity and the rate of disease progression in AD. We recently demonstrated that a dodecamer strain derived from synthetic Aβ42 propagates to morphologically distinct fibrils and selectively induces cerebral amyloid angiopathy phenotype in transgenic mice. This report supports the growing contention that stable oligomer strains can influence phenotypic outcomes by faithful propagation of their structures. Although we determined the mechanism of dodecamer propagation on a mesoscopic scale, the molecular details of the microscopic reactions remained unknown. Here, we have dissected and evaluated individually the kinetics of macroscopic phases in aggregation to gain insight into the process of strain propagation. The bulk rates determined experimentally in each phase were used to build an ensemble kinetic simulation model, which confirmed our observation that dodecamer seeds initially grow by monomer addition toward the formation of a key intermediate. This is followed by conversion of the intermediate to fibrils by oligomer elongation and association mechanisms. Overall, this report reveals important insights into the molecular details of oligomer strain propagation involved in AD pathology.
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Affiliation(s)
- Dexter N Dean
- Department of Chemistry and Biochemistry, University of Southern Mississippi, Hattiesburg, Mississippi
| | - Pratip Rana
- Department of Computer Science, Virginia Commonwealth University, Richmond, Virginia
| | - Ryan P Campbell
- Department of Chemistry and Biochemistry, University of Southern Mississippi, Hattiesburg, Mississippi
| | - Preetam Ghosh
- Department of Computer Science, Virginia Commonwealth University, Richmond, Virginia
| | - Vijayaraghavan Rangachari
- Department of Chemistry and Biochemistry, University of Southern Mississippi, Hattiesburg, Mississippi.
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6
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Honda R, Kuwata K. Evidence for a central role of PrP helix 2 in the nucleation of amyloid fibrils. FASEB J 2018; 32:3641-3652. [PMID: 29401635 DOI: 10.1096/fj.201701183rr] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Amyloid fibrils are filamentous protein aggregates associated with the pathogenesis of a wide variety of human diseases. The formation of such aggregates typically follows nucleation-dependent kinetics, wherein the assembly and structural conversion of amyloidogenic proteins into oligomeric aggregates (nuclei) is the rate-limiting step of the overall reaction. In this study, we sought to gain structural insights into the oligomeric nuclei of the human prion protein (PrP) by preparing a series of deletion mutants lacking 14-44 of the C-terminal 107 residues of PrP and examined the kinetics and thermodynamics of these mutants in amyloid formation. An analysis of the experimental data using the concepts of the Φ-value analysis indicated that the helix 2 region (residues 168-196) acquires an amyloid-like β-sheet during nucleation, whereas the other regions preserves a relatively disordered structure in the nuclei. This finding suggests that the helix 2 region serves as the nucleation site for the assembly of amyloid fibrils.-Honda, R., Kuwata, K. Evidence for a central role of PrP helix 2 in the nucleation of amyloid fibrils.
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Affiliation(s)
- Ryo Honda
- Department of Molecular Pathobiochemistry, Graduate School of Medicine, Gifu University, Gifu, Japan.,United Graduate School of Drug Discovery and Medical Information Sciences, Gifu University, Gifu, Japan
| | - Kazuo Kuwata
- United Graduate School of Drug Discovery and Medical Information Sciences, Gifu University, Gifu, Japan.,Department of Gene and Development, Graduate School of Medicine, Gifu University, Gifu, Japan
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7
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Lloret‐Villas A, Varusai TM, Juty N, Laibe C, Le NovÈre N, Hermjakob H, Chelliah V. The Impact of Mathematical Modeling in Understanding the Mechanisms Underlying Neurodegeneration: Evolving Dimensions and Future Directions. CPT Pharmacometrics Syst Pharmacol 2017; 6:73-86. [PMID: 28063254 PMCID: PMC5321808 DOI: 10.1002/psp4.12155] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2016] [Revised: 10/14/2016] [Accepted: 10/30/2016] [Indexed: 12/14/2022] Open
Abstract
Neurodegenerative diseases are a heterogeneous group of disorders that are characterized by the progressive dysfunction and loss of neurons. Here, we distil and discuss the current state of modeling in the area of neurodegeneration, and objectively compare the gaps between existing clinical knowledge and the mechanistic understanding of the major pathological processes implicated in neurodegenerative disorders. We also discuss new directions in the field of neurodegeneration that hold potential for furthering therapeutic interventions and strategies.
