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Wruck F, Avellaneda MJ, Koers EJ, Minde DP, Mayer MP, Kramer G, Mashaghi A, Tans SJ. Protein Folding Mediated by Trigger Factor and Hsp70: New Insights from Single-Molecule Approaches. J Mol Biol 2017; 430:438-449. [PMID: 28911846 DOI: 10.1016/j.jmb.2017.09.004] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2017] [Revised: 08/26/2017] [Accepted: 09/04/2017] [Indexed: 01/01/2023]
Abstract
Chaperones assist in protein folding, but what this common phrase means in concrete terms has remained surprisingly poorly understood. We can readily measure chaperone binding to unfolded proteins, but how they bind and affect proteins along folding trajectories has remained obscure. Here we review recent efforts by our labs and others that are beginning to pry into this issue, with a focus on the chaperones trigger factor and Hsp70. Single-molecule methods are central, as they allow the stepwise process of folding to be followed directly. First results have already revealed contrasts with long-standing paradigms: rather than acting only "early" by stabilizing unfolded chain segments, these chaperones can bind and stabilize partially folded structures as they grow to their native state. The findings suggest a fundamental redefinition of the protein folding problem and a more extensive functional repertoire of chaperones than previously assumed.
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Affiliation(s)
- Florian Wruck
- AMOLF, Science Park 104, 1098 XG Amsterdam, the Netherlands
| | | | - Eline J Koers
- AMOLF, Science Park 104, 1098 XG Amsterdam, the Netherlands
| | - David P Minde
- AMOLF, Science Park 104, 1098 XG Amsterdam, the Netherlands
| | - Matthias P Mayer
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Im Neuenheimer Feld 282, D-69120 Heidelberg, Germany; German Cancer Research Center (DKFZ), Im Neuenheimer Feld 282, D-69120 Heidelberg, Germany
| | - Günter Kramer
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, Im Neuenheimer Feld 282, D-69120 Heidelberg, Germany; German Cancer Research Center (DKFZ), Im Neuenheimer Feld 282, D-69120 Heidelberg, Germany
| | - Alireza Mashaghi
- Leiden Academic Centre for Drug Research, Faculty of Mathematics and Natural Sciences, Leiden University, Einsteinweg 55, 2333 CC Leiden, the Netherlands
| | - Sander J Tans
- AMOLF, Science Park 104, 1098 XG Amsterdam, the Netherlands.
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102
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Van Assche R, Borghgraef C, Vaneyck J, Dumoulin M, Schoofs L, Temmerman L. In vitro aggregating β-lactamase-polyQ chimeras do not induce toxic effects in an in vivo Caenorhabditis elegans model. J Negat Results Biomed 2017; 16:14. [PMID: 28830560 PMCID: PMC5568214 DOI: 10.1186/s12952-017-0080-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2016] [Accepted: 08/14/2017] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND A series of human diseases are caused by the misfolding and aggregation of specific proteins or peptides into amyloid fibrils; nine of these diseases, referred to as polyglutamine diseases, are associated with proteins carrying an expanded polyglutamine (polyQ) region. While the presence of this latter is thought to be the determinant factor for the development of polyQ diseases, the non-polyQ regions of the host proteins are thought to play a significant modulating role. METHOD In order to better understand the role of non-polyQ regions, the toxic effects of model proteins bearing different polyQ regions (containing up to 79 residues) embedded at two distinct locations within the β-lactamase (BlaP) host enzyme were evaluated in Caenorhabditis elegans. This small organism can be advantageous for the validation of in vitro findings, as it provides a multicellular context yet avoids the typical complexity of common studies relying on vertebrate models. Several phenotypic assays were performed in order to screen for potential toxic effects of the different BlaP-polyQ proteins. RESULTS Despite the significant in vitro aggregation of BlaP-polyQ proteins with long polyQ regions, none of the BlaP-polyQ chimeras aggregated in the generated transgenic in vivo models. CONCLUSION The absence of a toxic effect of the expression of BlaP-polyQ chimeras may find its cause in biochemical mechanisms present in vivo to cope with protein aggregation (e.g. presence of chaperones) or in C. elegans' limitations such as its short lifespan. It is plausible that the aggregation propensities of the different BlaP chimeras containing embedded polyQ sequences are too low in this in vivo environment to permit their aggregation. These experiments emphasize the need for several comparative and in vivo verification studies of biologically relevant in vitro findings, which reveal both the strengths and limitations of widely used model systems.
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Affiliation(s)
- Roel Van Assche
- Animal Physiology and Neurobiology, Department of Biology, KU Leuven (University of Leuven), Zoological Institute, Naamsestraat 59, 3000 Leuven, Belgium
| | - Charline Borghgraef
- Animal Physiology and Neurobiology, Department of Biology, KU Leuven (University of Leuven), Zoological Institute, Naamsestraat 59, 3000 Leuven, Belgium
| | - Jonathan Vaneyck
- Enzymology and Protein Folding, Center for Protein Engineering, InBioS, Institute of Chemistry, University of Liège, Sart-Tilman, 4000 Liège, Belgium
| | - Mireille Dumoulin
- Enzymology and Protein Folding, Center for Protein Engineering, InBioS, Institute of Chemistry, University of Liège, Sart-Tilman, 4000 Liège, Belgium
| | - Liliane Schoofs
- Animal Physiology and Neurobiology, Department of Biology, KU Leuven (University of Leuven), Zoological Institute, Naamsestraat 59, 3000 Leuven, Belgium
| | - Liesbet Temmerman
- Animal Physiology and Neurobiology, Department of Biology, KU Leuven (University of Leuven), Zoological Institute, Naamsestraat 59, 3000 Leuven, Belgium
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103
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Ambadipudi S, Biernat J, Riedel D, Mandelkow E, Zweckstetter M. Liquid-liquid phase separation of the microtubule-binding repeats of the Alzheimer-related protein Tau. Nat Commun 2017; 8:275. [PMID: 28819146 PMCID: PMC5561136 DOI: 10.1038/s41467-017-00480-0] [Citation(s) in RCA: 435] [Impact Index Per Article: 62.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Accepted: 06/30/2017] [Indexed: 02/08/2023] Open
Abstract
The protein Tau aggregates into tangles in the brain of patients with Alzheimer’s disease. In solution, however, Tau is intrinsically disordered, highly soluble, and binds to microtubules. It is still unclear what initiates the conversion from an innocuous phase of high solubility and functionality to solid-like neurotoxic deposits. Here, we show that the microtubule-binding repeats of Tau, which are lysine-rich, undergo liquid–liquid phase separation in solution. Liquid–liquid demixing causes molecular crowding of amyloid-promoting elements of Tau and drives electrostatic coacervation. Furthermore, we demonstrate that three-repeat and four-repeat isoforms of Tau differ in their ability for demixing. Alternative splicing of Tau can thus regulate the formation of Tau-containing membrane-less compartments. In addition, phosphorylation of Tau repeats promotes liquid–liquid phase separation at cellular protein conditions. The combined data propose a mechanism in which liquid droplets formed by the positively charged microtubule-binding domain of Tau undergo coacervation with negatively charged molecules to promote amyloid formation. Tau forms aggregates in the brains of Alzheimer patients. Here, the authors identify conditions, where the microtubule-binding repeats of Tau undergo a phosphorylation-dependent liquid–liquid phase separation, leading to molecular crowding in the formed Tau liquid droplets and characterize them by NMR and other biophysical methods.
