1
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Baek Y, Lee M. Exploring the complexity of amyloid-beta fibrils: structural polymorphisms and molecular interactions. Biochem Soc Trans 2024:BST20230854. [PMID: 39034652 DOI: 10.1042/bst20230854] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2024] [Revised: 07/09/2024] [Accepted: 07/12/2024] [Indexed: 07/23/2024]
Abstract
The aggregation of amyloid-beta (Aβ) peptides into cross-β structures forms a variety of distinct fibril conformations, potentially correlating with variations in neurodegenerative disease progression. Recent advances in techniques such as X-ray crystallography, solid-state NMR, and cryo-electron microscopy have enabled the development of high-resolution molecular structures of these polymorphic amyloid fibrils, which are either grown in vitro or isolated from human and transgenic mouse brain tissues. This article reviews our current understanding of the structural polymorphisms in amyloid fibrils formed by Aβ40 and Aβ42, as well as disease-associated mutants of Aβ peptides. The aim is to enhance our understanding of various molecular interactions, including hydrophobic and ionic interactions, within and among cross-β structures.
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Affiliation(s)
- Yoongyeong Baek
- Department of Chemistry, Drexel University, Philadelphia, PA 19104, U.S.A
| | - Myungwoon Lee
- Department of Chemistry, Drexel University, Philadelphia, PA 19104, U.S.A
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2
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Wagner WJ, Gross ML. Using mass spectrometry-based methods to understand amyloid formation and inhibition of alpha-synuclein and amyloid beta. MASS SPECTROMETRY REVIEWS 2024; 43:782-825. [PMID: 36224716 PMCID: PMC10090239 DOI: 10.1002/mas.21814] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Amyloid fibrils, insoluble β-sheets structures that arise from protein misfolding, are associated with several neurodegenerative disorders. Many small molecules have been investigated to prevent amyloid fibrils from forming; however, there are currently no therapeutics to combat these diseases. Mass spectrometry (MS) is proving to be effective for studying the high order structure (HOS) of aggregating proteins and for determining structural changes accompanying protein-inhibitor interactions. When combined with native MS (nMS), gas-phase ion mobility, protein footprinting, and chemical cross-linking, MS can afford regional and sometimes amino acid spatial resolution of the aggregating protein. The spatial resolution is greater than typical low-resolution spectroscopic, calorimetric, and the traditional ThT fluorescence methods used in amyloid research today. High-resolution approaches can struggle when investigating protein aggregation, as the proteins exist as complex oligomeric mixtures of many sizes and several conformations or polymorphs. Thus, MS is positioned to complement both high- and low-resolution approaches to studying amyloid fibril formation and protein-inhibitor interactions. This review covers basics in MS paired with ion mobility, continuous hydrogen-deuterium exchange (continuous HDX), pulsed hydrogen-deuterium exchange (pulsed HDX), fast photochemical oxidation of proteins (FPOP) and other irreversible labeling methods, and chemical cross-linking. We then review the applications of these approaches to studying amyloid-prone proteins with a focus on amyloid beta and alpha-synuclein. Another focus is the determination of protein-inhibitor interactions. The expectation is that MS will bring new insights to amyloid formation and thereby play an important role to prevent their formation.
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Affiliation(s)
- Wesley J Wagner
- Department of Chemistry, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Michael L Gross
- Department of Chemistry, Washington University in St. Louis, St. Louis, Missouri, USA
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3
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Whitfield JF, Rennie K, Chakravarthy B. Alzheimer's Disease and Its Possible Evolutionary Origin: Hypothesis. Cells 2023; 12:1618. [PMID: 37371088 DOI: 10.3390/cells12121618] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2023] [Revised: 05/29/2023] [Accepted: 06/08/2023] [Indexed: 06/29/2023] Open
Abstract
The enormous, 2-3-million-year evolutionary expansion of hominin neocortices to the current enormity enabled humans to take over the planet. However, there appears to have been a glitch, and it occurred without a compensatory expansion of the entorhinal cortical (EC) gateway to the hippocampal memory-encoding system needed to manage the processing of the increasing volume of neocortical data converging on it. The resulting age-dependent connectopathic glitch was unnoticed by the early short-lived populations. It has now surfaced as Alzheimer's disease (AD) in today's long-lived populations. With advancing age, processing of the converging neocortical data by the neurons of the relatively small lateral entorhinal cortex (LEC) inflicts persistent strain and high energy costs on these cells. This may result in their hyper-release of harmless Aβ1-42 monomers into the interstitial fluid, where they seed the formation of toxic amyloid-β oligomers (AβOs) that initiate AD. At the core of connectopathic AD are the postsynaptic cellular prion protein (PrPC). Electrostatic binding of the negatively charged AβOs to the positively charged N-terminus of PrPC induces hyperphosphorylation of tau that destroys synapses. The spread of these accumulating AβOs from ground zero is supported by Aβ's own production mediated by target cells' Ca2+-sensing receptors (CaSRs). These data suggest that an early administration of a strongly positively charged, AβOs-interacting peptide or protein, plus an inhibitor of CaSR, might be an effective AD-arresting therapeutic combination.
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Affiliation(s)
- James F Whitfield
- Human Health Therapeutics, National Research Council, Ottawa, ON K1A 0R6, Canada
| | - Kerry Rennie
- Human Health Therapeutics, National Research Council, Ottawa, ON K1A 0R6, Canada
| | - Balu Chakravarthy
- Human Health Therapeutics, National Research Council, Ottawa, ON K1A 0R6, Canada
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4
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Schilling S, Pradhan A, Heesch A, Helbig A, Blennow K, Koch C, Bertgen L, Koo EH, Brinkmalm G, Zetterberg H, Kins S, Eggert S. Differential effects of familial Alzheimer's disease-causing mutations on amyloid precursor protein (APP) trafficking, proteolytic conversion, and synaptogenic activity. Acta Neuropathol Commun 2023; 11:87. [PMID: 37259128 DOI: 10.1186/s40478-023-01577-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Accepted: 05/04/2023] [Indexed: 06/02/2023] Open
Abstract
The amyloid precursor protein (APP) is a key player in Alzheimer`s disease (AD) and the precursor of the Aβ peptide, which is generated by consecutive cleavages of β- and γ-secretases. Familial Alzheimer's disease (FAD) describes a hereditary subgroup of AD that represents a low percentage of AD cases with an early onset of the disease. Different APP FAD mutations are thought to have qualitatively different effects on its proteolytic conversion. However, few studies have explored the pathogenic and putative physiological differences in more detail. Here, we compared different FAD mutations, located at the β- (Swedish), α- (Flemish, Arctic, Iowa) or γ-secretase (Iberian) cleavage sites. We examined heterologous expression of APP WT and FAD mutants in non-neuronal cells and their impact on presynaptic differentiation in contacting axons of co-cultured neurons. To decipher the underlying molecular mechanism, we tested the subcellular localization, the endocytosis rate and the proteolytic processing in detail by immunoprecipitation-mass spectrometry. Interestingly, we found that only the Iberian mutation showed altered synaptogenic function. Furthermore, the APP Iowa mutant shows significantly decreased α-secretase processing which is in line with our results that APP carrying the Iowa mutation was significantly increased in early endosomes. However, most interestingly, immunoprecipitation-mass spectrometry analysis revealed that the amino acid substitutions of APP FAD mutants have a decisive impact on their processing reflected in altered Aβ profiles. Importantly, N-terminally truncated Aβ peptides starting at position 5 were detected preferentially for APP Flemish, Arctic, and Iowa mutants containing amino acid substitutions around the α-secretase cleavage site. The strongest change in the ratio of Aβ40/Aβ42 was observed for the Iberian mutation while APP Swedish showed a substantial increase in Aβ1-17 peptides. Together, our data indicate that familial AD mutations located at the α-, β-, and γ-secretase cleavage sites show considerable differences in the underlying pathogenic mechanisms.
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Affiliation(s)
- Sandra Schilling
- Department of Human Biology and Human Genetics, University of Kaiserslautern, 67663, Kaiserslautern, Germany
| | - Ajay Pradhan
- Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, The Sahlgrenska Academy at the University of Gothenburg, Mölndal, Sweden
| | - Amelie Heesch
- Department of Human Biology and Human Genetics, University of Kaiserslautern, 67663, Kaiserslautern, Germany
| | - Andrea Helbig
- Department of Human Biology and Human Genetics, University of Kaiserslautern, 67663, Kaiserslautern, Germany
| | - Kaj Blennow
- Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, The Sahlgrenska Academy at the University of Gothenburg, Mölndal, Sweden
| | - Christian Koch
- Department of Human Biology and Human Genetics, University of Kaiserslautern, 67663, Kaiserslautern, Germany
| | - Lea Bertgen
- Department of Human Biology and Human Genetics, University of Kaiserslautern, 67663, Kaiserslautern, Germany
| | - Edward H Koo
- San Diego (UCSD), Department of Neuroscience, University of California, La Jolla, CA, 92093-0662, USA
| | - Gunnar Brinkmalm
- Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, The Sahlgrenska Academy at the University of Gothenburg, Mölndal, Sweden
| | - Henrik Zetterberg
- Department of Psychiatry and Neurochemistry, Institute of Neuroscience and Physiology, The Sahlgrenska Academy at the University of Gothenburg, Mölndal, Sweden
- Clinical Neurochemistry Laboratory, Sahlgrenska University Hospital, Mölndal, Sweden
- Department of Neurodegenerative Disease, UCL Institute of Neurology, Queen Square, London, UK
- UK Dementia Research Institute at UCL, London, UK
- Hong Kong Center for Neurodegenerative Diseases, Clear Water Bay, Hong Kong, China
| | - Stefan Kins
- Department of Human Biology and Human Genetics, University of Kaiserslautern, 67663, Kaiserslautern, Germany
| | - Simone Eggert
- Department of Human Biology and Human Genetics, University of Kaiserslautern, 67663, Kaiserslautern, Germany.
- Department of Neurogenetics, Max Planck Institute for Multidisciplinary Sciences, City-Campus, Hermann-Rein-Str. 3, 37075, Göttingen, Germany.
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5
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Rezaei-Ghaleh N, Amininasab M, Giller K, Becker S. Familial Alzheimer's Disease-Related Mutations Differentially Alter Stability of Amyloid-Beta Aggregates. J Phys Chem Lett 2023; 14:1427-1435. [PMID: 36734539 PMCID: PMC9940190 DOI: 10.1021/acs.jpclett.2c03729] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Accepted: 01/31/2023] [Indexed: 06/18/2023]
Abstract
Amyloid-beta (Aβ) deposition as senile plaques is a pathological hallmark of Alzheimer's disease (AD). AD is characterized by a large level of heterogeneity in amyloid pathology, whose molecular origin is poorly understood. Here, we employ NMR spectroscopy and MD simulation at ambient and high pressures and investigate how AD-related mutations in Aβ peptide influence the stability of Aβ aggregates. The pressure-induced monomer dissociation from Aβ aggregates monitored by NMR demonstrated that the Iowa (D23N), Arctic (E22G), and Osaka (ΔE22) mutations altered the pressure stability of Aβ40 aggregates in distinct manners. While the NMR data of monomeric Aβ40 showed only small localized effects of mutations, the MD simulation of mutated Aβ fibrils revealed their distinct susceptibility to elevated pressure. Our data propose a structural basis for the distinct stability of various Aβ fibrils and highlights "stability" as a molecular property potentially contributing to the large heterogeneity of amyloid pathology in AD.
