1
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Housmans JAJ, Houben B, Monge-Morera M, Asvestas D, Nguyen HH, Tsaka G, Louros N, Carpentier S, Delcour JA, Rousseau F, Schymkowitz J. Investigating the Sequence Determinants of the Curling of Amyloid Fibrils Using Ovalbumin as a Case Study. Biomacromolecules 2022; 23:3779-3797. [PMID: 36027608 DOI: 10.1021/acs.biomac.2c00660] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Highly ordered, straight amyloid fibrils readily lend themselves to structure determination techniques and have therefore been extensively characterized. However, the less ordered curly fibrils remain relatively understudied, and the structural organization underlying their specific characteristics remains poorly understood. We found that the exemplary curly fibril-forming protein ovalbumin contains multiple aggregation prone regions (APRs) that form straight fibrils when isolated as peptides or when excised from the full-length protein through hydrolysis. In the context of the intact full-length protein, however, the regions separating the APRs facilitate curly fibril formation. In fact, a meta-analysis of previously reported curly fibril-forming proteins shows that their inter-APRs are significantly longer and more hydrophobic when compared to straight fibril-forming proteins, suggesting that they may cause strain in the amyloid state. Hence, inter-APRs driving curly fibril formation may not only apply to our model protein but rather constitute a more general mechanism.
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Affiliation(s)
- Joëlle A J Housmans
- Switch Laboratory, VIB-KU Leuven Center for Brain & Disease Research, Herestraat 49, 3000 Leuven, Belgium.,Department of Cellular and Molecular Medicine, KU Leuven, Herestraat 49, box 802, 3000 Leuven, Belgium
| | - Bert Houben
- Switch Laboratory, VIB-KU Leuven Center for Brain & Disease Research, Herestraat 49, 3000 Leuven, Belgium.,Department of Cellular and Molecular Medicine, KU Leuven, Herestraat 49, box 802, 3000 Leuven, Belgium
| | - Margarita Monge-Morera
- Laboratory of Food Chemistry and Biochemistry and Leuven Food Science and Nutrition Research Centre (LFoRCe), KU Leuven, Kasteelpark Arenberg 20, 3001 Leuven, Belgium
| | - Diego Asvestas
- Switch Laboratory, VIB-KU Leuven Center for Brain & Disease Research, Herestraat 49, 3000 Leuven, Belgium.,Department of Cellular and Molecular Medicine, KU Leuven, Herestraat 49, box 802, 3000 Leuven, Belgium
| | - Hung Huy Nguyen
- Switch Laboratory, VIB-KU Leuven Center for Brain & Disease Research, Herestraat 49, 3000 Leuven, Belgium.,Department of Cellular and Molecular Medicine, KU Leuven, Herestraat 49, box 802, 3000 Leuven, Belgium
| | - Grigoria Tsaka
- Switch Laboratory, VIB-KU Leuven Center for Brain & Disease Research, Herestraat 49, 3000 Leuven, Belgium.,Department of Cellular and Molecular Medicine, KU Leuven, Herestraat 49, box 802, 3000 Leuven, Belgium
| | - Nikolaos Louros
- Switch Laboratory, VIB-KU Leuven Center for Brain & Disease Research, Herestraat 49, 3000 Leuven, Belgium.,Department of Cellular and Molecular Medicine, KU Leuven, Herestraat 49, box 802, 3000 Leuven, Belgium
| | - Sebastien Carpentier
- Facility for Systems Biology Based Mass Spectrometry, KU Leuven, Herestraat 49, 3000 Leuven, Belgium
| | - Jan A Delcour
- Laboratory of Food Chemistry and Biochemistry and Leuven Food Science and Nutrition Research Centre (LFoRCe), KU Leuven, Kasteelpark Arenberg 20, 3001 Leuven, Belgium
| | - Frederic Rousseau
- Switch Laboratory, VIB-KU Leuven Center for Brain & Disease Research, Herestraat 49, 3000 Leuven, Belgium.,Department of Cellular and Molecular Medicine, KU Leuven, Herestraat 49, box 802, 3000 Leuven, Belgium
| | - Joost Schymkowitz
- Switch Laboratory, VIB-KU Leuven Center for Brain & Disease Research, Herestraat 49, 3000 Leuven, Belgium.,Department of Cellular and Molecular Medicine, KU Leuven, Herestraat 49, box 802, 3000 Leuven, Belgium
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2
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Howlett GJ, Ryan TM, Griffin MD. Lipid-apolipoprotein interactions in amyloid fibril formation and relevance to atherosclerosis. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2019; 1867:502-507. [DOI: 10.1016/j.bbapap.2018.08.010] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Revised: 08/06/2018] [Accepted: 08/27/2018] [Indexed: 01/08/2023]
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3
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Todorova N, Yarovsky I. The Enigma of Amyloid Forming Proteins: Insights From Molecular Simulations. Aust J Chem 2019. [DOI: 10.1071/ch19059] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Molecular level insight into the interplay between protein sequence, structure, and conformational dynamics is crucial for the comprehensive understanding of protein folding, misfolding, and aggregation phenomena that are pertinent to the formation of amyloid fibrils implicated in several degenerative diseases. Computational modelling provides insight into protein behaviour at spatial and temporal resolution still largely outside the reach of experiments. Herein we present an account of our theoretical modelling research conducted in collaboration with several experimental groups where we explored the effects of local environment on the structure and aggregation propensity of several types of amyloidogenic peptides and proteins, including apolipoprotein C-II, insulin, amylin, and amyloid-β using a variety of computational approaches.
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4
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Zlatic CO, Mao Y, Todorova N, Mok YF, Howlett GJ, Yarovsky I, Gooley PR, Griffin MDW. Polymorphism in disease-related apolipoprotein C-II amyloid fibrils: a structural model for rod-like fibrils. FEBS J 2018; 285:2799-2812. [PMID: 29791776 DOI: 10.1111/febs.14517] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Revised: 05/14/2018] [Accepted: 05/21/2018] [Indexed: 11/29/2022]
Abstract
Human apolipoprotein (apo) C-II is one of several plasma apolipoproteins that form amyloid deposits in vivo and is an independent risk factor for cardiovascular disease. Lipid-free apoC-II readily self-assembles into twisted-ribbon amyloid fibrils but forms straight, rod-like amyloid fibrils in the presence of low concentrations of micellar phospholipids. Charge mutations exerted significantly different effects on rod-like fibril formation compared to their effects on twisted-ribbon fibril formation. For instance, the double mutant, K30D-D69K apoC-II, readily formed twisted-ribbon fibrils, while the rate of rod-like fibril formation in the presence of micellar phospholipid was negligible. Structural analysis of rod-like apoC-II fibrils, using hydrogen-deuterium exchange and NMR analysis showed exchange protection consistent with a core cross-β structure comprising the C-terminal 58-76 region. Molecular dynamics simulations of fibril arrangements for this region favoured a parallel cross-β structure. X-ray fibre diffraction data for aligned rod-like fibrils showed a major meridional spacing at 4.6 Å and equatorial spacings at 9.7, 23.8 and 46.6 Å. The latter two equatorial spacings are not observed for aligned twisted-ribbon fibrils and are predicted for a model involving two cross-β fibrils in an off-set antiparallel structure with four apoC-II units per rise of the β-sheet. This model is consistent with the mutational effects on rod-like apoC-II fibril formation. The lipid-dependent polymorphisms exhibited by apoC-II fibrils could determine the properties of apoC-II in renal amyloid deposits and their potential role in the development of cardiovascular disease.