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Affiliation(s)
- A Lloret‐Villas
- European Bioinformatics Institute (EMBL‐EBI), European Molecular Biology LaboratoryWellcome Trust Genome Campus, HinxtonCambridgeUK
| | - TM Varusai
- European Bioinformatics Institute (EMBL‐EBI), European Molecular Biology LaboratoryWellcome Trust Genome Campus, HinxtonCambridgeUK
| | - N Juty
- European Bioinformatics Institute (EMBL‐EBI), European Molecular Biology LaboratoryWellcome Trust Genome Campus, HinxtonCambridgeUK
| | - C Laibe
- European Bioinformatics Institute (EMBL‐EBI), European Molecular Biology LaboratoryWellcome Trust Genome Campus, HinxtonCambridgeUK
| | - N Le NovÈre
- Babraham Institute, Babraham Research CampusCambridgeUK
| | - H Hermjakob
- European Bioinformatics Institute (EMBL‐EBI), European Molecular Biology LaboratoryWellcome Trust Genome Campus, HinxtonCambridgeUK
| | - V Chelliah
- European Bioinformatics Institute (EMBL‐EBI), European Molecular Biology LaboratoryWellcome Trust Genome Campus, HinxtonCambridgeUK
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8
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The role of the unusual threonine string in the conversion of prion protein. Sci Rep 2016; 6:38877. [PMID: 27982059 PMCID: PMC5159806 DOI: 10.1038/srep38877] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2016] [Accepted: 11/15/2016] [Indexed: 01/24/2023] Open
Abstract
The conversion of normal prion protein (PrP) into pathogenic PrP conformers is central to prion disease, but the mechanism remains unclear. The α-helix 2 of PrP contains a string of four threonines, which is unusual due to the high propensity of threonine to form β-sheets. This structural feature was proposed as the basis for initiating PrP conversion, but experimental results have been conflicting. We studied the role of the threonine string on PrP conversion by analyzing mouse Prnpa and Prnpb polymorphism that contains a polymorphic residue at the beginning of the threonine string, and PrP mutants in which threonine 191 was replaced by valine, alanine, or proline. The PMCA (protein misfolding cyclic amplification) assay was able to recapitulate the in vivo transmission barrier between PrPa and PrPb. Relative to PMCA, the amyloid fibril growth assay is less restrictive, but it did reflect certain properties of in vivo prion transmission. Our results suggest a plausible theory explaining the apparently contradictory results in the role of the threonine string in PrP conversion and provide novel insights into the complicated relationship among PrP stability, seeded conformational change, and prion structure, which is critical for understanding the molecular basis of prion infectivity.
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9
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Zapadka KL, Becher FJ, Uddin S, Varley PG, Bishop S, Gomes Dos Santos AL, Jackson SE. A pH-Induced Switch in Human Glucagon-like Peptide-1 Aggregation Kinetics. J Am Chem Soc 2016; 138:16259-16265. [PMID: 27998088 DOI: 10.1021/jacs.6b05025] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Aggregation and amyloid fibril formation of peptides and proteins is a widespread phenomenon. It has serious implications in a range of areas from biotechnological and pharmaceutical applications to medical disorders. The aim of this study was to develop a better understanding of the mechanism of aggregation and amyloid fibrillation of an important pharmaceutical, human glucagon-like peptide-1 (GLP-1). GLP-1 is a 31-residue hormone peptide that plays an important role regulating blood glucose levels, analogues of which are used for treatment of type 2 diabetes. Amyloid fibril formation of GLP-1 was monitored using thioflavin T fluorescence as a function of peptide concentration between pH 7.5 and 8.2. Results from these studies establish that there is a highly unusual pH-induced switch in GLP-1 aggregation kinetics. At pH 8.2, the kinetics are consistent with a nucleation-polymerization mechanism for fibril formation. However, at pH 7.5, highly unusual kinetics are observed, where the lag time increases with increasing peptide concentration. We attribute this result to the formation of off-pathway species together with an initial slow, unimolecular step where monomer converts to a different monomeric form that forms on-pathway oligomers and ultimately fibrils. Estimation of the pKa values of all the ionizable groups in GLP-1 suggest it is the protonation/deprotonation of the N-terminus that is responsible for the switch with pH. In addition, a range of biophysical techniques were used to characterize (1) the start point of the aggregation reaction and (2) the structure and stability of the fibrils formed. These results show that the off-pathway species form under conditions where GLP-1 is most prone to form oligomers.