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Affiliation(s)
- Nasrollah Rezaei-Ghaleh
- Institute
of Physical Biology, Heinrich Heine University
Düsseldorf, D-40225 Düsseldorf, Germany
- Institute
of Biological Information Processing, IBI-7: Structural Biochemistry, Forschungszentrum Jülich, D-52428 Jülich, Germany
- Department
of NMR-based Structural Biology, Max Planck
Institute for Multidisciplinary Sciences, D-37077 Göttingen, Germany
| | - Mehriar Amininasab
- Department
of Cell and Molecular Biology, School of Biology, College of Science, University of Tehran, 1417466191 Tehran, Iran
| | - Karin Giller
- Department
of NMR-based Structural Biology, Max Planck
Institute for Multidisciplinary Sciences, D-37077 Göttingen, Germany
| | - Stefan Becker
- Department
of NMR-based Structural Biology, Max Planck
Institute for Multidisciplinary Sciences, D-37077 Göttingen, Germany
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6
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Wilson Alphonse CR, Rajesh Kannan R, Nagarajan N. PITRM1 interaction studies with amyloidogenic nonapeptide mutants of familial Alzheimer's disease. J Biomol Struct Dyn 2022:1-12. [PMID: 35751131 DOI: 10.1080/07391102.2022.2092554] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Abstract
Amyloid β-protein (ABP) is found to be the major cause for the development of neurodegeneration which leads to Alzheimer's. The Aβ nonapeptide segment, QKLVFFAED (amino acids 15-23) is the highly amyloidogenic central region of Aβ. Familial mutation in Aβ increases the aggregation property of the peptide compared to the Native (Wild) amyloid-beta (Aβ) and these mutations fall on the Aβ nonapeptide segment. The catalytic activity of pitrilysin metallopeptidase 1(PITRM1) with familial mutant Aβ (Flemish, Arctic, Dutch, Italian and Iowa) during interaction is examined using molecular dynamic simulation. The molecular dynamics simulation of PITRM1 and the Aβ nonapeptide segment showed similar RMSD with respect to stability. The active site amino acid (AA) H108, hydrophobic pocket AA residues L111, F123, F124, and L127 and the basic pocket AA residues R888 and H896 showed similar interactions with both wild and familial Aβ. The molecular level interaction between amyloid beta and PITRM1 were similar in the wild and familial mutants except for the Arctic mutant. The hydrophobic interaction was commonly observed between the S1 hydrophobic pocket and the LVFF region, the Arctic mutant showed less hydrogen bond formation consistently when compared to other complexes. This molecular information on catalytic activity suggests that modulating inactive PITRM1 or an increase in expression of PITRM1 can help in eliminating different kinds of familial mutant Aβ in neurodegenerative cells.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Carlton Ranjith Wilson Alphonse
- Neuroscience Lab, Centre for Molecular and Nanomedical Sciences, Centre for Nanoscience and Nanotechnology, School of Bio and Chemical Engineering, Sathyabama Institute of Science and Technology, Chennai, Tamil Nadu, India
| | - Rajaretinam Rajesh Kannan
- Neuroscience Lab, Centre for Molecular and Nanomedical Sciences, Centre for Nanoscience and Nanotechnology, School of Bio and Chemical Engineering, Sathyabama Institute of Science and Technology, Chennai, Tamil Nadu, India
| | - Nagasundaram Nagarajan
- Neuroscience Lab, Centre for Molecular and Nanomedical Sciences, Centre for Nanoscience and Nanotechnology, School of Bio and Chemical Engineering, Sathyabama Institute of Science and Technology, Chennai, Tamil Nadu, India.,School of Biosciences and Technology, Vellore Institute of Technology, Vellore, Tamil Nadu, India
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7
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Simulations of Cross-Amyloid Aggregation of Amyloid-β and Islet Amyloid Polypeptide Fragments. Biophys J 2022; 121:2002-2013. [PMID: 35538665 DOI: 10.1016/j.bpj.2022.05.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 04/09/2022] [Accepted: 05/05/2022] [Indexed: 11/21/2022] Open
Abstract
Amyloid-beta (Aβ) and islet amyloid polypeptide (IAPP) are small peptides, classified as amyloids, that have the potential to self-assemble and form cytotoxic species, such as small soluble oligomers and large insoluble fibrils. The formation of Aβ aggregates facilitates the progression of Alzheimer's disease (AD), while IAPP aggregates induce pancreatic β-cell apoptosis, leading to exacerbation of Type 2 diabetes (T2D). Cross-amyloid interactions between Aβ and IAPP have been described both in vivo and in vitro, implying the role of Aβ or IAPP as modulators of cytotoxic self-aggregation of each species, and suggesting that Aβ-IAPP interactions are a potential molecular link between AD and T2D. Using molecular dynamics simulations, "hot spot" regions of the two peptides were studied to understand the formation of hexamers in a heterogenous and homogenous peptide-containing environment. Systems of only Aβ(16-22) peptides formed antiparallel, β-barrel-like structures, while systems of only IAPP(20-29) peptides formed stacked, parallel beta sheets and had relatively unstable aggregation structures after 2 μs of simulation time. Systems containing both Aβ and IAPP (1:1 ratio) hexamers showed antiparallel, β-barrel-like structures, with an interdigitated arrangement of Aβ(16-22) and IAPP(20-29). These β-barrel structures have features of cytotoxic amyloid species identified in previous literature. Ultimately, this work seeks to provide atomistic insight into both the mechanism behind cross-amyloid interactions and structural morphologies of these toxic amyloid species.
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8
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Illes-Toth E, Meisl G, Rempel DL, Knowles TPJ, Gross ML. Pulsed Hydrogen-Deuterium Exchange Reveals Altered Structures and Mechanisms in the Aggregation of Familial Alzheimer's Disease Mutants. ACS Chem Neurosci 2021; 12:1972-1982. [PMID: 33988976 DOI: 10.1021/acschemneuro.1c00072] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Mutations of the Amyloid Precursor Protein, from which the amyloid β peptide Aβ42 is cleaved, are associated with familial Alzheimer's disease. The disease-relevant familial mutations include the Arctic (E22G), Iowa (D23N), Italian (E22K), Dutch (E22Q), Japanese (D7N), English (D6R), and Flemish (A21G) variants. A detailed mechanistic understanding of the aggregation behavior of the mutant peptides at the residue level is, however, still lacking. We report here a study of the aggregation kinetics of these mutants in vitro by pulsed hydrogen-deuterium exchange mass spectrometry (HDX-MS) to obtain a temporally and sequence resolved picture of their self-assembly. For all variants, HDX occurs to give a bimodal distribution representing two soluble classes of aggregates, one protected and one solvent-exposed. There is no evidence of other classes of structural intermediates within the detection limits of the HDX approach. The fractional changes in the bimodal exchange profiles for several regions of Aβ42 reveal that the central and C-terminal peptides gain protection upon fibril formation, whereas the N-terminal regions remain largely solvent-accessible. For these mutants, all peptide fragments follow the same kinetics, acquiring solvent protection at the same time, further supporting that there are no significant populations of intermediate species under our experimental conditions. The results demonstrate the potential of pulsed HDX-MS for resolving the region-specific aggregation behavior of Aβ42 isoforms in solution where X-ray crystallography and solid-state NMR (ssNMR) are challenged.
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Affiliation(s)
- Eva Illes-Toth
- Washington University in St. Louis, Department of Chemistry, St. Louis, Missouri 63130, United States
| | - Georg Meisl
- University of Cambridge, Department of Chemistry, Lensfield Road, Cambridge CB2 1EW, UK
| | - Don L. Rempel
- Washington University in St. Louis, Department of Chemistry, St. Louis, Missouri 63130, United States
| | - Tuomas P. J. Knowles
- University of Cambridge, Department of Chemistry, Lensfield Road, Cambridge CB2 1EW, UK
| | - Michael L. Gross
- Washington University in St. Louis, Department of Chemistry, St. Louis, Missouri 63130, United States
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9
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Aggarwal L, Biswas P. Hydration Thermodynamics of the N-Terminal FAD Mutants of Amyloid-β. J Chem Inf Model 2021; 61:298-310. [PMID: 33440932 DOI: 10.1021/acs.jcim.0c01286] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The hydration thermodynamics of amyloid-β (Aβ) and its pathogenic familial Alzheimer's disease (FAD) mutants such as A2V, Taiwan (D7H), Tottori (D7N), and English (H6R) and the protective A2T mutant is investigated by a combination of all-atom, explicit water molecular dynamics (MD) simulations and the three-dimensional reference interaction site model (3D-RISM) theory. The change in the hydration free energy on mutation is decomposed into the energetic and entropic components, which comprise electrostatic and nonelectrostatic contributions. An increase in the hydration free energy is observed for A2V, D7H, D7N, and H6R mutations that increase the aggregation propensity of Aβ and lead to an early onset of Alzheimer's disease, while a reverse trend is noted for the protective A2T mutation. An antiphase correlation is found between the change in the hydration energy and the internal energy of Aβ upon mutation. A residue-wise decomposition analysis shows that the change in the hydration free energy of Aβ on mutation is primarily due to the hydration/dehydration of the side-chain atoms of the negatively charged residues. The decrease in the hydration of the negatively charged residues on mutation may decrease the solubility of the mutant, which increases the observed aggregation propensity of the FAD mutants. Results obtained from the theory show an excellent match with the experimentally reported data.
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Affiliation(s)
- Leena Aggarwal
- Department of Chemistry, University of Delhi, Delhi 110007, India
| | - Parbati Biswas
- Department of Chemistry, University of Delhi, Delhi 110007, India
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10
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Cawood EE, Karamanos TK, Wilson AJ, Radford SE. Visualizing and trapping transient oligomers in amyloid assembly pathways. Biophys Chem 2020; 268:106505. [PMID: 33220582 PMCID: PMC8188297 DOI: 10.1016/j.bpc.2020.106505] [Citation(s) in RCA: 81] [Impact Index Per Article: 20.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2020] [Revised: 10/29/2020] [Accepted: 11/01/2020] [Indexed: 12/31/2022]
Abstract
Oligomers which form during amyloid fibril assembly are considered to be key contributors towards amyloid disease. However, understanding how such intermediates form, their structure, and mechanisms of toxicity presents significant challenges due to their transient and heterogeneous nature. Here, we discuss two different strategies for addressing these challenges: use of (1) methods capable of detecting lowly-populated species within complex mixtures, such as NMR, single particle methods (including fluorescence and force spectroscopy), and mass spectrometry; and (2) chemical and biological tools to bias the amyloid energy landscape towards specific oligomeric states. While the former methods are well suited to following the kinetics of amyloid assembly and obtaining low-resolution structural information, the latter are capable of producing oligomer samples for high-resolution structural studies and inferring structure-toxicity relationships. Together, these different approaches should enable a clearer picture to be gained of the nature and role of oligomeric intermediates in amyloid formation and disease. Methods to study structure, toxicity, and kinetics of transient amyloid oligomers. NMR and single particle methods can characterize lowly-populated oligomers. Chemical tools/antibodies stabilize oligomers for structural and toxicity studies A combination of methods is needed to fully characterize amyloid assembly pathways.
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Affiliation(s)
- Emma E Cawood
- Astbury Centre for Structural Molecular Biology, School of Chemistry, University of Leeds, LS2 9JT, UK; Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, University of Leeds, LS2 9JT, UK
| | - Theodoros K Karamanos
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, University of Leeds, LS2 9JT, UK; Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Andrew J Wilson
- Astbury Centre for Structural Molecular Biology, School of Chemistry, University of Leeds, LS2 9JT, UK.
| | - Sheena E Radford
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, University of Leeds, LS2 9JT, UK.
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11
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Wille H, Dorosh L, Amidian S, Schmitt-Ulms G, Stepanova M. Combining molecular dynamics simulations and experimental analyses in protein misfolding. ADVANCES IN PROTEIN CHEMISTRY AND STRUCTURAL BIOLOGY 2020; 118:33-110. [PMID: 31928730 DOI: 10.1016/bs.apcsb.2019.10.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The fold of a protein determines its function and its misfolding can result in loss-of-function defects. In addition, for certain proteins their misfolding can lead to gain-of-function toxicities resulting in protein misfolding diseases such as Alzheimer's, Parkinson's, or the prion diseases. In all of these diseases one or more proteins misfold and aggregate into disease-specific assemblies, often in the form of fibrillar amyloid deposits. Most, if not all, protein misfolding diseases share a fundamental molecular mechanism that governs the misfolding and subsequent aggregation. A wide variety of experimental methods have contributed to our knowledge about misfolded protein aggregates, some of which are briefly described in this review. The misfolding mechanism itself is difficult to investigate, as the necessary timescale and resolution of the misfolding events often lie outside of the observable parameter space. Molecular dynamics simulations fill this gap by virtue of their intrinsic, molecular perspective and the step-by-step iterative process that forms the basis of the simulations. This review focuses on molecular dynamics simulations and how they combine with experimental analyses to provide detailed insights into protein misfolding and the ensuing diseases.
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Affiliation(s)
- Holger Wille
- Department of Biochemistry, University of Alberta, Edmonton, Canada; Centre for Prions and Protein Folding Diseases, University of Alberta, Edmonton, Canada; Neuroscience and Mental Health Institute, University of Alberta, Edmonton, Canada
| | - Lyudmyla Dorosh
- Department of Electrical and Computer Engineering, University of Alberta, Edmonton, Canada
| | - Sara Amidian
- Department of Biochemistry, University of Alberta, Edmonton, Canada; Centre for Prions and Protein Folding Diseases, University of Alberta, Edmonton, Canada
| | - Gerold Schmitt-Ulms
- Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada
| | - Maria Stepanova
- Department of Electrical and Computer Engineering, University of Alberta, Edmonton, Canada
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12
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Madhu P, Mukhopadhyay S. Preferential Recruitment of Conformationally Distinct Amyloid-β Oligomers by the Intrinsically Disordered Region of the Human Prion Protein. ACS Chem Neurosci 2020; 11:86-98. [PMID: 31808343 DOI: 10.1021/acschemneuro.9b00646] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Soluble oligomeric species of the amyloid-β (Aβ) peptide exhibit pronounced neurotoxic effects in Alzheimer's disease. Recent studies have indicated that the prion protein (PrP) is one of the cell-surface receptors, so-called a bad receptor, of Aβ oligomers that mediates downstream cellular toxicity. A rational classification of Aβ oligomers on the basis of conformation indicates that there are two distinct types of oligomers, namely, prefibrillar and fibrillar oligomers that are positive to A11 and OC conformation-dependent antibodies, respectively. The mechanism of heterotypic assembly of conformationally distinct oligomers and PrP is poorly understood. In this work, using an array of biophysical and biochemical tools, we dissect the molecular mechanism of the interaction of A11- and OC-positive Aβ42 oligomers with human PrP. Using site-specific binding titrations, we show that the recruitment of Aβ oligomers primarily occurs via the electrostatic interaction between the N-terminal intrinsically disordered region of PrP and Aβ oligomers. Our results demonstrate that OC-positive fibrillar oligomers possessing in-register parallel β-sheet packing displayed ∼30 times stronger binding with PrP compared to A11-positive oligomers. We also show that these OC-positive oligomers exacerbate their toxic effects on mammalian cells upon binding to PrP. On the contrary, the addition of PrP does not alter the toxicity exhibited by A11-positive oligomers. Our findings suggest that strategies targeting the interaction between PrP and OC-positive oligomers, which have been shown to be highly concentrated in the vicinity of amyloid plaques, may have therapeutic potential against Alzheimer's disease.
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13
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Wallin C, Friedemann M, Sholts SB, Noormägi A, Svantesson T, Jarvet J, Roos PM, Palumaa P, Gräslund A, Wärmländer SKTS. Mercury and Alzheimer's Disease: Hg(II) Ions Display Specific Binding to the Amyloid-β Peptide and Hinder Its Fibrillization. Biomolecules 2019; 10:E44. [PMID: 31892131 PMCID: PMC7022868 DOI: 10.3390/biom10010044] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Revised: 12/20/2019] [Accepted: 12/20/2019] [Indexed: 02/07/2023] Open
Abstract
Brains and blood of Alzheimer's disease (AD) patients have shown elevated mercury concentrations, but potential involvement of mercury exposure in AD pathogenesis has not been studied at the molecular level. The pathological hallmark of AD brains is deposition of amyloid plaques, consisting mainly of amyloid-β (Aβ) peptides aggregated into amyloid fibrils. Aβ peptide fibrillization is known to be modulated by metal ions such as Cu(II) and Zn(II). Here, we study in vitro the interactions between Aβ peptides and Hg(II) ions by multiple biophysical techniques. Fluorescence spectroscopy and atomic force microscopy (AFM) show that Hg(II) ions have a concentration-dependent inhibiting effect on Aβ fibrillization: at a 1:1 Aβ·Hg(II) ratio only non-fibrillar Aβ aggregates are formed. NMR spectroscopy shows that Hg(II) ions interact with the N-terminal region of Aβ(1-40) with a micromolar affinity, likely via a binding mode similar to that for Cu(II) and Zn(II) ions, i.e., mainly via the histidine residues His6, His13, and His14. Thus, together with Cu(II), Fe(II), Mn(II), Pb(IV), and Zn(II) ions, Hg(II) belongs to a family of metal ions that display residue-specific binding interactions with Aβ peptides and modulate their aggregation processes.