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Affiliation(s)
- Susmitha Ambadipudi
- Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), von-Siebold-Str. 3a, 37075, Göttingen, Germany
| | - Jacek Biernat
- Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), Ludwig-Erhard-Allee 2, 53175, Bonn, Germany
| | - Dietmar Riedel
- Max-Planck-Institut für Biophysikalische Chemie, Am Fassberg 11, 37077, Göttingen, Germany
| | - Eckhard Mandelkow
- Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), Ludwig-Erhard-Allee 2, 53175, Bonn, Germany.,CAESAR Research Center, Bonn, and MPI for Metabolism Research, Hamburg Outstation, 22607, Hamburg, Germany
| | - Markus Zweckstetter
- Deutsches Zentrum für Neurodegenerative Erkrankungen (DZNE), von-Siebold-Str. 3a, 37075, Göttingen, Germany. .,Max-Planck-Institut für Biophysikalische Chemie, Am Fassberg 11, 37077, Göttingen, Germany. .,Department of Neurology, University Medical Center Göttingen, University of Göttingen, Waldweg 33, 37073, Göttingen, Germany.
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104
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Kevei É, Pokrzywa W, Hoppe T. Repair or destruction-an intimate liaison between ubiquitin ligases and molecular chaperones in proteostasis. FEBS Lett 2017; 591:2616-2635. [PMID: 28699655 PMCID: PMC5601288 DOI: 10.1002/1873-3468.12750] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2017] [Revised: 07/04/2017] [Accepted: 07/06/2017] [Indexed: 12/11/2022]
Abstract
Cellular differentiation, developmental processes, and environmental factors challenge the integrity of the proteome in every eukaryotic cell. The maintenance of protein homeostasis, or proteostasis, involves folding and degradation of damaged proteins, and is essential for cellular function, organismal growth, and viability 1, 2. Misfolded proteins that cannot be refolded by chaperone machineries are degraded by specialized proteolytic systems. A major degradation pathway regulating cellular proteostasis is the ubiquitin (Ub)/proteasome system (UPS), which regulates turnover of damaged proteins that accumulate upon stress and during aging. Despite a large number of structurally unrelated substrates, Ub conjugation is remarkably selective. Substrate selectivity is mainly provided by the group of E3 enzymes. Several observations indicate that numerous E3 Ub ligases intimately collaborate with molecular chaperones to maintain the cellular proteome. In this review, we provide an overview of specialized quality control E3 ligases playing a critical role in the degradation of damaged proteins. The process of substrate recognition and turnover, the type of chaperones they team up with, and the potential pathogeneses associated with their malfunction will be further discussed.
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Affiliation(s)
- Éva Kevei
- School of Biological Sciences, University of Reading, Whiteknights, UK
| | - Wojciech Pokrzywa
- International Institute of Molecular and Cell Biology in Warsaw, Poland
| | - Thorsten Hoppe
- Institute for Genetics and Cologne Excellence Cluster on Cellular Stress Responses in Aging-Associated Diseases (CECAD), University of Cologne, Germany
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105
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Nanoscale Control of Amyloid Self-Assembly Using Protein Phase Transfer by Host-Guest Chemistry. Sci Rep 2017; 7:5710. [PMID: 28720896 PMCID: PMC5516018 DOI: 10.1038/s41598-017-06181-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2017] [Accepted: 06/09/2017] [Indexed: 12/19/2022] Open
Abstract
Amyloid fibrils have recently been highlighted for their diverse applications as functional nanomaterials in modern chemistry. However, tight control to obtain a targeted fibril length with low heterogeneity has not been achieved because of the complicated nature of amyloid fibrillation. Herein, we demonstrate that fibril assemblies can be homogeneously manipulated with desired lengths from ~40 nm to ~10 μm by a phase transfer of amyloid proteins based on host-guest chemistry. We suggest that host-guest interactions with cucurbit[6]uril induce a phase transfer of amyloid proteins (human insulin, human islet amyloid polypeptide, hen egg lysozyme, and amyloid-β 1–40 & 1–42) from the soluble state to insoluble state when the amount of cucurbit[6]uril exceeds its solubility limit in solution. The phase transfer of the proteins kinetically delays the nucleation of amyloid proteins, while the nuclei formed in the early stage are homogeneously assembled to fibrils. Consequently, supramolecular assemblies of amyloid proteins with heterogeneous kinetics can be controlled by protein phase transfer based on host-guest interactions.
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106
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Amyotrophic lateral sclerosis-like superoxide dismutase 1 proteinopathy is associated with neuronal loss in Parkinson's disease brain. Acta Neuropathol 2017; 134:113-127. [PMID: 28527045 DOI: 10.1007/s00401-017-1726-6] [Citation(s) in RCA: 73] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Revised: 05/10/2017] [Accepted: 05/12/2017] [Indexed: 12/13/2022]
Abstract
Neuronal loss in numerous neurodegenerative disorders has been linked to protein aggregation and oxidative stress. Emerging data regarding overlapping proteinopathy in traditionally distinct neurodegenerative diseases suggest that disease-modifying treatments targeting these pathological features may exhibit efficacy across multiple disorders. Here, we describe proteinopathy distinct from classic synucleinopathy, predominantly comprised of the anti-oxidant enzyme superoxide dismutase-1 (SOD1), in the Parkinson's disease brain. Significant expression of this pathology closely reflected the regional pattern of neuronal loss. The protein composition and non-amyloid macrostructure of these novel aggregates closely resembles that of neurotoxic SOD1 deposits in SOD1-associated familial amyotrophic lateral sclerosis (fALS). Consistent with the hypothesis that deposition of protein aggregates in neurodegenerative disorders reflects upstream dysfunction, we demonstrated that SOD1 in the Parkinson's disease brain exhibits evidence of misfolding and metal deficiency, similar to that seen in mutant SOD1 in fALS. Our data suggest common mechanisms of toxic SOD1 aggregation in both disorders and a potential role for SOD1 dysfunction in neuronal loss in the Parkinson's disease brain. This shared restricted proteinopathy highlights the potential translation of therapeutic approaches targeting SOD1 toxicity, already in clinical trials for ALS, into disease-modifying treatments for Parkinson's disease.