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Affiliation(s)
- Karolina L Zapadka
- Department of Chemistry, University of Cambridge , Cambridge CB2 1EW, U.K
| | - Frederik J Becher
- Department of Chemistry, University of Cambridge , Cambridge CB2 1EW, U.K
| | - Shahid Uddin
- Formulation Sciences, MedImmune Ltd. , Granta Park, Cambridge CB21 6GH, U.K
| | - Paul G Varley
- Formulation Sciences, MedImmune Ltd. , Granta Park, Cambridge CB21 6GH, U.K
| | - Steve Bishop
- Formulation Sciences, MedImmune , One MedImmune Way, Gaithersburg, Maryland 20878, United States
| | | | - Sophie E Jackson
- Department of Chemistry, University of Cambridge , Cambridge CB2 1EW, U.K
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10
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D’Orsogna MR, Lei Q, Chou T. First assembly times and equilibration in stochastic coagulation-fragmentation. J Chem Phys 2015; 143:014112. [DOI: 10.1063/1.4923002] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Affiliation(s)
- Maria R. D’Orsogna
- Department of Biomathematics, UCLA, Los Angeles, California 90095-1766, USA
- Department of Mathematics, CSUN, Los Angeles, California 91330-8313, USA
| | - Qi Lei
- Institute for Computational and Engineering Sciences, University of Texas, Austin, Texas 78712-1229, USA
| | - Tom Chou
- Department of Biomathematics, UCLA, Los Angeles, California 90095-1766, USA
- Department of Mathematics, UCLA, Los Angeles, California 90095-1555, USA
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11
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Davies HA, Madine J, Middleton DA. Comparisons with amyloid-β reveal an aspartate residue that stabilizes fibrils of the aortic amyloid peptide medin. J Biol Chem 2015; 290:7791-803. [PMID: 25614623 PMCID: PMC4367279 DOI: 10.1074/jbc.m114.602177] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2014] [Revised: 01/19/2015] [Indexed: 11/16/2022] Open
Abstract
Aortic medial amyloid (AMA) is the most common localized human amyloid, occurring in virtually all of the Caucasian population over the age of 50. The main protein component of AMA, medin, readily assembles into amyloid-like fibrils in vitro. Despite the prevalence of AMA, little is known about the self-assembly mechanism of medin or the molecular architecture of the fibrils. The amino acid sequence of medin is strikingly similar to the sequence of the Alzheimer disease (AD) amyloid-β (Aβ) polypeptides around the structural turn region of Aβ, where mutations associated with familial, early onset AD, have been identified. Asp(25) and Lys(30) of medin align with residues Asp(23) and Lys(28) of Aβ, which are known to form a stabilizing salt bridge in some fibril morphologies. Here we show that substituting Asp(25) of medin with asparagine (D25N) impedes assembly into fibrils and stabilizes non-cytotoxic oligomers. Wild-type medin, by contrast, aggregates into β-sheet-rich amyloid-like fibrils within 50 h. A structural analysis of wild-type fibrils by solid-state NMR suggests a molecular repeat unit comprising at least two extended β-strands, separated by a turn stabilized by a Asp(25)-Lys(30) salt bridge. We propose that Asp(25) drives the assembly of medin by stabilizing the fibrillar conformation of the peptide and is thus reminiscent of the influence of Asp(23) on the aggregation of Aβ. Pharmacological comparisons of wild-type medin and D25N will help to ascertain the pathological significance of this poorly understood protein.