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Affiliation(s)
- Courtney O Zlatic
- Department of Biochemistry and Molecular Biology, University of Melbourne, Parkville, Vic., Australia.,Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Vic., Australia
| | - Yu Mao
- Department of Biochemistry and Molecular Biology, University of Melbourne, Parkville, Vic., Australia.,Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Vic., Australia
| | - Nevena Todorova
- School of Engineering, RMIT University, Melbourne, Vic., Australia
| | - Yee-Foong Mok
- Department of Biochemistry and Molecular Biology, University of Melbourne, Parkville, Vic., Australia.,Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Vic., Australia
| | - Geoffrey J Howlett
- Department of Biochemistry and Molecular Biology, University of Melbourne, Parkville, Vic., Australia.,Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Vic., Australia
| | - Irene Yarovsky
- School of Engineering, RMIT University, Melbourne, Vic., Australia
| | - Paul R Gooley
- Department of Biochemistry and Molecular Biology, University of Melbourne, Parkville, Vic., Australia.,Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Vic., Australia
| | - Michael D W Griffin
- Department of Biochemistry and Molecular Biology, University of Melbourne, Parkville, Vic., Australia.,Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Vic., Australia
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5
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Sethi S, Dasari S, Plaisier E, Ronco P, Nasr SH, Brocheriou I, Theis JD, Vrana JA, Zimmermann MT, Quint PS, McPhail ED, Kurtin PJ. Apolipoprotein CII Amyloidosis Associated With p.Lys41Thr Mutation. Kidney Int Rep 2018; 3:1193-1201. [PMID: 30197986 PMCID: PMC6127408 DOI: 10.1016/j.ekir.2018.04.009] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Revised: 04/13/2018] [Accepted: 04/16/2018] [Indexed: 02/06/2023] Open
Abstract
Introduction Apolipoprotein CII amyloidosis (AApoCII) is a rare form of amyloidosis. Here, we report a novel mutation associated with AApoCII amyloidosis in 5 patients and describe their clinical, renal biopsy, and mass spectrometry findings. Methods Five patients with renal AApoCII p.Lys41Thr amyloidosis were identified from our amyloid mass spectrometry cohort. Clinical features, kidney biopsy, and mass spectrometry findings were analyzed in this rare type of amyloidosis. Results The patients were older adults (mean age of 71.6 years at diagnosis), presented with nephrotic-range proteinuria, and often had declining renal function. All renal biopsy specimens showed massive mesangial nodules composed of weakly eosinophilic, periodic acid−Schiff negative, Congo red–positive amyloid deposits. There were no interstitial, vascular, or medullary deposits. In all cases, immunofluorescence studies were negative for Igs and electron microscopy showed amyloid fibrils. Proteomic analysis of Congo red−positive amyloid deposits detected large amounts of apolipoprotein CII (APOC2) protein. We also detected APOC2 p.Lys41Thr mutant protein in amyloid deposits of all patients. DNA sequencing in 1 patient confirmed the presence of the mutation. Both mutant and wild-type forms of APOC2 were detected in amyloid deposits of all patients. Molecular dynamic simulations showed the variant mediating a collapse of the native structure of APOC2, thereby destabilizing the protein. Conclusion We propose that AApoCII p.Lys41Thr amyloidosis is a new form of amyloidosis seen in elderly individuals, histologically exhibiting massive glomerular involvement, leading to nephrotic-range proteinuria and progressive chronic kidney disease.
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Affiliation(s)
- Sanjeev Sethi
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Surendra Dasari
- Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota, USA
| | | | - Pierre Ronco
- Service de Néphrologie et Dialyses, Hôpital Tenon, Paris, France
| | - Samih H Nasr
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | | | - Jason D Theis
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Julie A Vrana
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | | | - Patrick S Quint
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Ellen D McPhail
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Paul J Kurtin
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
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6
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Amdursky N, Rashid MH, Stevens MM, Yarovsky I. Exploring the binding sites and proton diffusion on insulin amyloid fibril surfaces by naphthol-based photoacid fluorescence and molecular simulations. Sci Rep 2017; 7:6245. [PMID: 28740173 PMCID: PMC5524688 DOI: 10.1038/s41598-017-06030-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2017] [Accepted: 06/09/2017] [Indexed: 11/18/2022] Open
Abstract
The diffusion of protons along biological surfaces and the interaction of biological structures with water are fundamental areas of interest in biology and chemistry. Here, we examine the surface of insulin amyloid fibrils and follow the binding of small molecules (photoacids) that differ according to the number and location of their sulfonic groups. We use transient fluorescence combined with a spherically-symmetric diffusion theory to show that the binding mode of different photoacids determines the efficiency of proton dissociation from the photoacid and the dimensionality of the proton’s diffusion. We use molecular dynamics simulations to examine the binding mode and mechanism of the photoacids and its influence on the unique kinetic rates and diffusion properties of the photoacid’s dissociated proton, where we also suggest a proton transfer process between one of the photoacids to proximal histidine residues. We show that the photoacids can be used as fluorescent markers for following the progression of amyloidogenic processes. The detailed characterisation of different binding modes to the surface of amyloid fibrils paves the way for better understanding of the binding mechanism of small molecules to amyloid fibrils.
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Affiliation(s)
- Nadav Amdursky
- Department of Materials, Department of Bioengineering and Institute of Biomedical Engineering, Imperial College London, London, SW7 2AZ, United Kingdom. .,Schulich Faculty of Chemistry, Technion - Israel Institute of Technology, Haifa, 3200003, Israel.
| | - M Harunur Rashid
- School of Engineering, RMIT University, Melbourne, Victoria, 3001, Australia
| | - Molly M Stevens
- Department of Materials, Department of Bioengineering and Institute of Biomedical Engineering, Imperial College London, London, SW7 2AZ, United Kingdom
| | - Irene Yarovsky
- School of Engineering, RMIT University, Melbourne, Victoria, 3001, Australia.