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107
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Protein homeostasis of a metastable subproteome associated with Alzheimer's disease. Proc Natl Acad Sci U S A 2017; 114:E5703-E5711. [PMID: 28652376 DOI: 10.1073/pnas.1618417114] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Alzheimer's disease is the most common cause of dementia. A hallmark of this disease is the presence of aberrant deposits containing by the Aβ peptide (amyloid plaques) and the tau protein (neurofibrillary tangles) in the brains of affected individuals. Increasing evidence suggests that the formation of these deposits is closely associated with the age-related dysregulation of a large set of highly expressed and aggregation-prone proteins, which make up a metastable subproteome. To understand in more detail the origins of such dysregulation, we identify specific components of the protein homeostasis system associated with these metastable proteins by using a gene coexpression analysis. Our results reveal the particular importance of the protein trafficking and clearance mechanisms, including specific branches of the endosomal-lysosomal and ubiquitin-proteasome systems, in maintaining the homeostasis of the metastable subproteome associated with Alzheimer's disease.
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108
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Abstract
A healthy proteome is essential for cell survival. Protein misfolding is linked to a rapidly expanding list of human diseases, ranging from neurodegenerative diseases to aging and cancer. Many of these diseases are characterized by the accumulation of misfolded proteins in intra- and extracellular inclusions, such as amyloid plaques. The clear link between protein misfolding and disease highlights the need to better understand the elaborate machinery that manages proteome homeostasis, or proteostasis, in the cell. Proteostasis depends on a network of molecular chaperones and clearance pathways involved in the recognition, refolding, and/or clearance of aberrant proteins. Recent studies reveal that an integral part of the cellular management of misfolded proteins is their spatial sequestration into several defined compartments. Here, we review the properties, function, and formation of these compartments. Spatial sequestration plays a central role in protein quality control and cellular fitness and represents a critical link to the pathogenesis of protein aggregation-linked diseases.
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Affiliation(s)
| | - Rahul S Samant
- Department of Biology, Stanford University, Stanford, California 94305; , ,
| | - Judith Frydman
- Department of Biology, Stanford University, Stanford, California 94305; , ,
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109
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Dobson CM. The Amyloid Phenomenon and Its Links with Human Disease. Cold Spring Harb Perspect Biol 2017; 9:cshperspect.a023648. [PMID: 28062560 DOI: 10.1101/cshperspect.a023648] [Citation(s) in RCA: 84] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
The ability of normally soluble proteins to convert into amyloid fibrils is now recognized to be a generic phenomenon. The overall cross-β architecture of the core elements of such structures is closely similar for different amino acid sequences, as this architecture is dominated by interactions associated with the common polypeptide main chain. In contrast, the multiplicity of complex and intricate structures of the functional states of proteins is dictated by specific interactions involving the variable side chains, the sequence of which is unique to a given protein. Nevertheless, the side chains dictate important aspects of the amyloid structure, including the regions of the sequence that form the core elements of the fibrils and the kinetics and mechanism of the conversion process. The formation of the amyloid state of proteins is of particular importance in the context of a range of medical disorders that include Alzheimer's and Parkinson's diseases and type 2 diabetes. These disorders are becoming increasingly common in the modern world, primarily as a consequence of increasing life spans and changing lifestyles, and now affect some 500 million people worldwide. This review describes recent progress in our understanding of the molecular origins of these conditions and discusses emerging ideas for new and rational therapeutic strategies by which to combat their onset and progression.
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Affiliation(s)
- Christopher M Dobson
- Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
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110
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Using bicistronic constructs to evaluate the chaperone activities of heat shock proteins in cells. Sci Rep 2017; 7:2387. [PMID: 28539657 PMCID: PMC5443837 DOI: 10.1038/s41598-017-02459-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Accepted: 04/12/2017] [Indexed: 01/03/2023] Open
Abstract
Heat shock proteins (Hsps) are molecular chaperones that prevent the aggregation of client proteins by facilitating their refolding, or trafficking them for degradation. The chaperone activities of Hsps are dependent on dynamic protein-protein interactions, including their oligomerisation into large multi-subunit complexes. Thus, tagging Hsps with fluorescent proteins can interfere with their chaperone activity. To overcome this limitation, we have exploited bicistronic constructs for the concurrent expression of a non-tagged Hsp and fluorescent reporter from a single mRNA in cells. We used the Hsp-encoding bicistronic constructs in a cell-based model of protein aggregation, using a destabilised (mutant) form of firefly luciferase (mFluc) that forms inclusion bodies in cells. Expression of Hsp40, Hsp70, or Hsp40 and Hsp70 in cells expressing mFluc decreased the formation of inclusion bodies by 25–46% compared to controls. Moreover, there was a concentration-dependent decrease in the proportion of cells with inclusions when Hsp70, or Hsp40 and Hsp70 were co-expressed with mFluc in cells. The Hsp-encoding bicistronic constructs enable transfection efficiencies and concentration-dependent effects of Hsp expression to be determined using fluorescence based techniques, without the need to tag the Hsp with a fluorescent protein.