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Affiliation(s)
- Hannah A Davies
- From the Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool L69 7ZB, United Kingdom and
| | - Jillian Madine
- From the Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool L69 7ZB, United Kingdom and
| | - David A Middleton
- the Department of Chemistry, Lancaster University, Lancaster LA1 4YB, United Kingdom
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12
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Hingant E, Fontes P, Alvarez-Martinez MT, Arnaud JD, Liautard JP, Pujo-Menjouet L. A micellar on-pathway intermediate step explains the kinetics of prion amyloid formation. PLoS Comput Biol 2014; 10:e1003735. [PMID: 25101755 PMCID: PMC4125056 DOI: 10.1371/journal.pcbi.1003735] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2013] [Accepted: 06/05/2014] [Indexed: 11/19/2022] Open
Abstract
In a previous work by Alvarez-Martinez et al. (2011), the authors pointed out some fallacies in the mainstream interpretation of the prion amyloid formation. It appeared necessary to propose an original hypothesis able to reconcile the in vitro data with the predictions of a mathematical model describing the problem. Here, a model is developed accordingly with the hypothesis that an intermediate on-pathway leads to the conformation of the prion protein into an amyloid competent isoform thanks to a structure, called micelles, formed from hydrodynamic interaction. The authors also compare data to the prediction of their model and propose a new hypothesis for the formation of infectious prion amyloids. Understanding the mechanism of prions is an important issue. Indeed, it involves a mechanism modifying the structure of the proteins that are of high interest in theoretical biology. Knowing the underlying mechanism that leads to prion disease could help further investigations in the world of amyloid disease and for example the so-called Alzheimer's disease. The theory of prion, also known as Protein-Only, has been widely studied. Nevertheless no mathematical models are able to reproduce the phenomena in silico. This suggests a lack of information in the theory. Here we propose a new model, built with a new approach theory that fits experimental data in a very satisfactory way. This model, together with experiments, maintains the idea that an intermediate conformation of the protein helps the disease to spread. Besides, this work is an excellent example of a strong interaction between mathematical modelling and biological approach. Indeed, because of a strong discrepancy between theoretical results of the early original model and biological data on pathological prion formation, the team of biologists decided to investigate more closely their experiments. They came out with a new discovery: the crucial role of micelles in the pathological conformation of the prion protein.
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Affiliation(s)
- Erwan Hingant
- CIMA, Universidad de Concepción, Concepción, Chile
- * E-mail:
| | - Pascaline Fontes
- INSERM U710, Université Montpellier 2, Place E. Bataillon, 3eme étage, Montpellier, France
| | - Maria Teresa Alvarez-Martinez
- Etablissement Confiné d’Expérimentation, Plateforme RAM, UMS 3426-BioCampus, Place E. Bataillon, UM2, Montpellier, France
| | - Jacques-Damien Arnaud
- Etablissement Confiné d’Expérimentation, Plateforme RAM, UMS 3426-BioCampus, Place E. Bataillon, UM2, Montpellier, France
| | - Jean-Pierre Liautard
- Centre de Recherche sur les Pathogènes et Biologie pour la Santé, CPBS UMR5236, Université Montpellier 2, Place E. Bataillon, Montpellier, France
| | - Laurent Pujo-Menjouet
- Université de Lyon, CNRS, Université Lyon 1, Institut Camille Jordan UMR5208, Villeurbanne, France
- INRIA Team Dracula, Inria Center Grenoble Rhône-Alpes, France
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13
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Silva JL, Oliveira AC, Vieira TCRG, de Oliveira GAP, Suarez MC, Foguel D. High-Pressure Chemical Biology and Biotechnology. Chem Rev 2014; 114:7239-67. [DOI: 10.1021/cr400204z] [Citation(s) in RCA: 152] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Jerson L. Silva