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Affiliation(s)
- Cecilia Wallin
- Department of Biochemistry and Biophysics, Stockholm University, 10691 Stockholm, Sweden; (C.W.); (T.S.); (J.J.); (A.G.)
| | - Merlin Friedemann
- Department of Chemistry and Biotechnology, Tallinn University of Technology, 19086 Tallinn, Estonia; (M.F.); (A.N.); (P.P.)
| | - Sabrina B. Sholts
- Department of Anthropology, National Museum of Natural History, Smithsonian Institution, Washington, DC 20560, USA;
| | - Andra Noormägi
- Department of Chemistry and Biotechnology, Tallinn University of Technology, 19086 Tallinn, Estonia; (M.F.); (A.N.); (P.P.)
| | - Teodor Svantesson
- Department of Biochemistry and Biophysics, Stockholm University, 10691 Stockholm, Sweden; (C.W.); (T.S.); (J.J.); (A.G.)
| | - Jüri Jarvet
- Department of Biochemistry and Biophysics, Stockholm University, 10691 Stockholm, Sweden; (C.W.); (T.S.); (J.J.); (A.G.)
- The National Institute of Chemical Physics and Biophysics, 12618 Tallinn, Estonia
| | - Per M. Roos
- Institute of Environmental Medicine, Karolinska Institutet, 16765 Stockholm, Sweden;
- Department of Clinical Physiology, Capio St. Göran Hospital, 11219 Stockholm, Sweden
| | - Peep Palumaa
- Department of Chemistry and Biotechnology, Tallinn University of Technology, 19086 Tallinn, Estonia; (M.F.); (A.N.); (P.P.)
| | - Astrid Gräslund
- Department of Biochemistry and Biophysics, Stockholm University, 10691 Stockholm, Sweden; (C.W.); (T.S.); (J.J.); (A.G.)
| | - Sebastian K. T. S. Wärmländer
- Department of Biochemistry and Biophysics, Stockholm University, 10691 Stockholm, Sweden; (C.W.); (T.S.); (J.J.); (A.G.)
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14
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Vugmeyster L, Au DF, Ostrovsky D, Kierl B, Fu R, Hu ZW, Qiang W. Effect of Post-Translational Modifications and Mutations on Amyloid-β Fibrils Dynamics at N Terminus. Biophys J 2019; 117:1524-1535. [PMID: 31570231 PMCID: PMC6817547 DOI: 10.1016/j.bpj.2019.09.004] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Revised: 09/01/2019] [Accepted: 09/09/2019] [Indexed: 02/04/2023] Open
Abstract
We investigate the variability in the dynamics of the disordered N-terminal domain of amyloid-β fibrils (Aβ), comprising residues 1-16 of Aβ1-40, due to post-translational modifications and mutations in the β-bend regions known to modulate aggregation properties. Using 2H static solid-state NMR approaches, we compare the dynamics in the wild-type Aβ fibrils in the threefold symmetric polymorph with the fibrils from three post-translational modification sequences: isoaspartate-D7, the phosphorylation of S8, and an N-terminal truncation ΔE3. Additional comparisons are made with the mutants in the β-bend region (residues 21-23) corresponding to the familial Osaka E22Δ deletion and D23N Iowa mutation. We also include the aggregates induced by Zn2+ ions. The dynamics are probed at the F4 and G9 positions. The main motional model involves two free states undergoing diffusion and conformational exchanges with the bound state in which the diffusion is quenched because of transient interactions involving fibril core and other intrastrand contacts. The fraction of the bound state increases in a sigmoidal fashion with a decrease in temperature. There is clear variability in the dynamics: the phosphorylation of S8 variant is the most rigid at the G9 site in line with structural studies, the ΔE3 fibrils are more flexible at the G9 site in line with the morphological fragmentation pattern, the Zn-induced aggregates are the most mobile, and the two β-bend mutants have the strongest changes at the F4 site toward higher rigidity. Overall, the changes underlie the potential role of conformational ensembles in setting the stage for aggregation-prone states.
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Affiliation(s)
- Liliya Vugmeyster
- Department of Chemistry, University of Colorado Denver, Denver, Colorado.
| | - Dan F Au
- Department of Chemistry, University of Colorado Denver, Denver, Colorado
| | - Dmitry Ostrovsky
- Department of Mathematics, University of Colorado Denver, Denver, Colorado
| | - Brian Kierl
- Department of Chemistry, University of Colorado Denver, Denver, Colorado
| | - Riqiang Fu
- National High Field Magnetic Laboratory, Tallahassee, Florida
| | - Zhi-Wen Hu
- Department of Chemistry, Binghamton University, Binghamton, New York
| | - Wei Qiang
- Department of Chemistry, Binghamton University, Binghamton, New York
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15
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Abstract
Amyloid precursor A4 (770 amino acids (aa)) dimerizes and aggregates, as do its C-terminal (99 aa) and amyloid Aβ (40,42 aa Aβ40,Aβ42) fragments. The titled question has been discussed extensively, and here it is addressed further using thermodynamic scaling theory to analyze mutational trends in structural factors and kinetics. Special attention is given to Family Alzheimer's disease mutations in C99 outside Aβ42 centered on Aβ46. The scaling analysis is connected to extensive C99 docking simulations which included membranes ( Sun et al. J. Chem. Inf. Model. 2017 , 57 , 1375 - 1387 ), thereby confirming their C99 results and extending them to A4.
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Affiliation(s)
- James C. Phillips
- Department of Physics and Astronomy, Rutgers University, Piscataway, New Jersey 08854, United States
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16
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Querol-Vilaseca M, Colom-Cadena M, Pegueroles J, Nuñez-Llaves R, Luque-Cabecerans J, Muñoz-Llahuna L, Andilla J, Belbin O, Spires-Jones TL, Gelpi E, Clarimon J, Loza-Alvarez P, Fortea J, Lleó A. Nanoscale structure of amyloid-β plaques in Alzheimer's disease. Sci Rep 2019; 9:5181. [PMID: 30914681 PMCID: PMC6435662 DOI: 10.1038/s41598-019-41443-3] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2018] [Accepted: 03/08/2019] [Indexed: 12/15/2022] Open
Abstract
Soluble amyloid-β (Aβ) is considered to be a critical component in the pathogenesis of Alzheimer’s disease (AD). Evidence suggests that these non-fibrillar Aβ assemblies are implicated in synaptic dysfunction, neurodegeneration and cell death. However, characterization of these species comes mainly from studies in cellular or animal models, and there is little data in intact human samples due to the lack of adequate optical microscopic resolution to study these small structures. Here, to achieve super-resolution in all three dimensions, we applied Array Tomography (AT) and Stimulated Emission Depletion microscopy (STED), to characterize in postmortem human brain tissue non-fibrillar Aβ structures in amyloid plaques of cases with autosomal dominant and sporadic AD. Ultrathin sections scanned with super-resolution STED microscopy allowed the detection of small Aβ structures of the order of 100 nm. We reconstructed a whole human amyloid plaque and established that plaques are formed by a dense core of higher order Aβ species (~0.022 µm3) and a peripheral halo of smaller Aβ structures (~0.003 µm3). This work highlights the potential of AT-STED for human neuropathological studies.
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Affiliation(s)
- Marta Querol-Vilaseca
- Memory Unit, Department of Neurology, Institut d'Investigacions Biomèdiques Sant Pau - Hospital de Sant Pau, Universitat Autònoma de Barcelona, Barcelona, Spain.,Centro de Investigación Biomédica en Red en Enfermedades Neurodegenerativas (CIBERNED), Madrid, Spain
| | - Martí Colom-Cadena
- Memory Unit, Department of Neurology, Institut d'Investigacions Biomèdiques Sant Pau - Hospital de Sant Pau, Universitat Autònoma de Barcelona, Barcelona, Spain.,Centro de Investigación Biomédica en Red en Enfermedades Neurodegenerativas (CIBERNED), Madrid, Spain
| | - Jordi Pegueroles
- Memory Unit, Department of Neurology, Institut d'Investigacions Biomèdiques Sant Pau - Hospital de Sant Pau, Universitat Autònoma de Barcelona, Barcelona, Spain.,Centro de Investigación Biomédica en Red en Enfermedades Neurodegenerativas (CIBERNED), Madrid, Spain
| | - Raúl Nuñez-Llaves
- Memory Unit, Department of Neurology, Institut d'Investigacions Biomèdiques Sant Pau - Hospital de Sant Pau, Universitat Autònoma de Barcelona, Barcelona, Spain.,Centro de Investigación Biomédica en Red en Enfermedades Neurodegenerativas (CIBERNED), Madrid, Spain
| | - Joan Luque-Cabecerans
- Memory Unit, Department of Neurology, Institut d'Investigacions Biomèdiques Sant Pau - Hospital de Sant Pau, Universitat Autònoma de Barcelona, Barcelona, Spain.,Centro de Investigación Biomédica en Red en Enfermedades Neurodegenerativas (CIBERNED), Madrid, Spain
| | - Laia Muñoz-Llahuna
- Memory Unit, Department of Neurology, Institut d'Investigacions Biomèdiques Sant Pau - Hospital de Sant Pau, Universitat Autònoma de Barcelona, Barcelona, Spain.,Centro de Investigación Biomédica en Red en Enfermedades Neurodegenerativas (CIBERNED), Madrid, Spain
| | - Jordi Andilla
- ICFO-Institut de Ciències Fotòniques, The Barcelona Institute of Science and Technology, Castelldefels, Barcelona, Spain
| | - Olivia Belbin
- Memory Unit, Department of Neurology, Institut d'Investigacions Biomèdiques Sant Pau - Hospital de Sant Pau, Universitat Autònoma de Barcelona, Barcelona, Spain.,Centro de Investigación Biomédica en Red en Enfermedades Neurodegenerativas (CIBERNED), Madrid, Spain
| | - Tara L Spires-Jones
- The University of Edinburgh, UK Dementia Research Institute, Centre for Discovery Brain Sciences, Edinburgh, EH8 9JZ, UK
| | - Ellen Gelpi
- Neurological Tissue Bank of the Biobanc-Hospital Clinic-IDIBAPS, Barcelona, Spain.,Institute of Neurology, Medical University of Vienna, Vienna, Austria
| | - Jordi Clarimon
- Memory Unit, Department of Neurology, Institut d'Investigacions Biomèdiques Sant Pau - Hospital de Sant Pau, Universitat Autònoma de Barcelona, Barcelona, Spain.,Centro de Investigación Biomédica en Red en Enfermedades Neurodegenerativas (CIBERNED), Madrid, Spain
| | - Pablo Loza-Alvarez
- ICFO-Institut de Ciències Fotòniques, The Barcelona Institute of Science and Technology, Castelldefels, Barcelona, Spain
| | - Juan Fortea
- Memory Unit, Department of Neurology, Institut d'Investigacions Biomèdiques Sant Pau - Hospital de Sant Pau, Universitat Autònoma de Barcelona, Barcelona, Spain.,Centro de Investigación Biomédica en Red en Enfermedades Neurodegenerativas (CIBERNED), Madrid, Spain
| | - Alberto Lleó
- Memory Unit, Department of Neurology, Institut d'Investigacions Biomèdiques Sant Pau - Hospital de Sant Pau, Universitat Autònoma de Barcelona, Barcelona, Spain. .,Centro de Investigación Biomédica en Red en Enfermedades Neurodegenerativas (CIBERNED), Madrid, Spain.
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17
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Belikov AV. Age-related diseases as vicious cycles. Ageing Res Rev 2019; 49:11-26. [PMID: 30458244 DOI: 10.1016/j.arr.2018.11.002] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2018] [Revised: 10/05/2018] [Accepted: 11/15/2018] [Indexed: 02/07/2023]
Abstract
The mortality rates of age-related diseases (ARDs) increase exponentially with age. Processes described by the exponential growth function typically involve a branching chain reaction or, more generally, a positive feedback loop. Here I propose that each ARD is mediated by one or several positive feedback loops (vicious cycles). I then identify critical vicious cycles in five major ARDs: atherosclerosis, hypertension, diabetes, Alzheimer's and Parkinson's. I also propose that the progression of ARDs can be halted by selectively interrupting the vicious cycles and suggest the most promising targets.
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Affiliation(s)
- Aleksey V Belikov
- Laboratory of Innovative Medicine, School of Biological and Medical Physics, Moscow Institute of Physics and Technology, Institutsky per., 9, 141701 Dolgoprudny, Moscow Region, Russia.
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18
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Carballo-Pacheco M, Ismail AE, Strodel B. On the Applicability of Force Fields To Study the Aggregation of Amyloidogenic Peptides Using Molecular Dynamics Simulations. J Chem Theory Comput 2018; 14:6063-6075. [PMID: 30336669 DOI: 10.1021/acs.jctc.8b00579] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Molecular dynamics simulations play an essential role in understanding biomolecular processes such as protein aggregation at temporal and spatial resolutions which are not attainable by experimental methods. For a correct modeling of protein aggregation, force fields must accurately represent molecular interactions. Here, we study the effect of five different force fields on the oligomer formation of Alzheimer's Aβ16-22 peptide and two of its mutants: Aβ16-22(F19V,F20V), which does not form fibrils, and Aβ16-22(F19L) which forms fibrils faster than the wild type. We observe that while oligomer formation kinetics depends strongly on the force field, structural properties, such as the most relevant protein-protein contacts, are similar between them. The oligomer formation kinetics obtained with different force fields differ more from each other than the kinetics between aggregating and nonaggregating peptides simulated with a single force field. We discuss the difficulties in comparing atomistic simulations of amyloid oligomer formation with experimental observables.