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111
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Ciryam P, Lambert-Smith IA, Bean DM, Freer R, Cid F, Tartaglia GG, Saunders DN, Wilson MR, Oliver SG, Morimoto RI, Dobson CM, Vendruscolo M, Favrin G, Yerbury JJ. Spinal motor neuron protein supersaturation patterns are associated with inclusion body formation in ALS. Proc Natl Acad Sci U S A 2017; 114:E3935-E3943. [PMID: 28396410 PMCID: PMC5441770 DOI: 10.1073/pnas.1613854114] [Citation(s) in RCA: 83] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Amyotrophic lateral sclerosis (ALS) is a heterogeneous degenerative motor neuron disease linked to numerous genetic mutations in apparently unrelated proteins. These proteins, including SOD1, TDP-43, and FUS, are highly aggregation-prone and form a variety of intracellular inclusion bodies that are characteristic of different neuropathological subtypes of the disease. Contained within these inclusions are a variety of proteins that do not share obvious characteristics other than coaggregation. However, recent evidence from other neurodegenerative disorders suggests that disease-affected biochemical pathways can be characterized by the presence of proteins that are supersaturated, with cellular concentrations significantly greater than their solubilities. Here, we show that the proteins that form inclusions of mutant SOD1, TDP-43, and FUS are not merely a subset of the native interaction partners of these three proteins, which are themselves supersaturated. To explain the presence of coaggregating proteins in inclusions in the brain and spinal cord, we observe that they have an average supersaturation even greater than the average supersaturation of the native interaction partners in motor neurons, but not when scores are generated from an average of other human tissues. These results suggest that inclusion bodies in various forms of ALS result from a set of proteins that are metastable in motor neurons, and thus prone to aggregation upon a disease-related progressive collapse of protein homeostasis in this specific setting.
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Affiliation(s)
- Prajwal Ciryam
- Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom;
- Department of Molecular Biosciences, Rice Institute for Biomedical Research, Northwestern University, Evanston, IL 60208-3500
- Department of Medicine, Columbia University College of Physicans & Surgeons, New York, NY 10032-3784
| | - Isabella A Lambert-Smith
- Cambridge Systems Biology Centre, University of Cambridge, Cambridge CB2 1GA, United Kingdom
- Illawarra Health and Medical Research Institute, Wollongong, NSW 2522 Australia
- School of Biological Sciences, Faculty of Science, Medicine and Health, University of Wollongong, Wollongong, NSW 2522 Australia
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, United Kingdom
| | - Daniel M Bean
- Cambridge Systems Biology Centre, University of Cambridge, Cambridge CB2 1GA, United Kingdom
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, United Kingdom
| | - Rosie Freer
- Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
| | - Fernando Cid
- Centre for Genomic Regulation, The Barcelona Institute of Science and Technology, 08003 Barcelona, Spain
- Universitat Pompeu Fabra, 08003 Barcelona, Spain
| | - Gian Gaetano Tartaglia
- Centre for Genomic Regulation, The Barcelona Institute of Science and Technology, 08003 Barcelona, Spain
- Universitat Pompeu Fabra, 08003 Barcelona, Spain
- Institucio Catalana de Recerca i Estudis Avançats, 08010 Barcelona, Spain
| | - Darren N Saunders
- Faculty of Medicine, School of Medical Sciences, University of New South Wales, Sydney, NSW 2052, Australia
| | - Mark R Wilson
- Illawarra Health and Medical Research Institute, Wollongong, NSW 2522 Australia
- School of Biological Sciences, Faculty of Science, Medicine and Health, University of Wollongong, Wollongong, NSW 2522 Australia
| | - Stephen G Oliver
- Cambridge Systems Biology Centre, University of Cambridge, Cambridge CB2 1GA, United Kingdom
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, United Kingdom
| | - Richard I Morimoto
- Department of Molecular Biosciences, Rice Institute for Biomedical Research, Northwestern University, Evanston, IL 60208-3500
| | - Christopher M Dobson
- Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
| | - Michele Vendruscolo
- Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom
| | - Giorgio Favrin
- Cambridge Systems Biology Centre, University of Cambridge, Cambridge CB2 1GA, United Kingdom
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, United Kingdom
| | - Justin J Yerbury
- Illawarra Health and Medical Research Institute, Wollongong, NSW 2522 Australia;
- School of Biological Sciences, Faculty of Science, Medicine and Health, University of Wollongong, Wollongong, NSW 2522 Australia
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112
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113
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Aggregation landscapes of Huntingtin exon 1 protein fragments and the critical repeat length for the onset of Huntington's disease. Proc Natl Acad Sci U S A 2017; 114:4406-4411. [PMID: 28400517 DOI: 10.1073/pnas.1702237114] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Huntington's disease (HD) is a neurodegenerative disease caused by an abnormal expansion in the polyglutamine (polyQ) track of the Huntingtin (HTT) protein. The severity of the disease depends on the polyQ repeat length, arising only in patients with proteins having 36 repeats or more. Previous studies have shown that the aggregation of N-terminal fragments (encoded by HTT exon 1) underlies the disease pathology in mouse models and that the HTT exon 1 gene product can self-assemble into amyloid structures. Here, we provide detailed structural mechanisms for aggregation of several protein fragments encoded by HTT exon 1 by using the associative memory, water-mediated, structure and energy model (AWSEM) to construct their free energy landscapes. We find that the addition of the N-terminal 17-residue sequence ([Formula: see text]) facilitates polyQ aggregation by encouraging the formation of prefibrillar oligomers, whereas adding the C-terminal polyproline sequence ([Formula: see text]) inhibits aggregation. The combination of both terminal additions in HTT exon 1 fragment leads to a complex aggregation mechanism with a basic core that resembles that found for the aggregation of pure polyQ repeats using AWSEM. At the extrapolated physiological concentration, although the grand canonical free energy profiles are uphill for HTT exon 1 fragments having 20 or 30 glutamines, the aggregation landscape for fragments with 40 repeats has become downhill. This computational prediction agrees with the critical length found for the onset of HD and suggests potential therapies based on blocking early binding events involving the terminal additions to the polyQ repeats.