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7
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Todorova N, Zlatic CO, Mao Y, Yarovsky I, Howlett GJ, Gooley PR, Griffin MDW. Intra- and Intersubunit Ion-Pair Interactions Determine the Ability of Apolipoprotein C-II Mutants To Form Hybrid Amyloid Fibrils. Biochemistry 2017; 56:1757-1767. [DOI: 10.1021/acs.biochem.6b01146] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Nevena Todorova
- School
of Engineering, RMIT University, GPO Box 2476V, Melbourne, Victoria 3001, Australia
| | - Courtney O. Zlatic
- Department
of Biochemistry and Molecular Biology, University of Melbourne, Parkville, Victoria 3010, Australia
- Bio21
Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Yu Mao
- Department
of Biochemistry and Molecular Biology, University of Melbourne, Parkville, Victoria 3010, Australia
- Bio21
Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Irene Yarovsky
- School
of Engineering, RMIT University, GPO Box 2476V, Melbourne, Victoria 3001, Australia
| | - Geoffrey J. Howlett
- Department
of Biochemistry and Molecular Biology, University of Melbourne, Parkville, Victoria 3010, Australia
- Bio21
Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Paul R. Gooley
- Department
of Biochemistry and Molecular Biology, University of Melbourne, Parkville, Victoria 3010, Australia
- Bio21
Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Michael D. W. Griffin
- Department
of Biochemistry and Molecular Biology, University of Melbourne, Parkville, Victoria 3010, Australia
- Bio21
Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria 3010, Australia
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8
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Michaels TC, Dear AJ, Knowles TP. Scaling and dimensionality in the chemical kinetics of protein filament formation. INT REV PHYS CHEM 2016. [DOI: 10.1080/0144235x.2016.1239335] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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9
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Mao Y, Todorova N, Zlatic CO, Gooley PR, Griffin MDW, Howlett GJ, Yarovsky I. Solution Conditions Affect the Ability of the K30D Mutation To Prevent Amyloid Fibril Formation by Apolipoprotein C-II: Insights from Experiments and Theoretical Simulations. Biochemistry 2016; 55:3815-24. [DOI: 10.1021/acs.biochem.6b00266] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Yu Mao
- Department
of Biochemistry and Molecular Biology and Bio21 Molecular Science
and Biotechnology Institute, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Nevena Todorova
- School
of Engineering, RMIT University, GPO Box 2476V, Melbourne, Victoria 3001, Australia
| | - Courtney O. Zlatic
- Department
of Biochemistry and Molecular Biology and Bio21 Molecular Science
and Biotechnology Institute, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Paul R. Gooley
- Department
of Biochemistry and Molecular Biology and Bio21 Molecular Science
and Biotechnology Institute, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Michael D. W. Griffin
- Department
of Biochemistry and Molecular Biology and Bio21 Molecular Science
and Biotechnology Institute, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Geoffrey J. Howlett
- Department
of Biochemistry and Molecular Biology and Bio21 Molecular Science
and Biotechnology Institute, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Irene Yarovsky
- School
of Engineering, RMIT University, GPO Box 2476V, Melbourne, Victoria 3001, Australia
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10
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Nasr SH, Dasari S, Hasadsri L, Theis JD, Vrana JA, Gertz MA, Muppa P, Zimmermann MT, Grogg KL, Dispenzieri A, Sethi S, Highsmith WE, Merlini G, Leung N, Kurtin PJ. Novel Type of Renal Amyloidosis Derived from Apolipoprotein-CII. J Am Soc Nephrol 2016; 28:439-445. [PMID: 27297947 DOI: 10.1681/asn.2015111228] [Citation(s) in RCA: 50] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2015] [Accepted: 04/09/2016] [Indexed: 11/03/2022] Open
Abstract
Amyloidosis is characterized by extracellular deposition of misfolded proteins as insoluble fibrils. Most renal amyloidosis cases are Ig light chain, AA, or leukocyte chemotactic factor 2 amyloidosis, but rare hereditary forms can also involve the kidneys. Here, we describe the case of a 61-year-old woman who presented with nephrotic syndrome and renal impairment. Examination of the renal biopsy specimen revealed amyloidosis with predominant involvement of glomeruli and medullary interstitium. Proteomic analysis of Congo red-positive deposits detected large amounts of the Apo-CII protein. DNA sequencing of the APOC2 gene in the patient and one of her children detected a heterozygous c.206A→T transition, causing an E69V missense mutation. We also detected the mutant peptide in the proband's renal amyloid deposits. Using proteomics, we identified seven additional elderly patients with Apo-CII-rich amyloid deposits, all of whom had kidney involvement and histologically exhibited nodular glomerular involvement. Although prior in vitro studies have shown that Apo-CII can form amyloid fibrils and that certain mutations in this protein promote amyloid fibrillogenesis, there are no reports of this type of amyloidosis in humans. We propose that this study reveals a new form of hereditary amyloidosis (AApoCII) that is derived from the Apo-CII protein and appears to manifest in the elderly and preferentially affect the kidneys.
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Affiliation(s)
- Samih H Nasr
- Departments of Laboratory Medicine and Pathology
| | | | | | | | | | - Morie A Gertz
- Internal Medicine, Mayo Clinic, Rochester, Minnesota; and
| | | | | | | | - Angela Dispenzieri
- Departments of Laboratory Medicine and Pathology.,Internal Medicine, Mayo Clinic, Rochester, Minnesota; and
| | | | | | - Giampaolo Merlini
- Istituto di Ricovero e Cura a Carattere Scientifico Policlinico San Matteo and Department of Molecular Medicine, University of Pavia, Pavia, Italy
| | - Nelson Leung
- Internal Medicine, Mayo Clinic, Rochester, Minnesota; and
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11
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Ryan TM, Griffin MDW, McGillivray DJ, Knott RB, Wood K, Masters CL, Kirby N, Curtain CC. Apolipoprotein C-II Adopts Distinct Structures in Complex with Micellar and Submicellar Forms of the Amyloid-Inhibiting Lipid-Mimetic Dodecylphosphocholine. Biophys J 2016; 110:85-94. [PMID: 26745412 PMCID: PMC4805880 DOI: 10.1016/j.bpj.2015.11.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2015] [Revised: 11/03/2015] [Accepted: 11/09/2015] [Indexed: 01/21/2023] Open
Abstract
The formation of amyloid deposits is a common feature of a broad range of diseases, including atherosclerosis, Alzheimer's disease, and Parkinson's disease. The basis and role of amyloid deposition in the pathogenesis of these diseases is still being defined, however an interesting feature of amyloidogenic proteins is that the majority of the pathologically associated proteins are involved in lipid homeostasis, be it in lipid transport, incorporation into membranes, or the regulation of lipid pathways. Thus, amyloid-forming proteins commonly bind lipids, and lipids are generally involved in the proper folding of these proteins. However, understanding of the basis for these lipid-related aspects of amyloidogenesis is lacking. Thus, we have used the apolipoprotein C-II amyloid model system in conjunction with x-ray and neutron scattering analyses to address this problem. Apolipoprotein C-II is a well-studied model system of systemic amyloid fibril formation, with a clear and well-defined pathway for fibril formation, where the effects of lipid interaction are characterized, particularly for the lipid mimetic dodecylphosphocholine. We show that the micellar state of an inhibitory lipid can have a very significant effect on protein conformation, with micelles stabilizing a particular α-helical structure, whereas submicellar lipids stabilize a very different dimeric, α-helical structure. These results indicate that lipids may have an important role in the development and progression of amyloid-related diseases.
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Affiliation(s)
- Timothy M Ryan
- Australian Synchrotron, Clayton, Victoria, Australia; The Florey Institute, The University of Melbourne, Parkville, Victoria, Australia; The MacDiarmid Institute of Advanced Materials and Nanotechnology, Wellington, New Zealand.
| | - Michael D W Griffin
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, Victoria, Australia
| | - Duncan J McGillivray
- School of Chemical Science, The University of Auckland, Auckland, New Zealand; The MacDiarmid Institute of Advanced Materials and Nanotechnology, Wellington, New Zealand
| | - Robert B Knott
- Australian Nuclear Science and Technology Organisation, New South Wales, Australia
| | - Kathleen Wood
- Australian Nuclear Science and Technology Organisation, New South Wales, Australia
| | - Colin L Masters
- The Florey Institute, The University of Melbourne, Parkville, Victoria, Australia
| | - Nigel Kirby
- Australian Synchrotron, Clayton, Victoria, Australia
| | - Cyril C Curtain
- The Florey Institute, The University of Melbourne, Parkville, Victoria, Australia
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12
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Gorbenko G, Trusova V, Girych M, Adachi E, Mizuguchi C, Akaji K, Saito H. FRET evidence for untwisting of amyloid fibrils on the surface of model membranes. SOFT MATTER 2015; 11:6223-6234. [PMID: 26153461 DOI: 10.1039/c5sm00183h] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Apolipoprotein A-I (apoA-I) is an amyloid-forming protein whose amyloidogenic properties are attributed mainly to its N-terminal fragment. Cell membranes are thought to be the primary target for the toxic amyloid aggregates. In the present study Förster resonance energy transfer (FRET) between the membrane fluorescent probe Laurdan as a donor and amyloid-specific dye Thioflavin T (ThT) as an acceptor was employed to explore the interactions of amyloid fibrils from apoA-I variants 1-83/G26R and 1-83/G26R/W@8 with the model membranes composed of phosphatidylcholine and its mixture with cholesterol. The changes in FRET efficiency upon fibril-lipid binding were found to correlate with the extent of protein fibrillization. AFM imaging revealed the presence of two polymorphic states of fibrillar 1-83/G26R/W@8 with the helical and twisted ribbon morphologies. The simulation-based analysis of the experimental FRET profiles provided the arguments in favor of untwisting of fibrillar assemblies upon their interaction with the model membranes. Evidence for the face-on orientation and superficial bilayer location of the membrane-bound fragments of 1-83/G26R/W@8 fibrils was obtained.