- Instituto de Bioquímica Médica Leopoldo de Meis, Instituto
Nacional de Ciência e Tecnologia de Biologia Estrutural e Bioimagem,
Centro Nacional de Ressonância Magnética Nuclear Jiri
Jonas, and ‡Polo Xerém, Universidade Federal do Rio de Janeiro, Rio de Janeiro, 21941-902, Brazil
| | - Andrea C. Oliveira
- Instituto de Bioquímica Médica Leopoldo de Meis, Instituto
Nacional de Ciência e Tecnologia de Biologia Estrutural e Bioimagem,
Centro Nacional de Ressonância Magnética Nuclear Jiri
Jonas, and ‡Polo Xerém, Universidade Federal do Rio de Janeiro, Rio de Janeiro, 21941-902, Brazil
| | - Tuane C. R. G. Vieira
- Instituto de Bioquímica Médica Leopoldo de Meis, Instituto
Nacional de Ciência e Tecnologia de Biologia Estrutural e Bioimagem,
Centro Nacional de Ressonância Magnética Nuclear Jiri
Jonas, and ‡Polo Xerém, Universidade Federal do Rio de Janeiro, Rio de Janeiro, 21941-902, Brazil
| | - Guilherme A. P. de Oliveira
- Instituto de Bioquímica Médica Leopoldo de Meis, Instituto
Nacional de Ciência e Tecnologia de Biologia Estrutural e Bioimagem,
Centro Nacional de Ressonância Magnética Nuclear Jiri
Jonas, and ‡Polo Xerém, Universidade Federal do Rio de Janeiro, Rio de Janeiro, 21941-902, Brazil
| | - Marisa C. Suarez
- Instituto de Bioquímica Médica Leopoldo de Meis, Instituto
Nacional de Ciência e Tecnologia de Biologia Estrutural e Bioimagem,
Centro Nacional de Ressonância Magnética Nuclear Jiri
Jonas, and ‡Polo Xerém, Universidade Federal do Rio de Janeiro, Rio de Janeiro, 21941-902, Brazil
| | - Debora Foguel
- Instituto de Bioquímica Médica Leopoldo de Meis, Instituto
Nacional de Ciência e Tecnologia de Biologia Estrutural e Bioimagem,
Centro Nacional de Ressonância Magnética Nuclear Jiri
Jonas, and ‡Polo Xerém, Universidade Federal do Rio de Janeiro, Rio de Janeiro, 21941-902, Brazil
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14
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Madine J, Davies HA, Hughes E, Middleton DA. Heparin promotes the rapid fibrillization of a peptide with low intrinsic amyloidogenicity. Biochemistry 2013; 52:8984-92. [PMID: 24279288 DOI: 10.1021/bi401231u] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Amyloid deposits in vivo are complex mixtures composed of protein fibrils and nonfibrillar components, including polysaccharides of the glycosaminoglycan (GAG) class. It has been widely documented that GAGs influence the initiation and progress of self-assembly by several disease-associated amyloidogenic proteins and peptides in vitro. Here we investigated whether the GAG heparin can serve as a cofactor to induce amyloid-like fibril formation in a peptide predicted to have a weak propensity to aggregate and not associated with amyloid disorders. We selected the 23-residue peptide PLB(1-23), which corresponds to the acetylated cytoplasmic domain of the phospholamban transmembrane protein. PLB(1-23) remains unfolded in aqueous solution for >24 h and does not bind thioflavin T over this time period, in agreement with computer predictions that the peptide has a very low intrinsic amyloidogenicity. In the presence of low-molecular mass (5 kDa) heparin, which binds PLB(1-23) with micromolar affinity, the peptide undergoes spontaneous and rapid assembly into amyloid-like fibrils, the effect being more pronounced at pH 5.5 than at pH 7.4. At the lower pH, peptide aggregation is accompanied by a transition to a β-sheet rich structure. These results are consistent with the polyanionic heparin serving as a scaffold to enhance aggregation by aligning the peptide molecules in the correct orientation and with the appropriate periodicity. PLB(1-23) is toxic to cells when added in isolation, and promotion of fibril formation by heparin can reduce the toxicity of this peptide, consistent with the notion that amyloid-like fibrils represent a benign end stage of fibrillization. This work provides insight into the role that heparin and other glycosaminoglycans may play in amyloid formation and provides therapeutic avenues targeting the reduction of cytotoxicity of species along the amyloid formation pathway.