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114
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Alberti S, Mateju D, Mediani L, Carra S. Granulostasis: Protein Quality Control of RNP Granules. Front Mol Neurosci 2017; 10:84. [PMID: 28396624 PMCID: PMC5367262 DOI: 10.3389/fnmol.2017.00084] [Citation(s) in RCA: 87] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2017] [Accepted: 03/10/2017] [Indexed: 12/14/2022] Open
Abstract
Ribonucleoprotein (RNP) granules transport, store, or degrade messenger RNAs, thereby indirectly regulating protein synthesis. Normally, RNP granules are highly dynamic compartments. However, because of aging or severe environmental stress, RNP granules, in particular stress granules (SGs), convert into solid, aggregate-like inclusions. There is increasing evidence that such RNA-protein inclusions are associated with several age-related neurodegenerative diseases, such as amyotrophic lateral sclerosis (ALS), fronto-temporal dementia (FTD) and Alzheimer's disease (AD). Thus, understanding what triggers the conversion of RNP granules into aggregates and identifying the cellular players that control RNP granules will be critical to develop treatments for these diseases. In this review article, we discuss recent insight into RNP and SG formation. More specifically, we examine the evidence for liquid-liquid phase separation (LLPS) as an organizing principle of RNP granules and the role of aggregation-prone RNA-binding proteins (RBPs) in this process. We further discuss recent findings that liquid-like SGs can sequester misfolded proteins, which promote an aberrant conversion of liquid SGs into solid aggregates. Importantly, very recent studies show that a specific protein quality control (PQC) process prevents the accumulation of misfolding-prone proteins in SGs and, by doing so, maintains the dynamic state of SGs. This quality control process has been referred to as granulostasis and it relies on the specific action of the HSPB8-BAG3-HSP70 complex. Additional players such as p97/valosin containing protein (VCP) and other molecular chaperones (e.g., HSPB1) participate, directly or indirectly, in granulostasis, and ensure the timely elimination of defective ribosomal products and other misfolded proteins from SGs. Finally, we discuss recent findings that, in the stress recovery phase, SGs are preferentially disassembled with the assistance of chaperones, and we discuss evidence for a back-up system that targets aberrant SGs to the aggresome for autophagy-mediated clearance. Altogether the findings discussed here provide evidence for an intricate network of interactions between RNP granules and various components of the PQC machinery. Molecular chaperones in particular are emerging as key players that control the composition and dynamics of RNP granules, which may be important to protect against age-related diseases.
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Affiliation(s)
- Simon Alberti
- Alberti Lab, Max Planck Institute of Molecular Cell Biology and Genetics Dresden, Germany
| | - Daniel Mateju
- Alberti Lab, Max Planck Institute of Molecular Cell Biology and Genetics Dresden, Germany
| | - Laura Mediani
- Department of Biomedical, Metabolic and Neural Sciences, Center for Neuroscience and Nanotechnology, University of Modena and Reggio Emilia Modena, Italy
| | - Serena Carra
- Department of Biomedical, Metabolic and Neural Sciences, Center for Neuroscience and Nanotechnology, University of Modena and Reggio Emilia Modena, Italy
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115
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Krug L, Chatterjee N, Borges-Monroy R, Hearn S, Liao WW, Morrill K, Prazak L, Rozhkov N, Theodorou D, Hammell M, Dubnau J. Retrotransposon activation contributes to neurodegeneration in a Drosophila TDP-43 model of ALS. PLoS Genet 2017; 13:e1006635. [PMID: 28301478 PMCID: PMC5354250 DOI: 10.1371/journal.pgen.1006635] [Citation(s) in RCA: 128] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2016] [Accepted: 02/14/2017] [Indexed: 12/11/2022] Open
Abstract
Amyotrophic lateral sclerosis (ALS) and frontotemporal lobar degeneration (FTLD) are two incurable neurodegenerative disorders that exist on a symptomological spectrum and share both genetic underpinnings and pathophysiological hallmarks. Functional abnormality of TAR DNA-binding protein 43 (TDP-43), an aggregation-prone RNA and DNA binding protein, is observed in the vast majority of both familial and sporadic ALS cases and in ~40% of FTLD cases, but the cascade of events leading to cell death are not understood. We have expressed human TDP-43 (hTDP-43) in Drosophila neurons and glia, a model that recapitulates many of the characteristics of TDP-43-linked human disease including protein aggregation pathology, locomotor impairment, and premature death. We report that such expression of hTDP-43 impairs small interfering RNA (siRNA) silencing, which is the major post-transcriptional mechanism of retrotransposable element (RTE) control in somatic tissue. This is accompanied by de-repression of a panel of both LINE and LTR families of RTEs, with somewhat different elements being active in response to hTDP-43 expression in glia versus neurons. hTDP-43 expression in glia causes an early and severe loss of control of a specific RTE, the endogenous retrovirus (ERV) gypsy. We demonstrate that gypsy causes the degenerative phenotypes in these flies because we are able to rescue the toxicity of glial hTDP-43 either by genetically blocking expression of this RTE or by pharmacologically inhibiting RTE reverse transcriptase activity. Moreover, we provide evidence that activation of DNA damage-mediated programmed cell death underlies both neuronal and glial hTDP-43 toxicity, consistent with RTE-mediated effects in both cell types. Our findings suggest a novel mechanism in which RTE activity contributes to neurodegeneration in TDP-43-mediated diseases such as ALS and FTLD.
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Affiliation(s)
- Lisa Krug
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, United States of America
- Watson School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, United States of America
| | - Nabanita Chatterjee
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, United States of America
| | | | - Stephen Hearn
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, United States of America
| | - Wen-Wei Liao
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, United States of America
| | - Kathleen Morrill
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, United States of America
| | - Lisa Prazak
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, United States of America
- Department of Biology, Farmingdale State College, Farmingdale, NY United States of America
| | - Nikolay Rozhkov
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, United States of America
| | - Delphine Theodorou
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, United States of America
| | - Molly Hammell
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, United States of America
| | - Josh Dubnau
- Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, United States of America
- Watson School of Biological Sciences, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, United States of America
- Department of Anesthesiology, Stony Brook School of Medicine, Stony Brook, New York, United States of America
- Department of Neurobiology and Behavior, Stony Brook School of Medicine, Stony Brook, New York, United States of America
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116
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117
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Michel D, Ruelle P. Polylogarithmic equilibrium treatment of molecular aggregation and critical concentrations. Phys Chem Chem Phys 2017; 19:5273-5284. [DOI: 10.1039/c6cp08369b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A new modeling approach to molecular aggregation is proposed under the condition of generalized microreversibility.