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Affiliation(s)
- Martín Carballo-Pacheco
- Institute of Complex Systems: Structural Biochemistry (ICS-6) , Forschungszentrum Jülich GmbH , 52425 Jülich , Germany.,AICES Graduate School , RWTH Aachen University , Schinkelstraße 2 , 52062 Aachen , Germany
| | - Ahmed E Ismail
- AICES Graduate School , RWTH Aachen University , Schinkelstraße 2 , 52062 Aachen , Germany.,Aachener Verfahrenstechnik, Faculty of Mechanical Engineering , RWTH Aachen University , Schinkelstraße 2 , 52062 Aachen , Germany
| | - Birgit Strodel
- Institute of Complex Systems: Structural Biochemistry (ICS-6) , Forschungszentrum Jülich GmbH , 52425 Jülich , Germany.,Institute of Theoretical and Computational Chemistry , Heinrich Heine University Düsseldorf , Universitätstrasse 1 , 40225 Düsseldorf , Germany
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19
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Atrián-Blasco E, Gonzalez P, Santoro A, Alies B, Faller P, Hureau C. Cu and Zn coordination to amyloid peptides: From fascinating chemistry to debated pathological relevance. Coord Chem Rev 2018; 375:38-55. [PMID: 30262932 DOI: 10.1016/j.ccr.2018.04.007] [Citation(s) in RCA: 114] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Several diseases share misfolding of different peptides and proteins as a key feature for their development. This is the case of important neurodegenerative diseases such as Alzheimer's and Parkinson's diseases and type II diabetes mellitus. Even more, metal ions such as copper and zinc might play an important role upon interaction with amyloidogenic peptides and proteins, which could impact their aggregation and toxicity abilities. In this review, the different coordination modes proposed for copper and zinc with amyloid-β, α-synuclein and IAPP will be reviewed as well as their impact on the aggregation, and ROS production in the case of copper. In addition, a special focus will be given to the mutations that affect metal binding and lead to familial cases of the diseases. Different modifications of the peptides that have been observed in vivo and could be relevant for the coordination of metal ions are also described.
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Affiliation(s)
- Elena Atrián-Blasco
- CNRS, LCC (Laboratoire de Chimie de Coordination), 205 route de Narbonne, BP 44099 31077 Toulouse Cedex 4, France
- University of Toulouse, UPS, INPT, 31077 Toulouse Cedex 4, France
| | - Paulina Gonzalez
- Biometals and Biology Chemistry, Institut de Chimie (CNRS UMR7177), Université de Strasbourg, 4 rue B. Pascal, 67081 Strasbourg, France
- University of Strasbourg Institute for Advanced Study (USIAS), Strasbourg, France
| | - Alice Santoro
- Biometals and Biology Chemistry, Institut de Chimie (CNRS UMR7177), Université de Strasbourg, 4 rue B. Pascal, 67081 Strasbourg, France
- University of Strasbourg Institute for Advanced Study (USIAS), Strasbourg, France
| | - Bruno Alies
- Université de Bordeaux, ChemBioPharm INSERM U1212 CNRS UMR 5320, Bordeaux, France
| | - Peter Faller
- Biometals and Biology Chemistry, Institut de Chimie (CNRS UMR7177), Université de Strasbourg, 4 rue B. Pascal, 67081 Strasbourg, France
- University of Strasbourg Institute for Advanced Study (USIAS), Strasbourg, France
| | - Christelle Hureau
- CNRS, LCC (Laboratoire de Chimie de Coordination), 205 route de Narbonne, BP 44099 31077 Toulouse Cedex 4, France
- University of Toulouse, UPS, INPT, 31077 Toulouse Cedex 4, France
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20
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Sadakane Y, Kawahara M. Implications of Metal Binding and Asparagine Deamidation for Amyloid Formation. Int J Mol Sci 2018; 19:ijms19082449. [PMID: 30126231 PMCID: PMC6121660 DOI: 10.3390/ijms19082449] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2018] [Revised: 08/10/2018] [Accepted: 08/14/2018] [Indexed: 12/17/2022] Open
Abstract
Increasing evidence suggests that amyloid formation, i.e., self-assembly of proteins and the resulting conformational changes, is linked with the pathogenesis of various neurodegenerative disorders such as Alzheimer’s disease, prion diseases, and Lewy body diseases. Among the factors that accelerate or inhibit oligomerization, we focus here on two non-genetic and common characteristics of many amyloidogenic proteins: metal binding and asparagine deamidation. Both reflect the aging process and occur in most amyloidogenic proteins. All of the amyloidogenic proteins, such as Alzheimer’s β-amyloid protein, prion protein, and α-synuclein, are metal-binding proteins and are involved in the regulation of metal homeostasis. It is widely accepted that these proteins are susceptible to non-enzymatic posttranslational modifications, and many asparagine residues of these proteins are deamidated. Moreover, these two factors can combine because asparagine residues can bind metals. We review the current understanding of these two common properties and their implications in the pathogenesis of these neurodegenerative diseases.
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Affiliation(s)
- Yutaka Sadakane
- Graduate School of Pharmaceutical Sciences, Suzuka University of Medical Science, Suzuka 513-8670, Japan.
| | - Masahiro Kawahara
- Department of Bio-Analytical Chemistry, Faculty of Pharmacy, Musashino University, 1-1-20 Shinmachi, Nishitokyo, Tokyo 202-8585, Japan.
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21
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Sneha P, Panda PK, Gharemirshamlu FR, Bamdad K, Balaji S. Structural discordance in HIV-1 Vpu from brain isolate alarms amyloid fibril forming behavior- a computational perspective. J Theor Biol 2018; 451:35-45. [PMID: 29705491 DOI: 10.1016/j.jtbi.2018.04.033] [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: 08/29/2017] [Revised: 02/14/2018] [Accepted: 04/25/2018] [Indexed: 11/15/2022]
Abstract
HIV-1 being the most widespread type worldwide, its accounts for almost 95% of all infections including HIV associated dementia (HAD) that triggers neurological dysfunction and neurodegeneration in patients. The common features associated with HAD and other neurodegenerative diseases are accumulation of amyloid plaques, neuronal loss and deterioration of cognitive abilities, amongst which amyloid fibrillation is considered to be a hallmark. The success of effective therapeutics lies in the understanding of mechanisms leading to neurotoxicity. Few viral proteins like gp-120 are known to be involved in aggregation and enhancement of viral infectivity while comprehending the neurotoxic role of some other proteins is still underway. In the current study, amyloidogenic potential of HIV-1 Vpu protein from brain isolate is investigated through computational approaches. The aggregation propensity of brain derived HIV-1 Vpu was assessed by several amyloid prediction servers that projected the region 4-35 to be amyloidogenic. The protein structure was modeled and subjected to 70 ns molecular dynamics (MD) simulation to investigate the transformation of α-helical conformation of the predicted aggregate region into β-sheet, proposing the protein's ability to initiate fibril formation that is central to amyloidogenic proteins. The structural features of brain derived HIV-1 Vpu were consistent with the in silico amyloid prediction results that depicts the conformational change in the region 8-28 of which residues Ala8, Ile9, Val10, Ala19, Ile20 and Val21 constitutes β-sheet formation. The α-helix/β-sheet discordance of the predicted region was reflected in the simulation study highlighting the possible structural transition associated with HIV-1 Vpu protein of brain isolate.
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Affiliation(s)
- Patil Sneha
- School of Biotechnology and Bioinformatics, D.Y. Patil deemed to be University, CBD Belapur, Sector 15, Navi Mumbai, Maharashtra 400614, India; Research and Development Centre, Bharathiar University, Coimbatore 641046 India
| | - Pritam Kumar Panda
- School of Biotechnology and Bioinformatics, D.Y. Patil deemed to be University, CBD Belapur, Sector 15, Navi Mumbai, Maharashtra 400614, India
| | | | - Kourosh Bamdad
- Faculty of Science(,) Payame Noor University, 19395-4697 Iran
| | - Seetharaman Balaji
- Department of Biotechnology, Manipal Institute of Technology, Manipal Academy of Higher Education, Manipal, 576104 Karnataka, India.
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22
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Wang J, Wang C, Wu Z, Li X, Xu S, Liu J, Lan Q, Zhu Z, Xu J. Design, synthesis, biological evaluation, and docking study of 4-isochromanone hybrids bearing N
-benzyl pyridinium moiety as dual binding site acetylcholinesterase inhibitors (part II). Chem Biol Drug Des 2017; 91:756-762. [DOI: 10.1111/cbdd.13136] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2017] [Revised: 09/17/2017] [Accepted: 10/14/2017] [Indexed: 01/06/2023]
Affiliation(s)
- Jia Wang
- State Key Laboratory of Natural Medicines and Department of Medicinal Chemistry; China Pharmaceutical University; Nanjing China
| | - Chaolei Wang
- State Key Laboratory of Natural Medicines and Department of Medicinal Chemistry; China Pharmaceutical University; Nanjing China
| | - Zheng Wu
- State Key Laboratory of Natural Medicines and Department of Medicinal Chemistry; China Pharmaceutical University; Nanjing China
| | - Xinnan Li
- State Key Laboratory of Natural Medicines and Department of Medicinal Chemistry; China Pharmaceutical University; Nanjing China
| | - Shengtao Xu
- State Key Laboratory of Natural Medicines and Department of Medicinal Chemistry; China Pharmaceutical University; Nanjing China
| | - Jie Liu
- Department of Organic Chemistry; China Pharmaceutical University; Nanjing China
| | - Qinying Lan
- Life Science and Technique Base; Department of Life Science; Nanjing Agricultural University; Nanjing China
| | - Zheying Zhu
- Division of Molecular Therapeutics and Formulation; School of Pharmacy; The University of Nottingham, University Park Campus; Nottingham UK
| | - Jinyi Xu
- State Key Laboratory of Natural Medicines and Department of Medicinal Chemistry; China Pharmaceutical University; Nanjing China
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23
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Liu X, Shi D, Zhou S, Liu H, Liu H, Yao X. Molecular dynamics simulations and novel drug discovery. Expert Opin Drug Discov 2017; 13:23-37. [DOI: 10.1080/17460441.2018.1403419] [Citation(s) in RCA: 129] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Xuewei Liu
- State Key Laboratory of Applied Organic Chemistry and Department of Chemistry, Lanzhou University, Lanzhou, China
| | - Danfeng Shi
- State Key Laboratory of Applied Organic Chemistry and Department of Chemistry, Lanzhou University, Lanzhou, China
| | | | - Hongli Liu
- School of Pharmacy, Lanzhou University, Lanzhou, China
| | - Huanxiang Liu
- School of Pharmacy, Lanzhou University, Lanzhou, China
| | - Xiaojun Yao
- State Key Laboratory of Applied Organic Chemistry and Department of Chemistry, Lanzhou University, Lanzhou, China
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24
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25
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Wallin C, Sholts SB, Österlund N, Luo J, Jarvet J, Roos PM, Ilag L, Gräslund A, Wärmländer SKTS. Alzheimer's disease and cigarette smoke components: effects of nicotine, PAHs, and Cd(II), Cr(III), Pb(II), Pb(IV) ions on amyloid-β peptide aggregation. Sci Rep 2017; 7:14423. [PMID: 29089568 PMCID: PMC5663743 DOI: 10.1038/s41598-017-13759-5] [Citation(s) in RCA: 68] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2017] [Accepted: 09/05/2017] [Indexed: 12/14/2022] Open
Abstract
Cigarette smoking is a significant risk factor for Alzheimer's disease (AD), which is associated with extracellular brain deposits of amyloid plaques containing aggregated amyloid-β (Aβ) peptides. Aβ aggregation occurs via multiple pathways that can be influenced by various compounds. Here, we used AFM imaging and NMR, fluorescence, and mass spectrometry to monitor in vitro how Aβ aggregation is affected by the cigarette-related compounds nicotine, polycyclic aromatic hydrocarbons (PAHs) with one to five aromatic rings, and the metal ions Cd(II), Cr(III), Pb(II), and Pb(IV). All PAHs and metal ions modulated the Aβ aggregation process. Cd(II), Cr(III), and Pb(II) ions displayed general electrostatic interactions with Aβ, whereas Pb(IV) ions showed specific transient binding coordination to the N-terminal Aβ segment. Thus, Pb(IV) ions are especially prone to interact with Aβ and affect its aggregation. While Pb(IV) ions affected mainly Aβ dimer and trimer formation, hydrophobic toluene mainly affected formation of larger aggregates such as tetramers. The uncharged and hydrophilic nicotine molecule showed no direct interactions with Aβ, nor did it affect Aβ aggregation. Our Aβ interaction results suggest a molecular rationale for the higher AD prevalence among smokers, and indicate that certain forms of lead in particular may constitute an environmental risk factor for AD.
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Affiliation(s)
- Cecilia Wallin
- Department of Biochemistry and Biophysics, Arrhenius Laboratories, Stockholm University, 106 91, Stockholm, Sweden
| | - Sabrina B Sholts
- Department of Anthropology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA
| | - Nicklas Österlund
- Department of Biochemistry and Biophysics, Arrhenius Laboratories, Stockholm University, 106 91, Stockholm, Sweden
- Department of Environmental Science and Analytical Chemistry, Arrhenius Laboratories, Stockholm University, 106 91, Stockholm, Sweden
| | - Jinghui Luo
- Chemical Research Laboratory, University of Oxford, 12 Mansfield Road, Oxford Ox, 1 3TA, UK
| | - Jüri Jarvet
- Department of Biochemistry and Biophysics, Arrhenius Laboratories, Stockholm University, 106 91, Stockholm, Sweden
- The National Institute of Chemical Physics and Biophysics, Tallinn, Estonia
| | - Per M Roos
- Institute of Environmental Medicine, Karolinska Institutet, Nobels väg 13, 171 77, Stockholm, Sweden
- Department of Clinical Physiology, Capio St.Göran Hospital, St.Göransplan 1, 112 19, Stockholm, Sweden
| | - Leopold Ilag
- Department of Environmental Science and Analytical Chemistry, Arrhenius Laboratories, Stockholm University, 106 91, Stockholm, Sweden
| | - Astrid Gräslund
- Department of Biochemistry and Biophysics, Arrhenius Laboratories, Stockholm University, 106 91, Stockholm, Sweden
| | - Sebastian K T S Wärmländer
- Department of Biochemistry and Biophysics, Arrhenius Laboratories, Stockholm University, 106 91, Stockholm, Sweden.