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Affiliation(s)
- Galyna Gorbenko
- Department of Nuclear and Medical Physics, V.N. Karazin Kharkiv National University, 4 Svobody Sq., Kharkov, 61022, Ukraine.
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13
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Mao Y, Zlatic CO, Griffin MDW, Howlett GJ, Todorova N, Yarovsky I, Gooley PR. Hydrogen/Deuterium Exchange and Molecular Dynamics Analysis of Amyloid Fibrils Formed by a D69K Charge-Pair Mutant of Human Apolipoprotein C-II. Biochemistry 2015. [DOI: 10.1021/acs.biochem.5b00535] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Yu Mao
- Department of Biochemistry and
Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Courtney O. Zlatic
- Department of Biochemistry and
Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Michael D. W. Griffin
- Department of Biochemistry and
Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Geoffrey J. Howlett
- Department of Biochemistry and
Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Nevena Todorova
- Health Innovations
Research Institute, RMIT University, GPO
Box 2476, Melbourne, Victoria 3001, Australia
| | - Irene Yarovsky
- Health Innovations
Research Institute, RMIT University, GPO
Box 2476, Melbourne, Victoria 3001, Australia
| | - Paul R. Gooley
- Department of Biochemistry and
Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria 3010, Australia
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14
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Louros NN, Tsiolaki PL, Griffin MDW, Howlett GJ, Hamodrakas SJ, Iconomidou VA. Chameleon 'aggregation-prone' segments of apoA-I: A model of amyloid fibrils formed in apoA-I amyloidosis. Int J Biol Macromol 2015; 79:711-8. [PMID: 26049118 DOI: 10.1016/j.ijbiomac.2015.05.032] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2015] [Revised: 05/20/2015] [Accepted: 05/22/2015] [Indexed: 11/18/2022]
Abstract
Apolipoprotein A-I (apoA-I) is the major component of high density lipoproteins and plays a vital role in reverse cholesterol transport. Lipid-free apoA-I is the main constituent of amyloid deposits found in atherosclerotic plaques, an acquired type of amyloidosis, whereas its N-terminal fragments have been associated with a hereditary form, known as familial apoA-I amyloidosis. Here, we identified and verified four "aggregation-prone" segments of apoA-I with amyloidogenic properties, utilizing electron microscopy, X-ray fiber diffraction, ATR FT-IR spectroscopy and polarized light microscopy. These segments may act as conformational switches, possibly controlling the transition of the α-helical apoA-I content into the "cross-β" architecture of amyloid fibrils. A structural model illuminating the structure of amyloid fibrils formed by the N-terminal fragments of apoA-I is proposed, indicating that two of the identified chameleon segments may play a vital part in the formation of amyloid fibrils in familial apoA-I amyloidosis.
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Affiliation(s)
- Nikolaos N Louros
- Department of Cell Biology and Biophysics, Faculty of Biology, University of Athens, Panepistimiopolis, Athens 157 01, Greece
| | - Paraskevi L Tsiolaki
- Department of Cell Biology and Biophysics, Faculty of Biology, University of Athens, Panepistimiopolis, Athens 157 01, Greece
| | - Michael D W Griffin
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Geoffrey J Howlett
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, VIC 3010, Australia
| | - Stavros J Hamodrakas
- Department of Cell Biology and Biophysics, Faculty of Biology, University of Athens, Panepistimiopolis, Athens 157 01, Greece
| | - Vassiliki A Iconomidou
- Department of Cell Biology and Biophysics, Faculty of Biology, University of Athens, Panepistimiopolis, Athens 157 01, Greece.
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15
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Michaels TCT, Knowles TPJ. Role of filament annealing in the kinetics and thermodynamics of nucleated polymerization. J Chem Phys 2015; 140:214904. [PMID: 24908038 DOI: 10.1063/1.4880121] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
The formation of nanoscale protein filaments from soluble precursor molecules through nucleated polymerization is a common form of supra-molecular assembly phenomenon. This process underlies the generation of a range of both functional and pathological structures in nature. Filament breakage has emerged as a key process controlling the kinetics of the growth reaction since it increases the number of filament ends in the system that can act as growth sites. In order to ensure microscopic reversibility, however, the inverse process of fragmentation, end-to-end annealing of filaments, is a necessary component of a consistent description of such systems. Here, we combine Smoluchowski kinetics with nucleated polymerization models to generate a master equation description of protein fibrillization, where filamentous structures can undergo end-to-end association, in addition to elongation, fragmentation, and nucleation processes. We obtain self-consistent closed-form expressions for the growth kinetics and discuss the key physics that emerges from considering filament fusion relative to current fragmentation only models. Furthermore, we study the key time scales that describe relaxation to equilibrium.
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Affiliation(s)
- Thomas C T Michaels
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Tuomas P J Knowles
- Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
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16
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Mao Y, Teoh CL, Yang S, Zlatic CO, Rosenes ZK, Gooley PR, Howlett GJ, Griffin MDW. Charge and charge-pair mutations alter the rate of assembly and structural properties of apolipoprotein C-II amyloid fibrils. Biochemistry 2015; 54:1421-8. [PMID: 25609257 DOI: 10.1021/bi5014535] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The misfolding, aggregation, and accumulation of proteins as amyloid fibrils is a defining characteristic of several debilitating diseases. Human apolipoprotein C-II (apoC-II) amyloid fibrils are representative of the fibrils formed by a number of plasma apolipoproteins implicated in amyloid-related disease. Previous structural analyses identified a buried charge pair between residues K30 and D69 within apoC-II amyloid fibrils. We have investigated the effects of amino acid substitutions of these residues on apoC-II fibril formation. Two point mutations of apoC-II, D69K and K30D, as well as a reversed ion-pair mutant containing both mutations (KDDK) were generated. Fibril formation by the double mutant, apoC-II KDDK, and apoC-II D69K was enhanced compared to that of wild-type (WT) apoC-II, while apoC-II K30D lacked the ability to form fibrils under standard conditions. Structural analyses showed that WT apoC-II, apoC-II D69K, and apoC-II KDDK fibrils have similar secondary structures and morphologies. Size distribution analyses revealed that apoC-II D69K fibrils have a broader range of fibril sizes while apoC-II KDDK fibrils showed an increased frequency of closed fibrillar loops. ApoC-II D69K fibrils exhibited reduced thioflavin T binding capacity compared to that of fibrils formed by WT apoC-II and apoC-II KDDK. These results indicate that specific charge and charge-pair mutations within apoC-II significantly alter the ability to form fibrils and that position 69 within apoC-II plays a key role in the rate-limiting step of apoC-II fibril formation.
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Affiliation(s)
- Yu Mao
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne , Parkville, Victoria 3010, Australia
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17
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Interactions of Lipid Membranes with Fibrillar Protein Aggregates. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2015; 855:135-55. [PMID: 26149929 DOI: 10.1007/978-3-319-17344-3_6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Amyloid fibrils are an intriguing class of protein aggregates with distinct physicochemical, structural and morphological properties. They display peculiar membrane-binding behavior, thus adding complexity to the problem of protein-lipid interactions. The consensus that emerged during the past decade is that amyloid cytotoxicity arises from a continuum of cross-β-sheet assemblies including mature fibrils. Based on literature survey and our own data, in this chapter we address several aspects of fibril-lipid interactions, including (i) the effects of amyloid assemblies on molecular organization of lipid bilayer; (ii) competition between fibrillar and monomeric membrane-associating proteins for binding to the lipid surface; and (iii) the effects of lipids on the structural morphology of fibrillar aggregates. To illustrate some of the processes occurring in fibril-lipid systems, we present and analyze fluorescence data reporting on lipid bilayer interactions with fibrillar lysozyme and with the N-terminal 83-residue fragment of amyloidogenic mutant apolipoprotein A-I, 1-83/G26R/W@8. The results help understand possible mechanisms of interaction and mutual remodeling of amyloid fibers and lipid membranes, which may contribute to amyloid cytotoxicity.