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Affiliation(s)
- Denis Michel
- Universite de Rennes1-IRSET
- Campus de Villejean
- 3500 Rennes
- France
| | - Philippe Ruelle
- Université catholique de Louvain – Institut de Recherche en Mathématique et Physique
- Chemin du Cyclotron
- 2 B-1348 Louvain-la-Neuve
- Belgium
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118
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Pallarès I, Ventura S. Understanding and predicting protein misfolding and aggregation: Insights from proteomics. Proteomics 2016; 16:2570-2581. [PMID: 27479752 DOI: 10.1002/pmic.201500529] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2016] [Revised: 07/08/2016] [Accepted: 07/25/2016] [Indexed: 11/09/2022]
Abstract
Protein misfolding and aggregation are being found to be associated with an increasing number of human diseases and premature aging, either because they promote a loss of protein function or, more frequently, because the aggregated species gain a toxic activity. Despite potentially harmful, aggregation seems to be a generic property of polypeptide chains and aggregation-prone protein sequences seem to be ubiquitous, which, counterintuitively, suggests that they serve evolutionary conserved functions. The in vitro study of individual aggregation reactions of a large number of proteins has provided important insights on the structural and sequential determinants of this process. However, it is clear that understanding the role played by protein aggregation and its regulation in health and disease at the cellular, developmental, and evolutionary levels require more global approaches. The use of model organisms and their proteomic analysis hold the power to provide answers to such issues. In the present review, we address how, initially, computational large-scale analysis and, more recently, experimental proteomics are helping us to rationalize how, why and when proteins aggregate, as well as to decipher the strategies organisms have developed to control proteins aggregation propensities.
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Affiliation(s)
- Irantzu Pallarès
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, Bellaterra, Spain.,Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Salvador Ventura
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, Bellaterra, Spain. .,Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Bellaterra, Spain.
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119
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Wang Y, Shao Q, Hall CK. N-terminal Prion Protein Peptides (PrP(120-144)) Form Parallel In-register β-Sheets via Multiple Nucleation-dependent Pathways. J Biol Chem 2016; 291:22093-22105. [PMID: 27576687 DOI: 10.1074/jbc.m116.744573] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2016] [Indexed: 12/14/2022] Open
Abstract
The prion diseases are a family of fatal neurodegenerative diseases associated with the misfolding and accumulation of normal prion protein (PrPC) into its pathogenic scrapie form (PrPSc). Understanding the fundamentals of prion protein aggregation and the molecular architecture of PrPSc is key to unraveling the pathology of prion diseases. Our work investigates the early-stage aggregation of three prion protein peptides, corresponding to residues 120-144 of human (Hu), bank vole (BV), and Syrian hamster (SHa) prion protein, from disordered monomers to β-sheet-rich fibrillar structures. Using 12 μs discontinuous molecular dynamics simulations combined with the PRIME20 force field, we find that the Hu-, BV-, and SHaPrP(120-144) aggregate via multiple nucleation-dependent pathways to form U-shaped, S-shaped, and Ω-shaped protofilaments. The S-shaped HuPrP(120-144) protofilament is similar to the amyloid core structure of HuPrP(112-141) predicted by Zweckstetter. HuPrP(120-144) has a shorter aggregation lag phase than BVPrP(120-144) followed by SHaPrP(120-144), consistent with experimental findings. Two amino acid substitutions I138M and I139M retard the formation of parallel in-register β-sheet dimers during the nucleation stage by increasing side chain-side chain association and reducing side chain interaction specificity. On average, HuPrP(120-144) aggregates contain more parallel β-sheet content than those formed by BV- and SHaPrP(120-144). Deletion of the C-terminal residues 138-144 prevents formation of fibrillar structures in agreement with the experiment. This work sheds light on the amyloid core structures underlying prion strains and how I138M, I139M, and S143N affect prion protein aggregation kinetics.
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Affiliation(s)
- Yiming Wang
- From the Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina, 27695-7905
| | - Qing Shao
- From the Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina, 27695-7905
| | - Carol K Hall
- From the Department of Chemical and Biomolecular Engineering, North Carolina State University, Raleigh, North Carolina, 27695-7905
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120
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Abstract
Why do cells age? Recent advances show that the cytoplasm is organized into many membrane‐less compartments via a process known as phase separation, which ensures spatiotemporal control over diffusion‐limited biochemical reactions. Although phase separation is a powerful mechanism to organize biochemical reactions, it comes with the trade‐off that it is extremely sensitive to changes in physical‐chemical parameters, such as protein concentration, pH, or cellular energy levels. Here, we highlight recent findings showing that age‐related neurodegenerative diseases are linked to aberrant phase transitions in neurons. We discuss how these aberrant phase transitions could be tied to a failure to maintain physiological physical‐chemical conditions. We generalize this idea to suggest that the process of cellular aging involves a progressive loss of the organization of phase‐separated compartments in the cytoplasm.
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Affiliation(s)
- Simon Alberti
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany.
| | - Anthony A Hyman
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany.
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121
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Noda S, So M, Adachi M, Kardos J, Akazawa-Ogawa Y, Hagihara Y, Goto Y. Thioflavin T-Silent Denaturation Intermediates Support the Main-Chain-Dominated Architecture of Amyloid Fibrils. Biochemistry 2016; 55:3937-48. [PMID: 27345358 DOI: 10.1021/acs.biochem.6b00231] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Ultrasonication is considered one of the most effective agitations for inducing the spontaneous formation of amyloid fibrils. When we induced the ultrasonication-dependent fibrillation of β2-microglobulin and insulin monitored by amyloid-specific thioflavin T (ThT) fluorescence, both proteins showed a significant decrease in ThT fluorescence after the burst-phase increase. The decrease in ThT fluorescence was accelerated when the ultrasonic power was stronger, suggesting that this decrease was caused by the partial denaturation of preformed fibrils. The possible intermediates of denaturation retained amyloid-like morphologies, secondary structures, and seeding potentials. Similar denaturation intermediates were also observed when fibrils were denatured by guanidine hydrochloride or sodium dodecyl sulfate. The presence of these denaturation intermediates is consistent with the main-chain-dominated architecture of amyloid fibrils. Moreover, in the three types of denaturation experiments conducted, insulin fibrils were more stable than β2-microglobulin fibrils, suggesting that the relative stability of various fibrils is independent of the method of denaturation.