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26
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Ju Y, Asahi T, Sawamura N. Arctic Aβ40 blocks the nicotine-induced neuroprotective effect of CHRNA7 by inhibiting the ERK1/2 pathway in human neuroblastoma cells. Neurochem Int 2017; 110:49-56. [PMID: 28890319 DOI: 10.1016/j.neuint.2017.09.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2017] [Revised: 09/01/2017] [Accepted: 09/06/2017] [Indexed: 12/23/2022]
Abstract
Amyloid β protein (Aβ) plays a central role in Alzheimer's disease (AD) pathogenesis. Point mutations in the Aβ sequence, which cluster around the central hydrophobic core of the peptide, are associated with familial AD (FAD). Several mutations have been identified, with the Arctic mutation exhibiting a purely cognitive phenotype that is typical of AD. Our previous findings suggest that Arctic Aβ40 binds to and aggregates with CHRNA7, thereby inhibiting the calcium response and signaling pathways downstream of the receptor. Activation of CHRNA7 is neuroprotective both in vitro and in vivo. Therefore, in the present study, we investigated whether Arctic Aβ40 affects neuronal survival and/or death via CHRNA7. Using human neuroblastoma SH-SY5Y cells, we found that the neuroprotective function of CHRNA7 is blocked by CHRNA7 knockdown using RNA interference. Furthermore, Arctic Aβ40 blocked the neuroprotective effect of nicotine by inhibiting the ERK1/2 pathway downstream of CHRNA7. Moreover, we show that ERK1/2 activation mediates the neuroprotective effect of nicotine against oxidative stress. Collectively, our findings further our understanding of the molecular pathogenesis of Arctic FAD.
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Affiliation(s)
- Ye Ju
- Faculty of Science and Engineering, Waseda University, TWIns, 2-2 Wakamatsu, Shinjuku, Tokyo 162-8480, Japan
| | - Toru Asahi
- Faculty of Science and Engineering, Waseda University, TWIns, 2-2 Wakamatsu, Shinjuku, Tokyo 162-8480, Japan; Research Organization for Nano & Life Innovation, Waseda University #03C309, TWIns, 2-2 Wakamatsu, Shinjuku, Tokyo 162-8480, Japan
| | - Naoya Sawamura
- Faculty of Science and Engineering, Waseda University, TWIns, 2-2 Wakamatsu, Shinjuku, Tokyo 162-8480, Japan; Research Organization for Nano & Life Innovation, Waseda University #03C309, TWIns, 2-2 Wakamatsu, Shinjuku, Tokyo 162-8480, Japan.
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27
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de Almeida NEC, Do TD, LaPointe NE, Tro M, Feinstein SC, Shea JE, Bowers MT. 1,2,3,4,6-penta-O-galloyl-β-D-glucopyranose Binds to the N-terminal Metal Binding Region to Inhibit Amyloid β-protein Oligomer and Fibril Formation. INTERNATIONAL JOURNAL OF MASS SPECTROMETRY 2017; 420:24-34. [PMID: 29056865 PMCID: PMC5644501 DOI: 10.1016/j.ijms.2016.09.018] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
The early oligomerization of amyloid β-protein (Aβ) is a crucial step in the etiology of Alzheimer's disease (AD), in which soluble and highly neurotoxic oligomers are produced and accumulated inside neurons. In search of therapeutic solutions for AD treatment and prevention, potent inhibitors that remodel Aβ assembly and prevent neurotoxic oligomer formation offer a promising approach. In particular, several polyphenolic compounds have shown anti-aggregation properties and good efficacy on inhibiting oligomeric amyloid formation. 1,2,3,4,6-penta-O-galloyl-β-D-glucopyranose is a large polyphenol that has been shown to be effective at inhibiting aggregation of full-length Aβ1-40 and Aβ1-42, but has the opposite effect on the C-terminal fragment Aβ25-35. Here, we use a combination of ion mobility coupled to mass spectrometry (IMS-MS), transmission electron microscopy (TEM) and molecular dynamics (MD) simulations to elucidate the inhibitory effect of PGG on aggregation of full-length Aβ1-40 and Aβ1-42. We show that PGG interacts strongly with these two peptides, especially in their N-terminal metal binding regions, and suppresses the formation of Aβ1-40 tetramer and Aβ1-42 dodecamer. By exploring multiple facets of polyphenol-amyloid interactions, we provide a molecular basis for the opposing effects of PGG on full-length Aβ and its C-terminal fragments.
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Affiliation(s)
- Natália E. C. de Almeida
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106, United States
| | - Thanh D. Do
- Department of Chemistry and the Beckman Institute, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Nichole E. LaPointe
- Neuroscience Research Institute and Department of Molecular Cellular and Developmental Biology, University of California, Santa Barbara, California 93106, United States
| | - Michael Tro
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106, United States
| | - Stuart C. Feinstein
- Neuroscience Research Institute and Department of Molecular Cellular and Developmental Biology, University of California, Santa Barbara, California 93106, United States
| | - Joan-Emma Shea
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106, United States
| | - Michael T. Bowers
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106, United States
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28
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Kuo YC, Rajesh R. A critical overview of therapeutic strategy and advancement for Alzheimer's disease treatment. J Taiwan Inst Chem Eng 2017. [DOI: 10.1016/j.jtice.2017.05.011] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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29
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Sasaguri H, Nilsson P, Hashimoto S, Nagata K, Saito T, De Strooper B, Hardy J, Vassar R, Winblad B, Saido TC. APP mouse models for Alzheimer's disease preclinical studies. EMBO J 2017; 36:2473-2487. [PMID: 28768718 PMCID: PMC5579350 DOI: 10.15252/embj.201797397] [Citation(s) in RCA: 445] [Impact Index Per Article: 63.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2017] [Revised: 06/09/2017] [Accepted: 07/07/2017] [Indexed: 12/11/2022] Open
Abstract
Animal models of human diseases that accurately recapitulate clinical pathology are indispensable for understanding molecular mechanisms and advancing preclinical studies. The Alzheimer's disease (AD) research community has historically used first‐generation transgenic (Tg) mouse models that overexpress proteins linked to familial AD (FAD), mutant amyloid precursor protein (APP), or APP and presenilin (PS). These mice exhibit AD pathology, but the overexpression paradigm may cause additional phenotypes unrelated to AD. Second‐generation mouse models contain humanized sequences and clinical mutations in the endogenous mouse App gene. These mice show Aβ accumulation without phenotypes related to overexpression but are not yet a clinical recapitulation of human AD. In this review, we evaluate different APP mouse models of AD, and review recent studies using the second‐generation mice. We advise AD researchers to consider the comparative strengths and limitations of each model against the scientific and therapeutic goal of a prospective preclinical study.
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Affiliation(s)
- Hiroki Sasaguri
- Laboratory for Proteolytic Neuroscience, RIKEN Brain Science Institute, Wako, Japan .,Department of Neurology and Neurological Science, Graduate School of Medicine, Tokyo Medical and Dental University, Tokyo, Japan
| | - Per Nilsson
- Laboratory for Proteolytic Neuroscience, RIKEN Brain Science Institute, Wako, Japan.,Division of Neurogeriatrics, Department of Neurobiology, Care Sciences and Society, Center for Alzheimer Research, Karolinska Institutet, Huddinge, Sweden
| | - Shoko Hashimoto
- Laboratory for Proteolytic Neuroscience, RIKEN Brain Science Institute, Wako, Japan
| | - Kenichi Nagata
- Laboratory for Proteolytic Neuroscience, RIKEN Brain Science Institute, Wako, Japan
| | - Takashi Saito
- Laboratory for Proteolytic Neuroscience, RIKEN Brain Science Institute, Wako, Japan.,Department of Neuroscience and Pathobiology, Research Institute of Environmental Medicine, Nagoya University, Nagoya, Japan
| | - Bart De Strooper
- Dementia Research Institute, University College London, London, UK.,Department for Neurosciences, KU Leuven, Leuven, Belgium.,VIB Center for Brain and Disease Research, Leuven, Belgium
| | - John Hardy
- Reta Lila Research Laboratories and the Department of Molecular Neuroscience, University College London Institute of Neurology, London, UK
| | - Robert Vassar
- Department of Cell and Molecular Biology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Bengt Winblad
- Division of Neurogeriatrics, Department of Neurobiology, Care Sciences and Society, Center for Alzheimer Research, Karolinska Institutet, Huddinge, Sweden
| | - Takaomi C Saido
- Laboratory for Proteolytic Neuroscience, RIKEN Brain Science Institute, Wako, Japan
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30
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Young LM, Tu LH, Raleigh DP, Ashcroft AE, Radford SE. Understanding co-polymerization in amyloid formation by direct observation of mixed oligomers. Chem Sci 2017; 8:5030-5040. [PMID: 28970890 PMCID: PMC5613229 DOI: 10.1039/c7sc00620a] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2017] [Accepted: 05/03/2017] [Indexed: 12/15/2022] Open
Abstract
Although amyloid assembly in vitro is commonly investigated using single protein sequences, fibril formation in vivo can be more heterogeneous, involving co-assembly of proteins of different length, sequence and/or post-translational modifications. Emerging evidence suggests that co-polymerization can alter the rate and/or mechanism of aggregation and can contribute to pathogenicity. Electrospray ionization-ion mobility spectrometry-mass spectrometry (ESI-IMS-MS) is uniquely suited to the study of these heterogeneous ensembles. Here, ESI-IMS-MS combined with analysis of fibrillation rates using thioflavin T (ThT) fluorescence, is used to track the course of aggregation of variants of islet-amyloid polypeptide (IAPP) in isolation and in pairwise mixtures. We identify a sub-population of extended monomers as the key precursors of amyloid assembly, and reveal that the fastest aggregating sequence in peptide mixtures determines the lag time of fibrillation, despite being unable to cross-seed polymerization. The results demonstrate that co-polymerization of IAPP sequences radically alters the rate of amyloid assembly by altering the conformational properties of the mixed oligomers that form.
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Affiliation(s)
- Lydia M Young
- Astbury Centre for Structural Molecular Biology , School of Molecular and Cellular Biology , University of Leeds , Leeds LS2 9JT , UK .
| | - Ling-Hsien Tu
- Department of Chemistry , Stony Brook University , Stony Brook , New York 11794-3400 , USA
- Genomics Research Center , Academia Sinica , 128 Academia , Taipei 11529 , Taiwan
| | - Daniel P Raleigh
- Department of Chemistry , Stony Brook University , Stony Brook , New York 11794-3400 , USA
| | - Alison E Ashcroft
- Astbury Centre for Structural Molecular Biology , School of Molecular and Cellular Biology , University of Leeds , Leeds LS2 9JT , UK .
| | - Sheena E Radford
- Astbury Centre for Structural Molecular Biology , School of Molecular and Cellular Biology , University of Leeds , Leeds LS2 9JT , UK .
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31
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Bleiholder C, Bowers MT. The Solution Assembly of Biological Molecules Using Ion Mobility Methods: From Amino Acids to Amyloid β-Protein. ANNUAL REVIEW OF ANALYTICAL CHEMISTRY (PALO ALTO, CALIF.) 2017; 10:365-386. [PMID: 28375705 PMCID: PMC6287953 DOI: 10.1146/annurev-anchem-071114-040304] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
Ion mobility spectrometry-mass spectrometry (IMS-MS) methods are increasingly used to study noncovalent assemblies of peptides and proteins. This review focuses on the noncovalent self-assembly of amino acids and peptides, systems at the heart of the amyloid process that play a central role in a number of devastating diseases. Three different systems are discussed in detail: the 42-residue peptide amyloid-β42 implicated in the etiology of Alzheimer's disease, several amyloid-forming peptides with 6-11 residues, and the assembly of individual amino acids. We also discuss from a more fundamental perspective the processes that determine how quickly proteins and their assemblies denature when the analyte ion has been stripped of its solvent in an IMS-MS measurement and how to soften the measurement so that biologically meaningful data can be recorded.
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Affiliation(s)
- Christian Bleiholder
- Department of Chemistry and Biochemistry, Institute of Molecular Biophysics, Florida State University, Tallahassee, Florida 32306;
| | - Michael T Bowers
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106
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32
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Gleevec shifts APP processing from a β-cleavage to a nonamyloidogenic cleavage. Proc Natl Acad Sci U S A 2017; 114:1389-1394. [PMID: 28115709 DOI: 10.1073/pnas.1620963114] [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] [Indexed: 01/21/2023] Open
Abstract
Neurotoxic amyloid-β peptides (Aβ) are major drivers of Alzheimer's disease (AD) and are formed by sequential cleavage of the amyloid precursor protein (APP) by β-secretase (BACE) and γ-secretase. Our previous study showed that the anticancer drug Gleevec lowers Aβ levels through indirect inhibition of γ-secretase activity. Here we report that Gleevec also achieves its Aβ-lowering effects through an additional cellular mechanism. It renders APP less susceptible to proteolysis by BACE without inhibiting BACE enzymatic activity or the processing of other BACE substrates. This effect closely mimics the phenotype of APP A673T, a recently discovered mutation that protects carriers against AD and age-related cognitive decline. In addition, Gleevec induces formation of a specific set of APP C-terminal fragments, also observed in cells expressing the APP protective mutation and in cells exposed to a conventional BACE inhibitor. These Gleevec phenotypes require an intracellular acidic pH and are independent of tyrosine kinase inhibition, given that a related compound lacking tyrosine kinase inhibitory activity, DV2-103, exerts similar effects on APP metabolism. In addition, DV2-103 accumulates at high concentrations in the rodent brain, where it rapidly lowers Aβ levels. This study suggests that long-term treatment with drugs that indirectly modulate BACE processing of APP but spare other BACE substrates and achieve therapeutic concentrations in the brain might be effective in preventing or delaying the onset of AD and could be safer than nonselective BACE inhibitor drugs.