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18
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Amyloid-Forming Properties of Human Apolipoproteins: Sequence Analyses and Structural Insights. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2015; 855:175-211. [PMID: 26149931 DOI: 10.1007/978-3-319-17344-3_8] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Apolipoproteins are protein constituents of lipoproteins that transport cholesterol and fat in circulation and are central to cardiovascular health and disease. Soluble apolipoproteins can transiently dissociate from the lipoprotein surface in a labile free form that can misfold, potentially leading to amyloid disease. Misfolding of apoA-I, apoA-II, and serum amyloid A (SAA) causes systemic amyloidoses, apoE4 is a critical risk factor in Alzheimer's disease, and apolipoprotein misfolding is also implicated in cardiovascular disease. To explain why apolipoproteins are over-represented in amyloidoses, it was proposed that the amphipathic α-helices, which form the lipid surface-binding motif in this protein family, have high amyloid-forming propensity. Here, we use 12 sequence-based bioinformatics approaches to assess amyloid-forming potential of human apolipoproteins and to identify segments that are likely to initiate β-aggregation. Mapping such segments on the available atomic structures of apolipoproteins helps explain why some of them readily form amyloid while others do not. Our analysis shows that nearly all amyloidogenic segments: (i) are largely hydrophobic, (ii) are located in the lipid-binding amphipathic α-helices in the native structures of soluble apolipoproteins, (iii) are predicted in both native α-helices and β-sheets in the insoluble apoB, and (iv) are predicted to form parallel in-register β-sheet in amyloid. Most of these predictions have been verified experimentally for apoC-II, apoA-I, apoA-II and SAA. Surprisingly, the rank order of the amino acid sequence propensity to form amyloid (apoB>apoA-II>apoC-II≥apoA-I, apoC-III, SAA, apoC-I>apoA-IV, apoA-V, apoE) does not correlate with the proteins' involvement in amyloidosis. Rather, it correlates directly with the strength of the protein-lipid association, which increases with increasing protein hydrophobicity. Therefore, the lipid surface-binding function and the amyloid-forming propensity are both rooted in apolipoproteins' hydrophobicity, suggesting that functional constraints make it difficult to completely eliminate pathogenic apolipoprotein misfolding. We propose that apolipoproteins have evolved protective mechanisms against misfolding, such as the sequestration of the amyloidogenic segments via the native protein-lipid and protein-protein interactions involving amphipathic α-helices and, in case of apoB, β-sheets.
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19
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The Role of Lipid in Misfolding and Amyloid Fibril Formation by Apolipoprotein C-II. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2015; 855:157-74. [DOI: 10.1007/978-3-319-17344-3_7] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
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20
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PARK SJ, KIM JY, TEOH CL, KANG NY, CHANG YT. New Targets of Molecular Imaging in Atherosclerosis: Prehension of Current Status. ANAL SCI 2015; 31:245-55. [DOI: 10.2116/analsci.31.245] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Affiliation(s)
- Sung-Jin PARK
- Laboratory of Bioimaging Probe Development, Singapore Bioimaging Consortium, Agency for Science, Technology and Research
| | - Jun-Young KIM
- Laboratory of Bioimaging Probe Development, Singapore Bioimaging Consortium, Agency for Science, Technology and Research
| | - Chai Lean TEOH
- Laboratory of Bioimaging Probe Development, Singapore Bioimaging Consortium, Agency for Science, Technology and Research
| | - Nam-Young KANG
- Laboratory of Bioimaging Probe Development, Singapore Bioimaging Consortium, Agency for Science, Technology and Research
| | - Young-Tae CHANG
- Department of Chemistry & NUS MedChem Program of Life Sciences Institute, National University of Singapore
- Laboratory of Bioimaging Probe Development, Singapore Bioimaging Consortium, Agency for Science, Technology and Research
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21
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Moran SD, Zanni MT. How to Get Insight into Amyloid Structure and Formation from Infrared Spectroscopy. J Phys Chem Lett 2014; 5:1984-1993. [PMID: 24932380 PMCID: PMC4051309 DOI: 10.1021/jz500794d] [Citation(s) in RCA: 176] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2014] [Accepted: 05/16/2014] [Indexed: 05/17/2023]
Abstract
There is an enormous amount of interest in the structures and formation mechanisms of amyloid fibers. In this Perspective, we review the most common structural motifs of amyloid fibers and discuss how infrared spectroscopy and isotope labeling can be used to identify their structures and aggregation kinetics. We present three specific strategies, site-specific labeling to obtain residue-by-residue structural information, isotope dilution of uniformly labeled proteins for identifying structural folds and protein mixtures, and expressed protein ligation for studying the domain structures of large proteins. For each of these methods, vibrational couplings are the source of the identifying features in the infrared spectrum. Examples are provided using the proteins hIAPP, Aβ, polyglutamine, and γD-crystallin. We focus on FTIR spectroscopy but also describe new observables made possible by 2D IR spectroscopy.
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22
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Das M, Mei X, Jayaraman S, Atkinson D, Gursky O. Amyloidogenic mutations in human apolipoprotein A-I are not necessarily destabilizing - a common mechanism of apolipoprotein A-I misfolding in familial amyloidosis and atherosclerosis. FEBS J 2014; 281:2525-42. [PMID: 24702826 DOI: 10.1111/febs.12809] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2013] [Revised: 03/19/2014] [Accepted: 04/04/2014] [Indexed: 12/18/2022]
Abstract
High-density lipoproteins and their major protein, apolipoprotein A-I (apoA-I), remove excess cellular cholesterol and protect against atherosclerosis. However, in acquired amyloidosis, nonvariant full-length apoA-I deposits as fibrils in atherosclerotic plaques; in familial amyloidosis, N-terminal fragments of variant apoA-I deposit in vital organs, damaging them. Recently, we used the crystal structure of Δ(185-243)apoA-I to show that amyloidogenic mutations destabilize apoA-I and increase solvent exposure of the extended strand 44-55 that initiates β-aggregation. In the present study, we test this hypothesis by exploring naturally occurring human amyloidogenic mutations, W50R and G26R, within or close to this strand. The mutations caused small changes in the protein's α-helical content, stability, proteolytic pattern and protein-lipid interactions. These changes alone were unlikely to account for amyloidosis, suggesting the importance of other factors. Sequence analysis predicted several amyloid-prone segments that can initiate apoA-I misfolding. Aggregation studies using N-terminal fragments verified this prediction experimentally. Three predicted N-terminal amyloid-prone segments, mapped on the crystal structure, formed an α-helical cluster. Structural analysis indicates that amyloidogenic mutations or Met86 oxidation perturb native packing in this cluster. Taken together, the results suggest that structural perturbations in the amyloid-prone segments trigger α-helix to β-sheet conversion in the N-terminal ~ 75 residues forming the amyloid core. Polypeptide outside this core can be proteolysed to form 9-11 kDa N-terminal fragments found in familial amyloidosis. Our results imply that apoA-I misfolding in familial and acquired amyloidosis follows a similar mechanism that does not require significant structural destabilization or proteolysis. This novel mechanism suggests potential therapeutic interventions for apoA-I amyloidosis.