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Affiliation(s)
- Sayaka Noda
- Institute for Protein Research, Osaka University , Yamadaoka 3-2, Suita, Osaka 565-0871, Japan
| | - Masatomo So
- Institute for Protein Research, Osaka University , Yamadaoka 3-2, Suita, Osaka 565-0871, Japan
| | - Masayuki Adachi
- Institute for Protein Research, Osaka University , Yamadaoka 3-2, Suita, Osaka 565-0871, Japan
| | - József Kardos
- Department of Biochemistry and MTA-ELTE NAP B Neuroimmunology Research Group, Eötvös Loránd University , Pázmány sétány 1/C, Budapest 1117, Hungary
| | - Yoko Akazawa-Ogawa
- National Institute of Advanced Industrial Science and Technology (AIST) , 1-8-31 Midorigaoka, Ikeda, Osaka 563-8577, Japan
| | - Yoshihisa Hagihara
- National Institute of Advanced Industrial Science and Technology (AIST) , 1-8-31 Midorigaoka, Ikeda, Osaka 563-8577, Japan
| | - Yuji Goto
- Institute for Protein Research, Osaka University , Yamadaoka 3-2, Suita, Osaka 565-0871, Japan
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122
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A transcriptional signature of Alzheimer's disease is associated with a metastable subproteome at risk for aggregation. Proc Natl Acad Sci U S A 2016; 113:4753-8. [PMID: 27071083 DOI: 10.1073/pnas.1516604113] [Citation(s) in RCA: 70] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
It is well-established that widespread transcriptional changes accompany the onset and progression of Alzheimer's disease. Because of the multifactorial nature of this neurodegenerative disorder and its complex relationship with aging, however, it remains unclear whether such changes are the result of nonspecific dysregulation and multisystem failure or instead are part of a coordinated response to cellular dysfunction. To address this problem in a systematic manner, we performed a meta-analysis of about 1,600 microarrays from human central nervous system tissues to identify transcriptional changes upon aging and as a result of Alzheimer's disease. Our strategy to discover a transcriptional signature of Alzheimer's disease revealed a set of down-regulated genes that encode proteins metastable to aggregation. Using this approach, we identified a small number of biochemical pathways, notably oxidative phosphorylation, enriched in proteins vulnerable to aggregation in control brains and encoded by genes down-regulated in Alzheimer's disease. These results suggest that the down-regulation of a metastable subproteome may help mitigate aberrant protein aggregation when protein homeostasis becomes compromised in Alzheimer's disease.
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123
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CPAD, Curated Protein Aggregation Database: A Repository of Manually Curated Experimental Data on Protein and Peptide Aggregation. PLoS One 2016; 11:e0152949. [PMID: 27043825 PMCID: PMC4820268 DOI: 10.1371/journal.pone.0152949] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2016] [Accepted: 03/20/2016] [Indexed: 11/24/2022] Open
Abstract
Accurate distinction between peptide sequences that can form amyloid-fibrils or amorphous β-aggregates, identification of potential aggregation prone regions in proteins, and prediction of change in aggregation rate of a protein upon mutation(s) are critical to research on protein misfolding diseases, such as Alzheimer’s and Parkinson’s, as well as biotechnological production of protein based therapeutics. We have developed a Curated Protein Aggregation Database (CPAD), which has collected results from experimental studies performed by scientific community aimed at understanding protein/peptide aggregation. CPAD contains more than 2300 experimentally observed aggregation rates upon mutations in known amyloidogenic proteins. Each entry includes numerical values for the following parameters: change in rate of aggregation as measured by fluorescence intensity or turbidity, name and source of the protein, Uniprot and Protein Data Bank codes, single point as well as multiple mutations, and literature citation. The data in CPAD has been supplemented with five different types of additional information: (i) Amyloid fibril forming hexa-peptides, (ii) Amorphous β-aggregating hexa-peptides, (iii) Amyloid fibril forming peptides of different lengths, (iv) Amyloid fibril forming hexa-peptides whose crystal structures are available in the Protein Data Bank (PDB) and (v) Experimentally validated aggregation prone regions found in amyloidogenic proteins. Furthermore, CPAD is linked to other related databases and resources, such as Uniprot, Protein Data Bank, PUBMED, GAP, TANGO, WALTZ etc. We have set up a web interface with different search and display options so that users have the ability to get the data in multiple ways. CPAD is freely available at http://www.iitm.ac.in/bioinfo/CPAD/. The potential applications of CPAD have also been discussed.
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124
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Lin Y, Kardos J, Imai M, Ikenoue T, Kinoshita M, Sugiki T, Ishimori K, Goto Y, Lee YH. Amorphous Aggregation of Cytochrome c with Inherently Low Amyloidogenicity Is Characterized by the Metastability of Supersaturation and the Phase Diagram. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2016; 32:2010-2022. [PMID: 26824789 DOI: 10.1021/acs.langmuir.5b03810] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Despite extensive studies on the folding and function of cytochrome c, the mechanisms underlying its aggregation remain largely unknown. We herein examined the aggregation behavior of the physiologically relevant two types of cytochrome c, metal-bound cytochrome c, and its fragment with high amyloidogenicity as predicted in alcohol/water mixtures. Although the aggregation propensity of holo cytochrome c was low due to high solubility, markedly unfolded apo cytochrome c, lacking the heme prosthetic group, strongly promoted the propensity for amorphous aggregation with increases in hydrophobicity. Silver-bound apo cytochrome c increased the capacity of fibrillar aggregation (i.e., protofibrils or immature fibrils) due to subtle structural changes of apo cytochrome c by strong binding of silver. However, mature amyloid fibrils were not detected for any of the cytochrome c variants or its fragment, even with extensive ultrasonication, which is a powerful amyloid inducer. These results revealed the intrinsically low amyloidogenicity of cytochrome c, which is beneficial for its homeostasis and function by facilitating the folding and minimizing irreversible amyloid formation. We propose that intrinsically low amyloidogenicity of cytochrome c is attributed to the low metastability of supersaturation. The phase diagram constructed based on solubility and aggregate type is useful for a comprehensive understanding of protein aggregation. Furthermore, amorphous aggregation, which is also viewed as a generic property of proteins, and amyloid fibrillation can be distinguished from each other by the metastability of supersaturation.