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33
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Hatami A, Monjazeb S, Milton S, Glabe CG. Familial Alzheimer's Disease Mutations within the Amyloid Precursor Protein Alter the Aggregation and Conformation of the Amyloid-β Peptide. J Biol Chem 2017; 292:3172-3185. [PMID: 28049728 DOI: 10.1074/jbc.m116.755264] [Citation(s) in RCA: 97] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2016] [Revised: 12/28/2016] [Indexed: 11/06/2022] Open
Abstract
Most cases of Alzheimer's disease (AD) are sporadic, but a small percentage of AD cases, called familial AD (FAD), are associated with mutations in presenilin 1, presenilin 2, or the amyloid precursor protein. Amyloid precursor protein mutations falling within the amyloid-β (Aβ) sequence lead to a wide range of disease phenotypes. There is increasing evidence that distinct amyloid structures distinguished by amyloid conformation-dependent monoclonal antibodies have similarly distinct roles in pathology. It is possible that this phenotypic diversity of FAD associated with mutations within the Aβ sequence is due to differences in the conformations adopted by mutant Aβ peptides, but the effects of FAD mutations on aggregation kinetics and conformational and morphological changes of the Aβ peptide are poorly defined. To gain more insight into this possibility, we therefore investigated the effects of 11 FAD mutations on the aggregation kinetics of Aβ, as well as its ability to form distinct conformations recognized by a panel of amyloid conformation-specific monoclonal antibodies. We found that most FAD mutations increased the rate of aggregation of Aβ. The FAD mutations also led to the adoption of alternative amyloid conformations distinguished by monoclonal antibodies and resulted in the formation of distinct aggregate morphologies as determined by transmission electron microscopy. In addition, several of the mutant peptides displayed a large reduction in thioflavin T fluorescence, despite forming abundant fibrils indicating that thioflavin T is a probe of conformational polymorphisms rather than a reliable indicator of fibrillization. Taken together, these results indicate that FAD mutations falling within the Aβ sequence lead to dramatic changes in aggregation kinetics and influence the ability of Aβ to form immunologically and morphologically distinct amyloid structures.
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Affiliation(s)
- Asa Hatami
- Department of Molecular Biology and Biochemistry, University of California at Irvine, Irvine, California 92697; Department of Neurology, David Geffen School of Medicine at UCLA, Los Angeles, California 90095
| | - Sanaz Monjazeb
- Department of Molecular Biology and Biochemistry, University of California at Irvine, Irvine, California 92697
| | - Saskia Milton
- Department of Molecular Biology and Biochemistry, University of California at Irvine, Irvine, California 92697
| | - Charles G Glabe
- Department of Molecular Biology and Biochemistry, University of California at Irvine, Irvine, California 92697; Biochemistry Department, Faculty of Science and Experimental Biochemistry Unit, King Fahd Medical Research Center, King Abdulaziz University, 23218 Jeddah, Saudi Arabia.
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34
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Chakrabarti M, McDonald AJ, Will Reed J, Moss MA, Das BC, Ray SK. Molecular Signaling Mechanisms of Natural and Synthetic Retinoids for Inhibition of Pathogenesis in Alzheimer's Disease. J Alzheimers Dis 2016; 50:335-52. [PMID: 26682679 DOI: 10.3233/jad-150450] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Retinoids, which are vitamin A derivatives, interact through retinoic acid receptors (RARs) and retinoid X receptors (RXRs) and have profound effects on several physiological and pathological processes in the brain. The presence of retinoic acid signaling is extensively detected in the adult central nervous system, including the amygdala, cortex, hypothalamus, hippocampus, and other brain areas. Retinoids are primarily involved in neural patterning, differentiation, and axon outgrowth. Retinoids also play a key role in the preservation of the differentiated state of adult neurons. Impairment in retinoic acid signaling can result in neurodegeneration and progression of Alzheimer's disease (AD). Recent studies demonstrated severe deficiencies in spatial learning and memory in mice during retinoic acid (vitamin A) deprivation indicating its significance in preserving memory function. Defective cholinergic neurotransmission plays an important role in cognitive deficits in AD. All-trans retinoic acid is known to enhance the expression and activity of choline acetyltransferase in neuronal cell lines. Activation of RAR and RXR is also known to impede the pathogenesis of AD in mice by inhibiting accumulation of amyloids. In addition, retinoids have been shown to inhibit the expression of chemokines and pro-inflammatory cytokines in microglia and astrocytes, which are activated in AD. In this review article, we have described the chemistry and molecular signaling mechanisms of natural and synthetic retinoids and current understandings of their therapeutic potentials in prevention of AD pathology.
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Affiliation(s)
- Mrinmay Chakrabarti
- Department of Pathology, Microbiology, and Immunology, University of South Carolina School of Medicine, Columbia, SC, USA
| | - Alexander J McDonald
- Department of Pharmacology, Physiology, and Neuroscience, University of South Carolina School of Medicine, Columbia, SC, USA
| | - J Will Reed
- Department of Chemical Engineering, University of South Carolina, Columbia, SC, USA
| | - Melissa A Moss
- Department of Chemical Engineering, University of South Carolina, Columbia, SC, USA
| | - Bhaskar C Das
- Division of Hematology and Oncology, University of Kansas Medical Center, Kansas City, KS, USA
| | - Swapan K Ray
- Department of Pathology, Microbiology, and Immunology, University of South Carolina School of Medicine, Columbia, SC, USA
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35
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Girvan P, Miyake T, Teng X, Branch T, Ying L. Kinetics of the Interactions between Copper and Amyloid-β with FAD Mutations and Phosphorylation at the N terminus. Chembiochem 2016; 17:1732-7. [PMID: 27356100 PMCID: PMC5096041 DOI: 10.1002/cbic.201600255] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2016] [Indexed: 12/27/2022]
Abstract
Mutations and post‐translational modifications of amyloid‐β (Aβ) peptide in its N terminus have been shown to increase fibril formation, yet the molecular mechanism is not clear. Here we investigated the kinetics of the interactions of copper with two Aβ peptides containing Familial Alzheimer's disease (FAD) mutations (English (H6R) and Tottori (D7N)), as well as with Aβ peptide phosphorylated at serine 8 (pS8). All three peptides bind to copper with a similar rate as the wild‐type (wt). The dissociation rates follow the order pS8>H6R>wt>D7N; the interconversion between the two coordinating species occurs 50 % faster for H6R and pS8, whereas D7N had only a negligible effect. Interestingly, the rate of ternary complex (copper‐bridged heterodimer) formation for the modified peptides was significantly faster than that for wt, thus leading us to propose that FAD and sporadic AD might share a kinetic origin for the enhanced oligomerisation of Aβ.
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Affiliation(s)
- Paul Girvan
- Institute of Chemical Biology, Imperial College London, Exhibition Road, London, SW7 2AZ, UK.,Department of Chemistry, Imperial College London, Exhibition Road, London, SW7 2AZ, UK
| | - Toru Miyake
- Molecular Medicine, National Heart and Lung Institute, Imperial College London, Exhibition Road, London, SW7 2AZ, UK.,Faculty of Medicine, Tokyo Medical and Dental University, 1-5-45 Yushima, Bunkyo, Tokyo, 113-0034, Japan
| | - Xiangyu Teng
- Institute of Chemical Biology, Imperial College London, Exhibition Road, London, SW7 2AZ, UK.,Department of Chemistry, Imperial College London, Exhibition Road, London, SW7 2AZ, UK
| | - Thomas Branch
- Institute of Chemical Biology, Imperial College London, Exhibition Road, London, SW7 2AZ, UK.,Department of Chemistry, Imperial College London, Exhibition Road, London, SW7 2AZ, UK
| | - Liming Ying
- Molecular Medicine, National Heart and Lung Institute, Imperial College London, Exhibition Road, London, SW7 2AZ, UK. .,Institute of Chemical Biology, Imperial College London, Exhibition Road, London, SW7 2AZ, UK.
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36
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Chiricotto M, Tran TT, Nguyen PH, Melchionna S, Sterpone F, Derreumaux P. Coarse-grained and All-atom Simulations towards the Early and Late Steps of Amyloid Fibril Formation. Isr J Chem 2016. [DOI: 10.1002/ijch.201600048] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Mara Chiricotto
- Laboratoire de Biochimie Théorique, UPR 9080 CNRS; Université Paris Diderot, Sorbonne Paris Cité, IBPC; 13 Rue Pierre et Marie Curie 75005 Paris France
| | - Thanh Thuy Tran
- Laboratoire de Biochimie Théorique, UPR 9080 CNRS; Université Paris Diderot, Sorbonne Paris Cité, IBPC; 13 Rue Pierre et Marie Curie 75005 Paris France
| | - Phuong H. Nguyen
- Laboratoire de Biochimie Théorique, UPR 9080 CNRS; Université Paris Diderot, Sorbonne Paris Cité, IBPC; 13 Rue Pierre et Marie Curie 75005 Paris France
| | - Simone Melchionna
- Istituto Sistemi Complessi; Consiglio Nazionale delle Ricerche; P. le A. Moro 2 00185 Rome Italy
| | - Fabio Sterpone
- Laboratoire de Biochimie Théorique, UPR 9080 CNRS; Université Paris Diderot, Sorbonne Paris Cité, IBPC; 13 Rue Pierre et Marie Curie 75005 Paris France
| | - Philippe Derreumaux
- Laboratoire de Biochimie Théorique, UPR 9080 CNRS; Université Paris Diderot, Sorbonne Paris Cité, IBPC; 13 Rue Pierre et Marie Curie 75005 Paris France
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37
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Nehls M. Unified theory of Alzheimer's disease (UTAD): implications for prevention and curative therapy. J Mol Psychiatry 2016; 4:3. [PMID: 27429752 PMCID: PMC4947325 DOI: 10.1186/s40303-016-0018-8] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2016] [Accepted: 07/03/2016] [Indexed: 12/14/2022] Open
Abstract
The aim of this review is to propose a Unified Theory of Alzheimer's disease (UTAD) that integrates all key behavioural, genetic and environmental risk factors in a causal chain of etiological and pathogenetic events. It is based on three concepts that emanate from human's evolutionary history: (1) The grandmother-hypothesis (GMH), which explains human longevity due to an evolutionary advantage in reproduction by trans-generational transfer of acquired knowledge. Consequently it is argued that mental health at old-age must be the default pathway of humans' genetic program and not development of AD. (2) Therefore, mechanism like neuronal rejuvenation (NRJ) and adult hippocampal neurogenesis (AHN) that still function efficiently even at old age provide the required lifelong ability to memorize personal experiences important for survival. Cumulative evidence from a multitude of experimental and epidemiological studies indicate that behavioural and environmental risk factors, which impair productive AHN, result in reduced episodic memory performance and in reduced psychological resilience. This leads to avoidance of novelty, dysregulation of the hypothalamic-pituitary-adrenal (HPA)-axis and cortisol hypersecretion, which drives key pathogenic mechanisms of AD like the accumulation and oligomerization of synaptotoxic amyloid beta, chronic neuroinflammation and neuronal insulin resistance. (3) By applying to AHN the law of the minimum (LOM), which defines the basic requirements of biological growth processes, the UTAD explains why and how different lifestyle deficiencies initiate the AD process by impairing AHN and causing dysregulation of the HPA-axis, and how environmental and genetic risk factors such as toxins or ApoE4, respectively, turn into disease accelerators under these unnatural conditions. Consequently, the UTAD provides a rational strategy for the prevention of mental decline and a system-biological approach for the causal treatment of AD, which might even be curative if the systemic intervention is initiated early enough in the disease process. Hence an individualized system-biological treatment of patients with early AD is proposed as a test for the validity of UTAD and outlined in this review.
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Affiliation(s)
- Michael Nehls
- Independent Researcher, Allmendweg 1, 79279 Vörstetten, Germany
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38
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Luo J, Wärmländer SKTS, Gräslund A, Abrahams JP. Cross-interactions between the Alzheimer Disease Amyloid-β Peptide and Other Amyloid Proteins: A Further Aspect of the Amyloid Cascade Hypothesis. J Biol Chem 2016; 291:16485-93. [PMID: 27325705 DOI: 10.1074/jbc.r116.714576] [Citation(s) in RCA: 100] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Many protein folding diseases are intimately associated with accumulation of amyloid aggregates. The amyloid materials formed by different proteins/peptides share many structural similarities, despite sometimes large amino acid sequence differences. Some amyloid diseases constitute risk factors for others, and the progression of one amyloid disease may affect the progression of another. These connections are arguably related to amyloid aggregates of one protein being able to directly nucleate amyloid formation of another, different protein: the amyloid cross-interaction. Here, we discuss such cross-interactions between the Alzheimer disease amyloid-β (Aβ) peptide and other amyloid proteins in the context of what is known from in vitro and in vivo experiments, and of what might be learned from clinical studies. The aim is to clarify potential molecular associations between different amyloid diseases. We argue that the amyloid cascade hypothesis in Alzheimer disease should be expanded to include cross-interactions between Aβ and other amyloid proteins.