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Affiliation(s)
- Jillian Madine
- Institute of Integrative Biology, University of Liverpool , Crown Street, Liverpool L69 7ZB, United Kingdom
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15
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Choi I, Lee LP. Rapid detection of Aβ aggregation and inhibition by dual functions of gold nanoplasmic particles: catalytic activator and optical reporter. ACS NANO 2013; 7:6268-6277. [PMID: 23777418 DOI: 10.1021/nn402310c] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
One of the primary pathological hallmarks of Alzheimer's diseases (AD) is amyloid-β (Aβ) aggregation and its extracellular accumulation. However, current in vitro Aβ aggregation assays require time-consuming and labor-intensive steps, which delay the process of drug discovery and understanding the mechanism of Aβ induced neurotoxicity. Here, we propose a rapid detection method for studying Aβ aggregation and inhibition under an optimized acidic perturbation condition by dual functions of gold nanoplasmonic particles (GNPs): (1) catalytic activator and (2) optical reporter. Because of roles of GNPs as effective nucleation sites for fast-catalyzing Aβ aggregation and colorimetric optical reporters for tracking Aβ aggregation, we accomplished the fast aggregation assay in less than 1 min by the naked eyes. Our detection method is based on spontaneous clustering of unconjugated (unmodified) GNPs along with the aggregated Aβ network under an aggregation-promoting condition. As a proof-of-concept demonstration, we employed the acidic perturbation permitting rapid cooperative assemblies of GNPs and Aβ peptides via their surface charge modulation. Under the optimized acidic perturbation condition around pH 2 to 3, we characterized the concentration-dependent colorimetric responses for aggregation at physiologically relevant Aβ concentration levels (from 100 μM to 10 nM). We also demonstrated the GNP/acidic condition-based rapid inhibition assay of Aβ aggregation by using well-known binding reagents such as antibody and serum albumin. The proposed methodology can be a powerful alternative method for screening drugs for AD as well as studying molecular biophysics of protein aggregations, and further extended to explore other protein conformational diseases such as neurodegenerative disease.
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Affiliation(s)
- Inhee Choi
- Berkeley Sensor and Actuator Center, Department of Bioengineering, Department of Electrical Engineering and Computer Science, University of California at Berkeley, Berkeley, California 94720, USA
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16
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Chatterjee B, Lee CY, Lin C, Chen EHL, Huang CL, Yang CC, Chen RPY. Amyloid core formed of full-length recombinant mouse prion protein involves sequence 127-143 but not sequence 107-126. PLoS One 2013; 8:e67967. [PMID: 23844138 PMCID: PMC3700907 DOI: 10.1371/journal.pone.0067967] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2013] [Accepted: 05/23/2013] [Indexed: 12/23/2022] Open
Abstract
The principal event underlying the development of prion disease is the conversion of soluble cellular prion protein (PrP(C)) into its disease-causing isoform, PrP(Sc). This conversion is associated with a marked change in secondary structure from predominantly α-helical to a high β-sheet content, ultimately leading to the formation of aggregates consisting of ordered fibrillar assemblies referred to as amyloid. In vitro, recombinant prion proteins and short prion peptides from various species have been shown to form amyloid under various conditions and it has been proposed that, theoretically, any protein and peptide could form amyloid under appropriate conditions. To identify the peptide segment involved in the amyloid core formed from recombinant full-length mouse prion protein mPrP(23-230), we carried out seed-induced amyloid formation from recombinant prion protein in the presence of seeds generated from the short prion peptides mPrP(107-143), mPrP(107-126), and mPrP(127-143). Our results showed that the amyloid fibrils formed from mPrP(107-143) and mPrP(127-143), but not those formed from mPrP(107-126), were able to seed the amyloidogenesis of mPrP(23-230), showing that the segment residing in sequence 127-143 was used to form the amyloid core in the fibrillization of mPrP(23-230).