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Affiliation(s)
- Yuxi Lin
- Institute for Protein Research, Osaka University , Yamadaoka 3-2, Suita, Osaka 565-0871, Japan
| | - József Kardos
- MTA-ELTE NAP B Neuroimmunology Research Group, Department of Biochemistry, Eötvös Loránd University , Budapest H-1117, Hungary
| | - Mizue Imai
- Graduate School of Chemical Sciences and Engineering, Hokkaido University , Kita 13, Nishi 8, Kita-ku, Sapporo 060-8628, Japan
| | - Tatsuya Ikenoue
- Institute for Protein Research, Osaka University , Yamadaoka 3-2, Suita, Osaka 565-0871, Japan
| | - Misaki Kinoshita
- Institute for Protein Research, Osaka University , Yamadaoka 3-2, Suita, Osaka 565-0871, Japan
| | - Toshihiko Sugiki
- Institute for Protein Research, Osaka University , Yamadaoka 3-2, Suita, Osaka 565-0871, Japan
| | - Koichiro Ishimori
- Graduate School of Chemical Sciences and Engineering, Hokkaido University , Kita 13, Nishi 8, Kita-ku, Sapporo 060-8628, Japan
| | - Yuji Goto
- Institute for Protein Research, Osaka University , Yamadaoka 3-2, Suita, Osaka 565-0871, Japan
| | - Young-Ho Lee
- Institute for Protein Research, Osaka University , Yamadaoka 3-2, Suita, Osaka 565-0871, Japan
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125
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So M, Hall D, Goto Y. Revisiting supersaturation as a factor determining amyloid fibrillation. Curr Opin Struct Biol 2016; 36:32-9. [PMID: 26774801 DOI: 10.1016/j.sbi.2015.11.009] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2015] [Accepted: 11/20/2015] [Indexed: 10/22/2022]
Abstract
Amyloid fibrils involved in various diseases are formed by a nucleation-growth mechanism, similar to the crystallization of solutes from solution. Solubility and supersaturation are two of the most important factors determining crystallization of solutes. Moreover, crystallization competes with glass formation in which solutes collapse into amorphous aggregates. Recent studies on the formation of amyloid fibrils and amorphous aggregates indicate that the partition between distinct types of aggregates can be rationally explained by a kinetic and thermodynamic competition between them. Understanding the role of supersaturation in determining aggregation-based phase transitions of denatured proteins provides an important complementary point of view to structural studies of protein aggregates.
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Affiliation(s)
- Masatomo So
- Institute for Protein Research, Osaka University, Yamadaoka 3-2, Suita, Osaka 565-0871, Japan
| | - Damien Hall
- Institute for Protein Research, Osaka University, Yamadaoka 3-2, Suita, Osaka 565-0871, Japan; Research School of Chemistry, Australian National University, Acton, ACT 2601, Australia
| | - Yuji Goto
- Institute for Protein Research, Osaka University, Yamadaoka 3-2, Suita, Osaka 565-0871, Japan.
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126
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The Crowded Cytosol. Evol Bioinform Online 2016. [DOI: 10.1007/978-3-319-28755-3_16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022] Open
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127
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Crespo R, Villar-Alvarez E, Taboada P, Rocha FA, Damas AM, Martins PM. What Can the Kinetics of Amyloid Fibril Formation Tell about Off-pathway Aggregation? J Biol Chem 2015; 291:2018-2032. [PMID: 26601940 DOI: 10.1074/jbc.m115.699348] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2015] [Indexed: 11/06/2022] Open
Abstract
Some of the most prevalent neurodegenerative diseases are characterized by the accumulation of amyloid fibrils in organs and tissues. Although the pathogenic role of these fibrils has not been completely established, increasing evidence suggests off-pathway aggregation as a source of toxic/detoxicating deposits that still remains to be targeted. The present work is a step toward the development of off-pathway modulators using the same amyloid-specific dyes as those conventionally employed to screen amyloid inhibitors. We identified a series of kinetic signatures revealing the quantitative importance of off-pathway aggregation relative to amyloid fibrillization; these include non-linear semilog plots of amyloid progress curves, highly variable end point signals, and half-life coordinates weakly influenced by concentration. Molecules that attenuate/intensify the magnitude of these signals are considered promising off-pathway inhibitors/promoters. An illustrative example shows that amyloid deposits of lysozyme are only the tip of an iceberg hiding a crowd of insoluble aggregates. Thoroughly validated using advanced microscopy techniques and complementary measurements of dynamic light scattering, CD, and soluble protein depletion, the new analytical tools are compatible with the high-throughput methods currently employed in drug discovery.
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Affiliation(s)
- Rosa Crespo
- From the Laboratório de Engenharia de Processos, Ambiente, Biotecnologia e Energia, Departamento de Engenharia Química, Faculdade de Engenharia da Universidade do Porto, Rua Dr. Roberto Frias, 4200-465 Porto, Portugal
| | - Eva Villar-Alvarez
- the Departamento de Física de la Materia Condensada, Facultad de Física, Universidad de Santiago de Compostela, 15782 Spain, and
| | - Pablo Taboada
- the Departamento de Física de la Materia Condensada, Facultad de Física, Universidad de Santiago de Compostela, 15782 Spain, and
| | - Fernando A Rocha
- From the Laboratório de Engenharia de Processos, Ambiente, Biotecnologia e Energia, Departamento de Engenharia Química, Faculdade de Engenharia da Universidade do Porto, Rua Dr. Roberto Frias, 4200-465 Porto, Portugal
| | - Ana M Damas
- the Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, 4050-313 Porto, Portugal
| | - Pedro M Martins
- From the Laboratório de Engenharia de Processos, Ambiente, Biotecnologia e Energia, Departamento de Engenharia Química, Faculdade de Engenharia da Universidade do Porto, Rua Dr. Roberto Frias, 4200-465 Porto, Portugal,; the Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, 4050-313 Porto, Portugal.
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128
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Biophysical chemistry of the ageing eye lens. Biophys Rev 2015; 7:353-368. [PMID: 28510099 DOI: 10.1007/s12551-015-0176-4] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2015] [Accepted: 06/23/2015] [Indexed: 12/24/2022] Open
Abstract
This review examines both recent and historical literature related to the biophysical chemistry of the proteins in the ageing eye, with a particular focus on cataract development. The lens is a vital component of the eye, acting as an optical focusing device to form clear images on the retina. The lens maintains the necessary high transparency and refractive index by expressing crystallin proteins in high concentration and eliminating all large cellular structures that may cause light scattering. This has the consequence of eliminating lens fibre cell metabolism and results in mature lens fibre cells having no mechanism for protein expression and a complete absence of protein recycling or turnover. As a result, the crystallins are some of the oldest proteins in the human body. Lack of protein repair or recycling means the lens tends to accumulate damage with age in the form of protein post-translational modifications. The crystallins can be subject to a wide range of age-related changes, including isomerisation, deamidation and racemisation. Many of these modification are highly correlated with cataract formation and represent a biochemical mechanism for age-related blindness.
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129
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Dobson CM. Alzheimer’s disease: addressing a twenty-first century plague. RENDICONTI LINCEI-SCIENZE FISICHE E NATURALI 2015. [DOI: 10.1007/s12210-015-0453-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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130
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Jalles A, Maciel P. The disruption of proteostasis in neurodegenerative disorders. AIMS MOLECULAR SCIENCE 2015. [DOI: 10.3934/molsci.2015.3.259] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
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