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Affiliation(s)
- Jinghui Luo
- From the Chemical Research Laboratory, University of Oxford, Oxford OX1 3TA, United Kingdom,
| | | | - Astrid Gräslund
- the Department of Biochemistry and Biophysics, Stockholm University, SE-10691 Stockholm, Sweden
| | - Jan Pieter Abrahams
- the Biozentrum, University of Basel, CH-4056 Basel, Switzerland, and the Laboratory of Biomolecular Research, Paul Scherrer Institute, CH-5232 Villigen, Switzerland
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39
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Feinstein HE, Benbow SJ, LaPointe NE, Patel N, Ramachandran S, Do TD, Gaylord MR, Huskey NE, Dressler N, Korff M, Quon B, Cantrell KL, Bowers MT, Lal R, Feinstein SC. Oligomerization of the microtubule-associated protein tau is mediated by its N-terminal sequences: implications for normal and pathological tau action. J Neurochem 2016; 137:939-54. [PMID: 26953146 PMCID: PMC4899250 DOI: 10.1111/jnc.13604] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2015] [Revised: 02/10/2016] [Accepted: 03/06/2016] [Indexed: 11/28/2022]
Abstract
Despite extensive structure-function analyses, the molecular mechanisms of normal and pathological tau action remain poorly understood. How does the C-terminal microtubule-binding region regulate microtubule dynamics and bundling? In what biophysical form does tau transfer trans-synaptically from one neuron to another, promoting neurodegeneration and dementia? Previous biochemical/biophysical work led to the hypothesis that tau can dimerize via electrostatic interactions between two N-terminal 'projection domains' aligned in an anti-parallel fashion, generating a multivalent complex capable of interacting with multiple tubulin subunits. We sought to test this dimerization model directly. Native gel analyses of full-length tau and deletion constructs demonstrate that the N-terminal region leads to multiple bands, consistent with oligomerization. Ferguson analyses of native gels indicate that an N-terminal fragment (tau(45-230) ) assembles into heptamers/octamers. Ferguson analyses of denaturing gels demonstrates that tau(45-230) can dimerize even in sodium dodecyl sulfate. Atomic force microscopy reveals multiple levels of oligomerization by both full-length tau and tau(45-230) . Finally, ion mobility-mass spectrometric analyses of tau(106-144) , a small peptide containing the core of the hypothesized dimerization region, also demonstrate oligomerization. Thus, multiple independent strategies demonstrate that the N-terminal region of tau can mediate higher order oligomerization, which may have important implications for both normal and pathological tau action. The microtubule-associated protein tau is essential for neuronal development and maintenance, but is also central to Alzheimer's and related dementias. Unfortunately, the molecular mechanisms underlying normal and pathological tau action remain poorly understood. Here, we demonstrate that tau can homo-oligomerize, providing novel mechanistic models for normal tau action (promoting microtubule growth and bundling, suppressing microtubule shortening) and pathological tau action (poisoning of oligomeric complexes).
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Affiliation(s)
- H Eric Feinstein
- Neuroscience Research Institute, University of California, Santa Barbara, California, USA
- Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, California, USA
| | - Sarah J Benbow
- Neuroscience Research Institute, University of California, Santa Barbara, California, USA
- Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, California, USA
| | - Nichole E LaPointe
- Neuroscience Research Institute, University of California, Santa Barbara, California, USA
| | - Nirav Patel
- Department of Bioengineering, Department of Mechanical Engineering and Materials Science Graduate Program, University of California, San Diego, California, USA
| | - Srinivasan Ramachandran
- Department of Bioengineering, Department of Mechanical Engineering and Materials Science Graduate Program, University of California, San Diego, California, USA
| | - Thanh D Do
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California, USA
| | - Michelle R Gaylord
- Neuroscience Research Institute, University of California, Santa Barbara, California, USA
- Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, California, USA
| | - Noelle E Huskey
- Neuroscience Research Institute, University of California, Santa Barbara, California, USA
- Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, California, USA
| | - Nicolette Dressler
- Department of Chemistry, Westmont College, Santa Barbara, California, USA
| | - Megan Korff
- Department of Chemistry, Westmont College, Santa Barbara, California, USA
| | - Brady Quon
- Department of Chemistry, Westmont College, Santa Barbara, California, USA
| | | | - Michael T Bowers
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California, USA
| | - Ratnesh Lal
- Department of Bioengineering, Department of Mechanical Engineering and Materials Science Graduate Program, University of California, San Diego, California, USA
| | - Stuart C Feinstein
- Neuroscience Research Institute, University of California, Santa Barbara, California, USA
- Department of Molecular, Cellular and Developmental Biology, University of California, Santa Barbara, California, USA
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40
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Phosphorylation of the amyloid β-peptide at Ser26 stabilizes oligomeric assembly and increases neurotoxicity. Acta Neuropathol 2016; 131:525-37. [PMID: 26898910 PMCID: PMC4789232 DOI: 10.1007/s00401-016-1546-0] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2015] [Revised: 02/10/2016] [Accepted: 02/10/2016] [Indexed: 10/25/2022]
Abstract
Aggregation and toxicity of the amyloid β-peptide (Aβ) are considered as critical events in the initiation and progression of Alzheimer's disease (AD). Recent evidence indicated that soluble oligomeric Aβ assemblies exert pronounced toxicity, rather than larger fibrillar aggregates that deposit in the forms of extracellular plaques. While some rare mutations in the Aβ sequence that cause early-onset AD promote the oligomerization, molecular mechanisms that induce the formation or stabilization of oligomers of the wild-type Aβ remain unclear. Here, we identified an Aβ variant phosphorylated at Ser26 residue (pSer26Aβ) in transgenic mouse models of AD and in human brain that shows contrasting spatio-temporal distribution as compared to non-phosphorylated Aβ (npAβ) or other modified Aβ species. pSer26Aβ is particularly abundant in intraneuronal deposits at very early stages of AD, but much less in extracellular plaques. pSer26Aβ assembles into a specific oligomeric form that does not proceed further into larger fibrillar aggregates, and accumulates in characteristic intracellular compartments of granulovacuolar degeneration together with TDP-43 and phosphorylated tau. Importantly, pSer26Aβ oligomers exert increased toxicity in human neurons as compared to other known Aβ species. Thus, pSer26Aβ could represent a critical species in the neurodegeneration during AD pathogenesis.
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41
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de Almeida NEC, Do TD, Tro M, LaPointe NE, Feinstein SC, Shea JE, Bowers MT. Opposing Effects of Cucurbit[7]uril and 1,2,3,4,6-Penta-O-galloyl-β-d-glucopyranose on Amyloid β25-35 Assembly. ACS Chem Neurosci 2016; 7:218-26. [PMID: 26629788 PMCID: PMC4758880 DOI: 10.1021/acschemneuro.5b00280] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Alzheimer's disease (AD) is a neurodegenerative disease characterized by extracellular deposits of amyloid β protein (Aβ) in the brain. The conversion of soluble monomers to amyloid Aβ fibrils is a complicated process and involves several transient oligomeric species, which are widely believed to be highly toxic and play a crucial role in the etiology of AD. The development of inhibitors to prevent formation of small and midsized oligomers is a promising strategy for AD treatment. In this work, we employ ion mobility spectrometry (IMS), transmission electron microscopy (TEM), and molecular dynamics (MD) simulations to elucidate the structural modulation promoted by two potential inhibitors of Aβ oligomerization, cucurbit[7]uril (CB[7]) and 1,2,3,4,6-penta-O-galloyl-β-d-glucopyranose (PGG), on early oligomer and fibril formation of the Aβ25-35 fragment. One and two CB[7] molecules bind to Aβ25-35 monomers and dimers, respectively, and suppress aggregation by remodeling early oligomer structures and inhibiting the formation of higher-order oligomers. On the other hand, nonselective binding was observed between PGG and Aβ25-35. The interactions between PGG and Aβ25-35, surprisingly, enhanced the formation of Aβ aggregates by promoting extended Aβ25-35 conformations in both homo- and hetero-oligomers. When both ligands were present, the inhibitory effect of CB[7] overrode the stimulatory effect of PGG on Aβ25-35 aggregation, suppressing the formation of large amyloid oligomers and eliminating the structural conversion from isotropic to β-rich topologies induced by PGG. Our results provide mechanistic insights into CB[7] and PGG action on Aβ oligomerization. They also demonstrate the power of the IMS technique to investigate mechanisms of multiple small-molecule agents on the amyloid formation process.
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Affiliation(s)
- Natália E. C. de Almeida
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106, United States
| | - Thanh D. Do
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106, United States
| | - Michael Tro
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106, United States
| | - Nichole E. LaPointe
- Neuroscience Research Institute and Department of Molecular Cellular and Developmental Biology, University of California, Santa Barbara, California 93106, United States
| | - Stuart C. Feinstein
- Neuroscience Research Institute and Department of Molecular Cellular and Developmental Biology, University of California, Santa Barbara, California 93106, United States
| | - Joan-Emma Shea
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106, United States
| | - Michael T. Bowers
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106, United States
- Corresponding author: Michael T. Bowers. Tel: +1-805-893-2673;
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42
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Young LM, Saunders JC, Mahood RA, Revill CH, Foster RJ, Ashcroft AE, Radford SE. ESI-IMS-MS: A method for rapid analysis of protein aggregation and its inhibition by small molecules. Methods 2016; 95:62-9. [PMID: 26007606 PMCID: PMC4769093 DOI: 10.1016/j.ymeth.2015.05.017] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2015] [Revised: 03/26/2015] [Accepted: 05/07/2015] [Indexed: 11/21/2022] Open
Abstract
Electrospray ionisation-ion mobility spectrometry-mass spectrometry (ESI-IMS-MS) is a powerful method for the study of conformational changes in protein complexes, including oligomeric species populated during protein self-aggregation into amyloid fibrils. Information on the mass, stability, cross-sectional area and ligand binding capability of each transiently populated intermediate, present in the heterogeneous mixture of assembling species, can be determined individually in a single experiment in real-time. Determining the structural characterisation of oligomeric species and alterations in self-assembly pathways observed in the presence of small molecule inhibitors is of great importance, given the urgent demand for effective therapeutics. Recent studies have demonstrated the capability of ESI-IMS-MS to identify small molecule modulators of amyloid assembly and to determine the mechanism by which they interact (positive, negative, non-specific binding, or colloidal) in a high-throughput format. Here, we demonstrate these advances using self-assembly of Aβ40 as an example, and reveal two new inhibitors of Aβ40 fibrillation.
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Affiliation(s)
- Lydia M Young
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom; School of Molecular and Cellular Biology, University of Leeds, LS2 9JT, United Kingdom.
| | - Janet C Saunders
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom; School of Molecular and Cellular Biology, University of Leeds, LS2 9JT, United Kingdom.
| | - Rachel A Mahood
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom; School of Molecular and Cellular Biology, University of Leeds, LS2 9JT, United Kingdom.
| | - Charlotte H Revill
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom; School of Chemistry, University of Leeds, LS2 9JT, United Kingdom.
| | - Richard J Foster
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom; School of Chemistry, University of Leeds, LS2 9JT, United Kingdom.
| | - Alison E Ashcroft
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom; School of Molecular and Cellular Biology, University of Leeds, LS2 9JT, United Kingdom.
| | - Sheena E Radford
- Astbury Centre for Structural Molecular Biology, University of Leeds, Leeds LS2 9JT, United Kingdom; School of Molecular and Cellular Biology, University of Leeds, LS2 9JT, United Kingdom.
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43
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Radko SP, Khmeleva SA, Suprun EV, Kozin SA, Bodoev NV, Makarov AA, Archakov AI, Shumyantseva VV. [Physico-chemical methods for studing β-amyloid aggregation]. BIOMEDIT︠S︡INSKAI︠A︡ KHIMII︠A︡ 2015; 61:203-18. [PMID: 25978387 DOI: 10.18097/pbmc20156102203] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Alzheimer's disease is the most prevalent neurodegenerative pathology. According to the amyloid cascade hypothesis, a key event of the Alzheimer's disease pathogenesis is a transition of the β-amyloid peptide (Аβ) from the monomeric form to the aggregated state. The mechanism of Аβ aggregation is intensively studied in vitro, by means of synthetic peptides and various physico-chemical methods allowing evaluation of size, molecular structure, and morphology of the formed aggregates. The paper reviews both the well-known and recently introduced physico-chemical methods for analysis of Аβ aggregation, including microscopу, optical and fluorescent methods, method of electron paramagnetic resonance, electrochemical and electrophoretic methods, gel-filtration, and mass spectrometric methods. Merits and drawbacks of the methods are discussed. The unique possibility to simultaneously observe Аβ monomers as well oligomers and large aggregates by means of atomic force microscopy or fluorescence correlation spectroscopy is emphasized. The high detection sensitivity of the latter method, monitoring the aggregation process in Аβ solutions at low peptide concentrations is underlined. Among mass spectrometric methods, the ion mobility mass spectrometry is marked out as a method enabling to obtain information about both the spectrum of Аβ oligomers and their structure. It is pointed out that the use of several methods giving the complementary data about Аβ aggregates is the best experimental approach to studying the process of b-amyloid peptide aggregation in vitro.
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Affiliation(s)
- S P Radko
- Institute of Biomedical Chemistry, Moscow, Russia; Engelhardt Institute of Molecular Biology, Moscow, Russia
| | - S A Khmeleva
- Institute of Biomedical Chemistry, Moscow, Russia
| | - E V Suprun
- Institute of Biomedical Chemistry, Moscow, Russia
| | - S A Kozin
- Engelhardt Institute of Molecular Biology, Moscow, Russia
| | - N V Bodoev
- Institute of Biomedical Chemistry, Moscow, Russia
| | - A A Makarov
- Engelhardt Institute of Molecular Biology, Moscow, Russia
| | - A I Archakov
- Institute of Biomedical Chemistry, Moscow, Russia
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44
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Roychaudhuri R, Zheng X, Lomakin A, Maiti P, Condron MM, Benedek GB, Bitan G, Bowers MT, Teplow DB. Role of Species-Specific Primary Structure Differences in Aβ42 Assembly and Neurotoxicity. ACS Chem Neurosci 2015; 6:1941-55. [PMID: 26421877 PMCID: PMC4844016 DOI: 10.1021/acschemneuro.5b00180] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
A variety of species express the amyloid β-protein (Aβ (the term "Aβ" refers both to Aβ40 and Aβ42, whereas "Aβ40" and "Aβ42" refer to each isoform specifically). Those species expressing Aβ with primary structure identical to that expressed in humans have been found to develop amyloid deposits and Alzheimer's disease-like neuropathology. In contrast, the Aβ sequence in mice and rats contains three amino acid substitutions, Arg5Gly, His13Arg, and Tyr10Phe, which apparently prevent the development of AD-like neuropathology. Interestingly, the brush-tailed rat, Octodon degus, expresses Aβ containing only one of these substitutions, His13Arg, and does develop AD-like pathology. We investigate here the biophysical and biological properties of Aβ peptides from humans, mice (Mus musculus), and rats (Octodon degus). We find that each peptide displays statistical coil → β-sheet secondary structure transitions, transitory formation of hydrophobic surfaces, oligomerization, formation of annuli, protofibrils, and fibrils, and an inverse correlation between rate of aggregation and aggregate size (faster aggregation produced smaller aggregates). The rank order of assembly rate was mouse > rat > Aβ42. The rank order of neurotoxicity of assemblies formed by each peptide immediately after preparation was Aβ42 > mouse ≈ rat. These data do not support long-standing hypotheses that the primary factor controlling development of AD-like neuropathology in rodents is Aβ sequence. Instead, the data support a hypothesis that assembly quaternary structure and organismal responses to toxic peptide assemblies mediate neuropathogenetic effects. The implication of this hypothesis is that a valid understanding of disease causation within a given system (organism, tissue, etc.) requires the coevaluation of both biophysical and cell biological properties of that system.