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Affiliation(s)
| | - Chung-Yu Lee
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
- Institute of Biochemical Sciences, National Taiwan University, Taipei, Taiwan
| | - Chen Lin
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
| | - Eric H.-L. Chen
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
| | - Chao-Li Huang
- Department of Biochemical Science and Technology, National Taiwan University, Taipei, Taiwan
| | - Chien-Chih Yang
- Department of Biochemical Science and Technology, National Taiwan University, Taipei, Taiwan
| | - Rita P.-Y. Chen
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan
- Institute of Biochemical Sciences, National Taiwan University, Taipei, Taiwan
- * E-mail:
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17
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Cortez LM, Kumar J, Renault L, Young HS, Sim VL. Mouse prion protein polymorphism Phe-108/Val-189 affects the kinetics of fibril formation and the response to seeding: evidence for a two-step nucleation polymerization mechanism. J Biol Chem 2013; 288:4772-81. [PMID: 23283973 DOI: 10.1074/jbc.m112.414581] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Prion diseases are fatal neurodegenerative disorders associated with the polymerization of the cellular form of prion protein (PrP(C)) into an amyloidogenic β-sheet infectious form (PrP(Sc)). The sequence of host PrP is the major determinant of host prion disease susceptibility. In mice, the presence of allele a (Prnp(a), encoding the polymorphism Leu-108/Thr-189) or b (Prnp(b), Phe-108/Val-189) is associated with short or long incubation times, respectively, following infection with PrP(Sc). The molecular bases linking PrP sequence, infection susceptibility, and convertibility of PrP(C) into PrP(Sc) remain unclear. Here we show that recombinant PrP(a) and PrP(b) aggregate and respond to seeding differently in vitro. Our kinetic studies reveal differences during the nucleation phase of the aggregation process, where PrP(b) exhibits a longer lag phase that cannot be completely eliminated by seeding the reaction with preformed fibrils. Additionally, PrP(b) is more prone to propagate features of the seeds, as demonstrated by conformational stability and electron microscopy studies of the formed fibrils. We propose a model of polymerization to explain how the polymorphisms at positions 108 and 189 produce the phenotypes seen in vivo. This model also provides insight into phenomena such as species barrier and prion strain generation, two phenomena also influenced by the primary structure of PrP.
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Affiliation(s)
- Leonardo M Cortez
- Centre for Prions and Protein Folding Diseases, University of Alberta, Edmonton, Alberta T6G 2M8, Canada
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18
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Prigent S, Ballesta A, Charles F, Lenuzza N, Gabriel P, Tine LM, Rezaei H, Doumic M. An efficient kinetic model for assemblies of amyloid fibrils and its application to polyglutamine aggregation. PLoS One 2012; 7:e43273. [PMID: 23152746 PMCID: PMC3496744 DOI: 10.1371/journal.pone.0043273] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2012] [Accepted: 07/18/2012] [Indexed: 11/23/2022] Open
Abstract
Protein polymerization consists in the aggregation of single monomers into polymers that may fragment. Fibrils assembly is a key process in amyloid diseases. Up to now, protein aggregation was commonly mathematically simulated by a polymer size-structured ordinary differential equations (ODE) system, which is infinite by definition and therefore leads to high computational costs. Moreover, this Ordinary Differential Equation-based modeling approach implies biological assumptions that may be difficult to justify in the general case. For example, whereas several ordinary differential equation models use the assumption that polymerization would occur at a constant rate independently of polymer size, it cannot be applied to certain protein aggregation mechanisms. Here, we propose a novel and efficient analytical method, capable of modelling and simulating amyloid aggregation processes. This alternative approach consists of an integro-Partial Differential Equation (PDE) model of coalescence-fragmentation type that was mathematically derived from the infinite differential system by asymptotic analysis. To illustrate the efficiency of our approach, we applied it to aggregation experiments on polyglutamine polymers that are involved in Huntington’s disease. Our model demonstrates the existence of a monomeric structural intermediate acting as a nucleus and deriving from a non polymerizing monomer (). Furthermore, we compared our model to previously published works carried out in different contexts and proved its accuracy to describe other amyloid aggregation processes.