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Affiliation(s)
- Madhurima Das
- Department of Physiology and Biophysics, Boston University School of Medicine, Boston, MA, USA
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23
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Gursky O. Hot spots in apolipoprotein A-II misfolding and amyloidosis in mice and men. FEBS Lett 2014; 588:845-50. [PMID: 24561203 DOI: 10.1016/j.febslet.2014.01.066] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2013] [Revised: 01/08/2014] [Accepted: 01/27/2014] [Indexed: 01/06/2023]
Abstract
ApoA-II is the second-major protein of high-density lipoproteins. C-terminal extension in human apoA-II or point substitutions in murine apoA-II cause amyloidosis. The molecular mechanism of apolipoprotein misfolding, from the native predominantly α-helical conformation to cross-β-sheet in amyloid, is unknown. We used 12 sequence-based prediction algorithms to identify two ten-residue segments in apoA-II that probably initiate β-aggregation. Previous studies of apoA-II fragments experimentally verify this prediction. Together, experimental and bioinformatics studies explain why the C-terminal extension in human apoA-II causes amyloidosis and why, unlike murine apoA-II, human apoA-II normally does not cause amyloidosis despite its unusually high sequence propensity for β-aggregation.
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Affiliation(s)
- Olga Gursky
- Department of Physiology and Biophysics, Boston University School of Medicine, W329, 700 Albany Street, Boston, MA 02118, United States.
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24
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Moran SD, Zhang TO, Zanni MT. An alternative structural isoform in amyloid-like aggregates formed from thermally denatured human γD-crystallin. Protein Sci 2014; 23:321-31. [PMID: 24415662 DOI: 10.1002/pro.2422] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2013] [Revised: 01/06/2014] [Accepted: 01/08/2014] [Indexed: 11/11/2022]
Abstract
The eye lens protein γD-crystallin contributes to cataract formation in the lens. In vitro experiments show that γD-crystallin has a high propensity to form amyloid fibers when denatured, and that denaturation by acid or UV-B photodamage results in its C-terminal domain forming the β-sheet core of amyloid fibers. Here, we show that thermal denaturation results in sheet-like aggregates that contain cross-linked oligomers of the protein, according to transmission electron microscopy and SDS-PAGE. We use two-dimensional infrared spectroscopy to show that these aggregates have an amyloid-like secondary structure with extended β-sheets, and use isotope dilution experiments to show that each protein contributes approximately one β-strand to each β-sheet in the aggregates. Using segmental (13) C labeling, we show that the organization of the protein's two domains in thermally induced aggregates results in a previously unobserved structure in which both the N-terminal and C-terminal domains contribute to β-sheets. We propose a model for the structural organization of the aggregates and attribute the recruitment of the N-terminal domain into the fiber structure to intermolecular cross linking.
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Affiliation(s)
- Sean D Moran
- Department of Chemistry, University of Wisconsin-Madison, Madison, WI, 53706
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25
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Interaction of Thioflavin T with amyloid fibrils of apolipoprotein A-I N-terminal fragment: Resonance energy transfer study. J Struct Biol 2014; 185:116-24. [DOI: 10.1016/j.jsb.2013.10.017] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2013] [Revised: 10/08/2013] [Accepted: 10/25/2013] [Indexed: 11/23/2022]
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26
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Todorova N, Makarucha AJ, Hine NDM, Mostofi AA, Yarovsky I. Dimensionality of carbon nanomaterials determines the binding and dynamics of amyloidogenic peptides: multiscale theoretical simulations. PLoS Comput Biol 2013; 9:e1003360. [PMID: 24339760 PMCID: PMC3854483 DOI: 10.1371/journal.pcbi.1003360] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2013] [Accepted: 10/09/2013] [Indexed: 12/22/2022] Open
Abstract
Experimental studies have demonstrated that nanoparticles can affect the rate of protein self-assembly, possibly interfering with the development of protein misfolding diseases such as Alzheimer's, Parkinson's and prion disease caused by aggregation and fibril formation of amyloid-prone proteins. We employ classical molecular dynamics simulations and large-scale density functional theory calculations to investigate the effects of nanomaterials on the structure, dynamics and binding of an amyloidogenic peptide apoC-II(60-70). We show that the binding affinity of this peptide to carbonaceous nanomaterials such as C60, nanotubes and graphene decreases with increasing nanoparticle curvature. Strong binding is facilitated by the large contact area available for π-stacking between the aromatic residues of the peptide and the extended surfaces of graphene and the nanotube. The highly curved fullerene surface exhibits reduced efficiency for π-stacking but promotes increased peptide dynamics. We postulate that the increase in conformational dynamics of the amyloid peptide can be unfavorable for the formation of fibril competent structures. In contrast, extended fibril forming peptide conformations are promoted by the nanotube and graphene surfaces which can provide a template for fibril-growth.
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Affiliation(s)
| | | | - Nicholas D. M. Hine
- Department of Materials and the Thomas Young Centre for Theory and Simulation of Materials, Imperial College London, London, United Kingdom
| | - Arash A. Mostofi
- Department of Materials and the Thomas Young Centre for Theory and Simulation of Materials, Imperial College London, London, United Kingdom
| | - Irene Yarovsky
- Health Innovations Research Institute, Melbourne, Australia
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27
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Gillam JE, MacPhee CE. Modelling amyloid fibril formation kinetics: mechanisms of nucleation and growth. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2013; 25:373101. [PMID: 23941964 DOI: 10.1088/0953-8984/25/37/373101] [Citation(s) in RCA: 86] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Amyloid and amyloid-like fibrils are self-assembling protein nanostructures, of interest for their robust material properties and inherent biological compatibility as well as their putative role in a number of debilitating mammalian disorders. Understanding fibril formation is essential to the development of strategies to control, manipulate or prevent fibril growth. As such, this area of research has attracted significant attention over the last half century. This review describes a number of different models that have been formulated to describe the kinetics of fibril assembly. We describe the macroscopic implications of mechanisms in which secondary processes such as secondary nucleation, fragmentation or branching dominate the assembly pathway, compared to mechanisms dominated by the influence of primary nucleation. We further describe how experimental data can be analysed with respect to the predictions of kinetic models.
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Affiliation(s)
- J E Gillam
- School of Physics and Astronomy, The University of Edinburgh, Mayfield Road, Edinburgh EH9 3JZ, UK
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28
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Burke KA, Yates EA, Legleiter J. Biophysical insights into how surfaces, including lipid membranes, modulate protein aggregation related to neurodegeneration. Front Neurol 2013; 4:17. [PMID: 23459674 PMCID: PMC3585431 DOI: 10.3389/fneur.2013.00017] [Citation(s) in RCA: 81] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2012] [Accepted: 02/09/2013] [Indexed: 11/13/2022] Open
Abstract
There are a vast number of neurodegenerative diseases, including Alzheimer’s disease (AD), Parkinson’s disease (PD), and Huntington’s disease (HD), associated with the rearrangement of specific proteins to non-native conformations that promotes aggregation and deposition within tissues and/or cellular compartments. These diseases are commonly classified as protein-misfolding or amyloid diseases. The interaction of these proteins with liquid/surface interfaces is a fundamental phenomenon with potential implications for protein-misfolding diseases. Kinetic and thermodynamic studies indicate that significant conformational changes can be induced in proteins encountering surfaces, which can play a critical role in nucleating aggregate formation or stabilizing specific aggregation states. Surfaces of particular interest in neurodegenerative diseases are cellular and subcellular membranes that are predominately comprised of lipid components. The two-dimensional liquid environments provided by lipid bilayers can profoundly alter protein structure and dynamics by both specific and non-specific interactions. Importantly for misfolding diseases, these bilayer properties can not only modulate protein conformation, but also exert influence on aggregation state. A detailed understanding of the influence of (sub)cellular surfaces in driving protein aggregation and/or stabilizing specific aggregate forms could provide new insights into toxic mechanisms associated with these diseases. Here, we review the influence of surfaces in driving and stabilizing protein aggregation with a specific emphasis on lipid membranes.