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Affiliation(s)
| | - Annabelle Ballesta
- Institut National de Recherche en Informatique et Automatique, Rocquencourt, France
| | | | | | - Pierre Gabriel
- Institut National de Recherche en Informatique et Automatique Rhônes-Alpes, Lyon, France
| | | | - Human Rezaei
- Institut National de Recherche Agronomique, Jouy-en-Josas, France
| | - Marie Doumic
- Institut National de Recherche en Informatique et Automatique, Rocquencourt, France
- * E-mail:
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19
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Lee CF, Bird S, Shaw M, Jean L, Vaux DJ. Combined effects of agitation, macromolecular crowding, and interfaces on amyloidogenesis. J Biol Chem 2012; 287:38006-19. [PMID: 22988239 PMCID: PMC3488071 DOI: 10.1074/jbc.m112.400580] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2012] [Revised: 09/17/2012] [Indexed: 11/06/2022] Open
Abstract
Amyloid formation and accumulation is a hallmark of protein misfolding diseases and is associated with diverse pathologies including type II diabetes and Alzheimer's disease (AD). In vitro, amyloidogenesis is widely studied in conditions that do not simulate the crowded and viscous in vivo environment. A high volume fraction of most biological fluids is occupied by various macromolecules, a phenomenon known as macromolecular crowding. For some amyloid systems (e.g. α-synuclein) and under shaking condition, the excluded volume effect of macromolecular crowding favors aggregation, whereas increased viscosity reduces the kinetics of these reactions. Amyloidogenesis can also be catalyzed by hydrophobic-hydrophilic interfaces, represented by the air-water interface in vitro and diverse heterogeneous interfaces in vivo (e.g. membranes). In this study, we investigated the effects of two different crowding polymers (dextran and Ficoll) and two different experimental conditions (with and without shaking) on the fibrilization of amyloid-β peptide, a major player in AD pathogenesis. Specifically, we demonstrate that, during macromolecular crowding, viscosity dominates over the excluded volume effect only when the system is spatially non homogeneous (i.e. an air-water interface is present). We also show that the surfactant activity of the crowding agents can critically influence the outcome of macromolecular crowding and that the structure of the amyloid species formed may depend on the polymer used. This suggests that, in vivo, the outcome of amyloidogenesis may be affected by both macromolecular crowding and spatial heterogeneity (e.g. membrane turn-over). More generally, our work suggests that any factors causing changes in crowding may be susceptibility factors in AD.
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Affiliation(s)
- Chiu Fan Lee
- the Max Planck Institute for the Physics of Complex Systems, Noethnitzerstr. 38, Dresden 01187, Germany, and
| | - Sarah Bird
- the Medical School, Medical Sciences Office, John Radcliffe Hospital, Oxford University Clinical School, Oxford, OX3 9DU, United Kingdom
| | - Michael Shaw
- From the Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, United Kingdom
| | - Létitia Jean
- From the Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, United Kingdom
| | - David J. Vaux
- From the Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, United Kingdom
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20
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Invernizzi G, Papaleo E, Sabate R, Ventura S. Protein aggregation: mechanisms and functional consequences. Int J Biochem Cell Biol 2012; 44:1541-54. [PMID: 22713792 DOI: 10.1016/j.biocel.2012.05.023] [Citation(s) in RCA: 98] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2012] [Revised: 05/09/2012] [Accepted: 05/27/2012] [Indexed: 12/31/2022]
Abstract
Understanding the mechanisms underlying protein misfolding and aggregation has become a central issue in biology and medicine. Compelling evidence show that the formation of amyloid aggregates has a negative impact in cell function and is behind the most prevalent human degenerative disorders, including Alzheimer's Parkinson's and Huntington's diseases or type 2 diabetes. Surprisingly, the same type of macromolecular assembly is used for specialized functions by different organisms, from bacteria to human. Here we address the conformational properties of these aggregates, their formation pathways, their role in human diseases, their functional properties and how bioinformatics tools might be of help to study these protein assemblies.
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Affiliation(s)
- Gaetano Invernizzi
- Dipartimento di Biotecnologie e Bioscienze, Università di Milano-Bicocca, Milan, Italy
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