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Affiliation(s)
- Kathleen A Burke
- C. Eugene Bennett Department of Chemistry, West Virginia University Morgantown, WV, USA
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29
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"Janus" cyclic peptides: a new approach to amyloid fibril inhibition? PLoS One 2013; 8:e57437. [PMID: 23437387 PMCID: PMC3577749 DOI: 10.1371/journal.pone.0057437] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2012] [Accepted: 01/22/2013] [Indexed: 11/19/2022] Open
Abstract
Cyclic peptides are increasingly being shown as powerful inhibitors of fibril formation, and have the potential to be therapeutic agents for combating many debilitating amyloid-related diseases. One such example is a cyclic peptide derivative from the human apolipoprotein C-II, which has the ability to inhibit fibril formation by the fibrillogenic peptide apoC-II(60–70). Using classical molecular dynamics and electronic structure calculations, we were able to provide insight into the interaction between the amyloidogenic peptide apoC-II(60–70) and its cyclic derivative, cyc(60–70). Our results showed that cyc(60–70) induced increased flexibility in apoC-II(60–70), suggesting that one mechanism by which cyc(60–70) inhibits fibrillisation is by destabilising apoC-II(60–70) structure, rendering it incapable of adopting fibril favouring conformations. In contrast, cyc(60–70) shows less flexibility upon binding to apoC-II(60–70), which is predominantly mediated by hydrophobic interactions between the aromatic rings of the peptides. This effectively creates a cap around the fibril-forming region of apoC-II(60–70) and generates an outer hydrophilic shell that discourages further apoC-II(60–70) peptide self-association. We showed that apoC-II(60–70) exhibited stronger binding affinity for the hydrophobic face of cyc(60–70) and weakest binding affinity for the hydrophilic side. This suggests that cyc(60–70) can be an effective fibril inhibitor due to its amphipathic character, like that of the "Janus"-type particles. This property can be exploited in the design of specific inhibitors of amyloid fibril formation.
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30
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Moran SD, Decatur SM, Zanni MT. Structural and sequence analysis of the human γD-crystallin amyloid fibril core using 2D IR spectroscopy, segmental 13C labeling, and mass spectrometry. J Am Chem Soc 2012; 134:18410-6. [PMID: 23082813 DOI: 10.1021/ja307898g] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Identifying the sequence and structural content of residues that compose the core of amyloid fibrils is important because core regions likely control the process of fibril extension and provide potential drug targets. Human γD-crystallin is an eye lens protein that aggregates into amyloid fibrils under acidic conditions. In this manuscript, we use a pepsin enzymatic digest to isolate the core of the amyloid fibrils. The sequence of the core is identified with MALDI MS/MS and its structure is probed with 2D IR spectroscopy and (13)C isotope labeling. Mass spectrometry of the digest identifies residues 80-163 as the amyloid core, which spans most of the C-terminal domain, the linker, and a small portion of the N-terminal domain. From 2D IR spectroscopy of the digested fibrils, we learn that only the C-terminal domain contributes to the amyloid β-sheets while the N-terminal and linker residues are disordered. A comparison to the native crystal structure reveals that loops and α-helices in the native state must undergo conformational transitions to β-strands upon aggregation. These locations may be good drug binding targets. Besides providing new information about γD-crystallin, this study demonstrates the complementarity of mass spectrometry and 2D IR spectroscopy to obtain both sequence and structure information that neither technique provides individually, which will be especially useful for samples only available in microgram quantities.
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Affiliation(s)
- Sean D Moran
- Department of Chemistry, University of Wisconsin-Madison, 1101 University Avenue, Madison, Wisconsin 53706, USA
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31
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Kei AA, Filippatos TD, Tsimihodimos V, Elisaf MS. A review of the role of apolipoprotein C-II in lipoprotein metabolism and cardiovascular disease. Metabolism 2012; 61:906-21. [PMID: 22304839 DOI: 10.1016/j.metabol.2011.12.002] [Citation(s) in RCA: 94] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/26/2011] [Revised: 12/06/2011] [Accepted: 12/08/2011] [Indexed: 12/21/2022]
Abstract
The focus of this review is on the role of apolipoprotein C-II (apoC-II) in lipoprotein metabolism and the potential effects on the risk of cardiovascular disease (CVD). We searched PubMed/Scopus for articles regarding apoC-II and its role in lipoprotein metabolism and the risk of CVD. Apolipoprotein C-II is a constituent of chylomicrons, very low-density lipoprotein, low-density lipoprotein, and high-density lipoprotein (HDL). Apolipoprotein C-II contains 3 amphipathic α-helices. The lipid-binding domain of apoC-II is located in the N-terminal, whereas the C-terminal helix of apoC-II is responsible for the interaction with lipoprotein lipase (LPL). At intermediate concentrations (approximately 4 mg/dL) and in normolipidemic subjects, apoC-II activates LPL. In contrast, both an excess and a deficiency of apoC-II are associated with reduced LPL activity and hypertriglyceridemia. Furthermore, excess apoC-II has been associated with increased triglyceride-rich particles and alterations in HDL particle distribution, factors that may increase the risk of CVD. However, there is not enough current evidence to clarify whether increased apoC-II causes hypertriglyceridemia or is an epiphenomenon reflecting hypertriglyceridemia. A number of pharmaceutical interventions, including statins, fibrates, ezetimibe, nicotinic acid, and orlistat, have been shown to reduce the increased apoC-II concentrations. An excess of apoC-II is associated with increased triglyceride-rich particles and alterations in HDL particle distribution. However, prospective trials are needed to assess if apoC-II is a CVD marker or a risk factor in high-risk patients.
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Affiliation(s)
- Anastazia A Kei
- Department of Internal Medicine, School of Medicine, University of Ioannina, 45 110 Ioannina, Greece
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32
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Wong YQ, Binger KJ, Howlett GJ, Griffin MD. Identification of an amyloid fibril forming peptide comprising residues 46-59 of apolipoprotein A-I. FEBS Lett 2012; 586:1754-8. [DOI: 10.1016/j.febslet.2012.05.007] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2012] [Revised: 05/02/2012] [Accepted: 05/03/2012] [Indexed: 11/28/2022]
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33
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Yang S, Griffin MDW, Binger KJ, Schuck P, Howlett GJ. An equilibrium model for linear and closed-loop amyloid fibril formation. J Mol Biol 2012; 421:364-77. [PMID: 22370559 DOI: 10.1016/j.jmb.2012.02.026] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2011] [Revised: 02/08/2012] [Accepted: 02/18/2012] [Indexed: 11/30/2022]
Abstract
Amyloid fibrils and their soluble oligomeric intermediates are implicated in several age-related diseases including Alzheimer's and Parkinson's diseases. The distribution of oligomers and fibrils is related to toxicity and is dependent on the pathways for fibril assembly, generally considered to occur via a slow nucleation step that precedes fibril elongation. Human apolipoprotein (apo) C-II forms amyloid fibrils via a reversible self-assembly process accompanied by closed-loop formation and fibril breaking and joining. Our fluorescence quenching and sedimentation velocity experiments with Alexa488-labeled apoC-II indicated a time-dependent subunit interchange for both linear and closed-loop fibrils, while dilution experiments using mature fibrils indicated a shift to smaller size distributions consistent with a reversible assembly pathway. To account for this behavior, we developed an equilibrium self-association model that describes the final size distributions of apoC-II fibrils formed at different starting concentrations. The model proposes a reversible isomerization of apoC-II monomer to form an active conformer that self-assembles into fibrils via an isodesmic self-association pathway coupled to fibril length-dependent closed-loop formation. The model adequately described fibril size distributions and the proportion of closed loops as a function of total apoC-II concentration over the concentration range 0.1-0.5 mg/ml. Extension of the model to include the rates of isomerization, self-association and fibril breaking and joining provided satisfactory global fits to kinetic data on fibril formation and changes in average fibril size at different apoC-II starting concentrations. The model provides a simple thermodynamic description of the processes governing the size distribution of apoC-II fibrils at equilibrium and the formation of discrete oligomeric intermediates.
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Affiliation(s)
- Shuo Yang
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Victoria 3010, Australia
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Hu Y, Su B, Zheng H, Kim JR. A peptide probe for detection of various beta-amyloid oligomers. MOLECULAR BIOSYSTEMS 2012; 8:2741-52. [DOI: 10.1039/c2mb25148e] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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Abstract
In this chapter we provided the overall background to the subject of protein aggregation and fibrillogenesis in amyloidogenesis, with introduction and brief discussion of the various topics that are included with the coming chapters. The division of the book into basic science and clinical science sections enables correlation of the topics to be made. The many proteins and peptides that have currently been found to undergo fibrillogenesis are tabulated. A broad technical survey is made, to indicate the vast array of techniques currently available to study aspects of protein oligomerization, aggregation and fibrillogenesis. These are split into three groups and tabulated, as the microscopical techniques, the analytical and biophysical methods, and the biochemical and cellular techniques. A few techniques are discussed, but in most cases only a link to relevant recent literature is provided.
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Hernandez M, Golbert S, Zhang LG, Kim JR. Creation of aggregation-defective α-synuclein variants by engineering the sequence connecting β-strand-forming domains. Chembiochem 2011; 12:2630-9. [PMID: 21998035 DOI: 10.1002/cbic.201100430] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2011] [Indexed: 12/18/2022]
Abstract
The aggregation of α-synuclein (αS), which is implicated in the pathology of Parkinson's disease, produces fibrils in which layers of parallel, in-register β-sheet-loop-β-sheets are formed. The effects of sequence variation in the loop-forming region (referred to as the linker region) on αS aggregation have yet to be systematically studied. In the study described here, we created and characterized αS variants containing mutations in the linker regions. Our results indicate that although the physicochemical properties of the linker region, evaluated based on an intrinsic property of a single amino acid, still play a significant role in aggregation, additional factors can also determine aggregation of αS linker mutants. Our analyses suggest that these factors include a pairwise potential for parallel in-register β-sheet formation. A linker variant displaying significantly reduced self-aggregation interfered with αS aggregation by inhibiting the conversion of αS soluble species to αS insoluble fibrils. We anticipate that linker mutations could serve as a novel method of creating αS variants that are aggregation-defective and/or inhibit αS aggregation.
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Affiliation(s)
- Michael Hernandez
- Othmer-Jacobs Department of Chemical and Biological Engineering, Polytechnic Institute of New York University, 6 MetroTech Center, Brooklyn, NY 11201, USA
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Ryan TM, Griffin MDW, Bailey MF, Schuck P, Howlett GJ. NBD-labeled phospholipid accelerates apolipoprotein C-II amyloid fibril formation but is not incorporated into mature fibrils. Biochemistry 2011; 50:9579-86. [PMID: 21985034 DOI: 10.1021/bi201192r] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Human apolipoprotein (apo) C-II is one of several lipid-binding proteins that self-assemble into fibrils and accumulate in disease-related amyloid deposits. A general characteristic of these amyloid deposits is the presence of lipids, known to modulate individual steps in amyloid fibril formation. ApoC-II fibril formation is activated by submicellar phospholipids but inhibited by micellar lipids. We examined the mechanism for the activation by submicellar lipids using the fluorescently labeled, short-chain phospholipid 1-dodecyl-[(7-nitro-2-1,3-benzoxadiazol-4-yl)amino]-2-hydroxyglycero-3-phosphocholine (NBD-lyso-12-PC). Addition of submicellar NBD-lyso-12-PC increased the rate of fibril formation by apoC-II approximately 2-fold. Stopped flow kinetic analysis using fluorescence detection and low, non-fibril-forming concentrations of apoC-II indicated NBD-lyso-12-PC binds rapidly, on the millisecond time scale, followed by the slower formation of discrete apoC-II tetramers. Sedimentation velocity analysis showed NBD-lyso-12-PC binds to both apoC-II monomers and tetramers at approximately five sites per monomer with an average dissociation constant of approximately 10 μM. Mature apoC-II fibrils formed in the presence of NBD-lyso-12-PC were devoid of lipid, indicating a purely catalytic role for submicellar lipids in the activation of apoC-II fibril formation. These studies demonstrate the catalytic potential of small amphiphilic molecules in controlling protein folding and fibril assembly pathways.
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Affiliation(s)
- Timothy M Ryan
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, Victoria 3010, Australia
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Teoh CL, Bekard IB, Asimakis P, Griffin MDW, Ryan TM, Dunstan DE, Howlett GJ. Shear flow induced changes in apolipoprotein C-II conformation and amyloid fibril formation. Biochemistry 2011; 50:4046-57. [PMID: 21476595 DOI: 10.1021/bi2002482] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
The misfolding and self-assembly of proteins into amyloid fibrils that occur in several debilitating diseases are affected by a variety of environmental factors, including mechanical factors associated with shear flow. We examined the effects of shear flow on amyloid fibril formation by human apolipoprotein C-II (apoC-II). Shear fields (150, 300, and 500 s(-1)) accelerated the rate of apoC-II fibril formation (1 mg/mL) approximately 5-10-fold. Fibrils produced at shear rates of 150 and 300 s(-1) were similar to the twisted ribbon fibrils formed in the absence of shear, while at 500 s(-1), tangled ropelike structures were observed. The mechanism of the shear-induced acceleration of amyloid fibril formation was investigated at low apoC-II concentrations (50 μg/mL) where fibril formation does not occur. Circular dichroism and tryptophan fluorescence indicated that shear induced an irreversible change in apoC-II secondary structure. Fluorescence resonance energy transfer experiments using the single tryptophan residue in apoC-II as the donor and covalently attached acceptors showed that shear flow increased the distance between the donor and acceptor molecules. Shear-induced higher-order oligomeric species were identified by sedimentation velocity experiments using fluorescence detection, while fibril seeding experiments showed that species formed during shear flow are on the fibril formation pathway. These studies suggest that physiological shear flow conditions and conditions experienced during protein manufacturing can exert significant effects on protein conformation, leading to protein misfolding, aggregation, and amyloid fibril formation.
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Affiliation(s)
- Chai Lean Teoh
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, Victoria 3010, Australia
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Teoh CL, Griffin MDW, Howlett GJ. Apolipoproteins and amyloid fibril formation in atherosclerosis. Protein Cell 2011; 2:116-27. [PMID: 21400045 DOI: 10.1007/s13238-011-1013-6] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2011] [Accepted: 01/29/2011] [Indexed: 10/18/2022] Open
Abstract
Amyloid fibrils arise from the aggregation of misfolded proteins into highly-ordered structures. The accumulation of these fibrils along with some non-fibrillar constituents within amyloid plaques is associated with the pathogenesis of several human degenerative diseases. A number of plasma apolipoproteins, including apolipoprotein (apo) A-I, apoA-II, apoC-II and apoE are implicated in amyloid formation or influence amyloid formation by other proteins. We review present knowledge of amyloid formation by apolipoproteins in disease, with particular focus on atherosclerosis. Further insights into the molecular mechanisms underlying their amyloidogenic propensity are obtained from in vitro studies which describe factors affecting apolipoprotein amyloid fibril formation and interactions. Additionally, we outline the evidence that amyloid fibril formation by apolipoproteins might play a role in the development and progression of atherosclerosis, and highlight possible molecular mechanisms that could contribute to the pathogenesis of this disease.
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Affiliation(s)
- Chai Lean Teoh
- Department of Biochemistry and Molecular Biology, University of Melbourne, Parkville, Victoria 3010, Australia
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