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Affiliation(s)
- Robin Roychaudhuri
- Department of Neurology, David Geffen School of Medicine at UCLA, Los Angeles, CA
| | - Xueyun Zheng
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106
| | - Aleksey Lomakin
- Department of Physics and Center for Materials Science and Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Panchanan Maiti
- Department of Neurology, David Geffen School of Medicine at UCLA, Los Angeles, CA
| | - Margaret M. Condron
- Department of Neurology, David Geffen School of Medicine at UCLA, Los Angeles, CA
| | - George B. Benedek
- Department of Physics and Center for Materials Science and Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Gal Bitan
- Department of Neurology, David Geffen School of Medicine at UCLA, Los Angeles, CA
- Molecular Biology Institute and Brain Research Institute, University of California, Los Angeles, California 90095
| | - Michael T. Bowers
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106
| | - David B. Teplow
- Department of Neurology, David Geffen School of Medicine at UCLA, Los Angeles, CA
- Molecular Biology Institute and Brain Research Institute, University of California, Los Angeles, California 90095
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45
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Eschmann NA, Do TD, LaPointe NE, Shea JE, Feinstein SC, Bowers MT, Han S. Tau Aggregation Propensity Engrained in Its Solution State. J Phys Chem B 2015; 119:14421-32. [PMID: 26484390 PMCID: PMC4645975 DOI: 10.1021/acs.jpcb.5b08092] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
![]()
A peptide fragment of the human tau
protein which stacks to form
neat cross β-sheet fibrils, resembling that found in pathological
aggregation, 273GKVQIINKKLDL284 (here
“R2/WT”), was modified with a spin-label at the N-terminus.
With the resulting peptide, R2/G273C-SL, we probed events at time
scales spanning seconds to hours after aggregation is initiated using
transmission electron microscopy (TEM), thioflavin T (THT) fluorescence,
ion mobility mass spectrometry (IMMS), electron paramagnetic resonance
(EPR), and Overhauser dynamic nuclear polarization (ODNP) to determine
if deliberate changes to its conformational states and population
in solution influence downstream propensity to form fibrillar aggregates.
We find varying solution conditions by adding the osmolyte urea or
TMAO, or simply using different buffers (acetate buffer, phosphate
buffer, or water), produces significant differences in early monomer/dimer
populations and conformations. Crucially, these characteristics of
the peptide in solution state before aggregation
is initiated dictate the fibril formation propensity after aggregation. We conclude the driving forces that accelerate aggregation,
when heparin is added, do not override the subtle intra- or interprotein
interactions induced by the initial solvent conditions. In other words,
the balance of protein–protein vs protein–solvent interactions
present in the initial solution conditions is a critical driving force
for fibril formation.
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Affiliation(s)
- Neil A Eschmann
- Department of Chemistry and Biochemistry and ‡Neuroscience Research Institute and Department of Molecular, Cellular and Developmental Biology, University of California at Santa Barbara , Santa Barbara, California 93106, United States
| | - Thanh D Do
- Department of Chemistry and Biochemistry and ‡Neuroscience Research Institute and Department of Molecular, Cellular and Developmental Biology, University of California at Santa Barbara , Santa Barbara, California 93106, United States
| | - Nichole E LaPointe
- Department of Chemistry and Biochemistry and ‡Neuroscience Research Institute and Department of Molecular, Cellular and Developmental Biology, University of California at Santa Barbara , Santa Barbara, California 93106, United States
| | - Joan-Emma Shea
- Department of Chemistry and Biochemistry and ‡Neuroscience Research Institute and Department of Molecular, Cellular and Developmental Biology, University of California at Santa Barbara , Santa Barbara, California 93106, United States
| | - Stuart C Feinstein
- Department of Chemistry and Biochemistry and ‡Neuroscience Research Institute and Department of Molecular, Cellular and Developmental Biology, University of California at Santa Barbara , Santa Barbara, California 93106, United States
| | - Michael T Bowers
- Department of Chemistry and Biochemistry and ‡Neuroscience Research Institute and Department of Molecular, Cellular and Developmental Biology, University of California at Santa Barbara , Santa Barbara, California 93106, United States
| | - Songi Han
- Department of Chemistry and Biochemistry and ‡Neuroscience Research Institute and Department of Molecular, Cellular and Developmental Biology, University of California at Santa Barbara , Santa Barbara, California 93106, United States
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46
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Young LM, Mahood RA, Saunders JC, Tu LH, Raleigh DP, Radford SE, Ashcroft AE. Insights into the consequences of co-polymerisation in the early stages of IAPP and Aβ peptide assembly from mass spectrometry. Analyst 2015; 140:6990-9. [PMID: 26193839 PMCID: PMC4626081 DOI: 10.1039/c5an00865d] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The precise molecular mechanisms by which different peptides and proteins assemble into highly ordered amyloid deposits remain elusive. The fibrillation of human amylin (also known as islet amyloid polypeptide, hIAPP) and the amyloid-beta peptide (Aβ-40) are thought to be pathogenic factors in Type 2 diabetes mellitus (T2DM) and Alzheimer's disease (AD), respectively. Amyloid diseases may involve co-aggregation of different protein species, in addition to the self-assembly of single precursor sequences. Here we investigate the formation of heterogeneous pre-fibrillar, oligomeric species produced by the co-incubation of hIAPP and Aβ-40 using electrospray ionisation-ion mobility spectrometry-mass spectrometry (ESI-IMS-MS)-based methods. Conformational properties and gas-phase stabilities of amyloid oligomers formed from hIAPP or Aβ40 alone, and from a 1 : 1 mixture of hIAPP and Aβ40 monomers, were determined and compared. We show that co-assembly of the two sequences results in hetero-oligomers with distinct properties and aggregation kinetics properties compared with the homo-oligomers present in solution. The observations may be of key significance to unravelling the mechanisms of amyloid formation in vivo and elucidating how different sequences and/or assembly conditions can result in different fibril structures and/or pathogenic outcomes.
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Affiliation(s)
- Lydia M. Young
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, University of Leeds, LS2 9JT, UK
| | - Rachel A. Mahood
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, University of Leeds, LS2 9JT, UK
| | - Janet C. Saunders
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, University of Leeds, LS2 9JT, UK
| | - Ling-Hsien Tu
- Department of Chemistry, Stony Brook University, Stony Brook, New York 11794-3400, USA
| | - Daniel P. Raleigh
- Department of Chemistry, Stony Brook University, Stony Brook, New York 11794-3400, USA
- Research Department of Structural and Molecule Biology, University College London, Gower Street, London, WC1E 6BT, UK
| | - Sheena E. Radford
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, University of Leeds, LS2 9JT, UK
| | - Alison E. Ashcroft
- Astbury Centre for Structural Molecular Biology, School of Molecular and Cellular Biology, University of Leeds, LS2 9JT, UK
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47
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Zheng X, Liu D, Roychaudhuri R, Teplow DB, Bowers MT. Amyloid β-Protein Assembly: Differential Effects of the Protective A2T Mutation and Recessive A2V Familial Alzheimer's Disease Mutation. ACS Chem Neurosci 2015; 6:1732-40. [PMID: 26244608 DOI: 10.1021/acschemneuro.5b00171] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Oligomeric states of the amyloid β-protein (Aβ) appear to be causally related to Alzheimer's disease (AD). Recently, two familial mutations in the amyloid precursor protein gene have been described, both resulting in amino acid substitutions at Ala2 (A2) within Aβ. An A2V mutation causes autosomal recessive early onset AD. Interestingly, heterozygotes enjoy some protection against development of the disease. An A2T substitution protects against AD and age-related cognitive decline in non-AD patients. Here, we use ion mobility-mass spectrometry (IM-MS) to examine the effects of these mutations on Aβ assembly. These studies reveal different assembly pathways for early oligomer formation for each peptide. A2T Aβ42 formed dimers, tetramers, and hexamers, but dodecamer formation was inhibited. In contrast, no significant effects on Aβ40 assembly were observed. A2V Aβ42 also formed dimers, tetramers, and hexamers, but it did not form dodecamers. However, A2V Aβ42 formed trimers, unlike A2T or wild-type (wt) Aβ42. In addition, the A2V substitution caused Aβ40 to oligomerize similar to that of wt Aβ42, as evidenced by the formation of dimers, tetramers, hexamers, and dodecamers. In contrast, wt Aβ40 formed only dimers and tetramers. These results provide a basis for understanding how these two mutations lead to, or protect against, AD. They also suggest that the Aβ N-terminus, in addition to the oft discussed central hydrophobic cluster and C-terminus, can play a key role in controlling disease susceptibility.
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Affiliation(s)
- Xueyun Zheng
- Department
of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106, United States
| | - Deyu Liu
- Department
of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106, United States
| | - Robin Roychaudhuri
- Department of Neurology, David Geffen School
of Medicine, Molecular Biology Institute and Brain Research Institute, University of California Los Angeles, Los Angeles, California 90095, United States
| | - David B. Teplow
- Department of Neurology, David Geffen School
of Medicine, Molecular Biology Institute and Brain Research Institute, University of California Los Angeles, Los Angeles, California 90095, United States
| | - Michael T. Bowers
- Department
of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106, United States
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48
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Zheng X, Wu C, Liu D, Li H, Bitan G, Shea JE, Bowers MT. Mechanism of C-Terminal Fragments of Amyloid β-Protein as Aβ Inhibitors: Do C-Terminal Interactions Play a Key Role in Their Inhibitory Activity? J Phys Chem B 2015; 120:1615-23. [PMID: 26439281 DOI: 10.1021/acs.jpcb.5b08177] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Targeting the early oligomerization of amyloid β protein (Aβ) is a promising therapeutic strategy for Alzheimer's disease (AD). Recently, certain C-terminal fragments (CTFs) derived from Aβ42 were shown to be potent inhibitors of Aβ-induced toxicity. The shortest peptide studied, Aβ(39-42), has been shown to modulate Aβ oligomerization and inhibit Aβ toxicity. Understanding the mechanism of these CTFs, especially Aβ(39-42), is of significance for future therapeutic development of AD and peptidomimetic-based drug development. Here we used ion mobility spectrometry-mass spectrometry to investigate the interactions between two modified Aβ(39-42) derivatives, VVIA-NH2 and Ac-VVIA, and full-length Aβ42. VVIA-NH2 was previously shown to inhibit Aβ toxicity, whereas Ac-VVIA did not. Our mass spectrometry analysis revealed that VVIA-NH2 binds directly to Aβ42 monomer and small oligomers while Ac-VVIA binds only to Aβ42 monomer. Ion mobility studies showed that VVIA-NH2 modulates Aβ42 oligomerization by not only inhibiting the dodecamer formation but also disaggregating preformed Aβ42 dodecamer. Ac-VVIA also inhibits and removes preformed Aβ42 dodecamer. However, the Aβ42 sample with the addition of Ac-VVIA clogged the nanospray tip easily, indicating that larger aggregates are formed in the solution in the presence of Ac-VVIA. Molecular dynamics simulations suggested that VVIA-NH2 binds specifically to the C-terminal region of Aβ42 while Ac-VVIA binds dispersedly to multiple regions of Aβ42. This work implies that C-terminal interactions and binding to Aβ oligomers are important for C-terminal fragment inhibitors.
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Affiliation(s)
- Xueyun Zheng
- Department of Chemistry and Biochemistry and ∥Department of Physics, University of California , Santa Barbara, California 93106, United States.,Department of Neurology, David Geffen School of Medicine, §Brain Research Institute, and Molecular Biology Institute, University of California at Los Angeles , Los Angeles, California 90095, United States
| | - Chun Wu
- Department of Chemistry and Biochemistry and ∥Department of Physics, University of California , Santa Barbara, California 93106, United States.,Department of Neurology, David Geffen School of Medicine, §Brain Research Institute, and Molecular Biology Institute, University of California at Los Angeles , Los Angeles, California 90095, United States
| | - Deyu Liu
- Department of Chemistry and Biochemistry and ∥Department of Physics, University of California , Santa Barbara, California 93106, United States.,Department of Neurology, David Geffen School of Medicine, §Brain Research Institute, and Molecular Biology Institute, University of California at Los Angeles , Los Angeles, California 90095, United States
| | - Huiyuan Li
- Department of Chemistry and Biochemistry and ∥Department of Physics, University of California , Santa Barbara, California 93106, United States.,Department of Neurology, David Geffen School of Medicine, §Brain Research Institute, and Molecular Biology Institute, University of California at Los Angeles , Los Angeles, California 90095, United States
| | - Gal Bitan
- Department of Chemistry and Biochemistry and ∥Department of Physics, University of California , Santa Barbara, California 93106, United States.,Department of Neurology, David Geffen School of Medicine, §Brain Research Institute, and Molecular Biology Institute, University of California at Los Angeles , Los Angeles, California 90095, United States
| | - Joan-Emma Shea
- Department of Chemistry and Biochemistry and ∥Department of Physics, University of California , Santa Barbara, California 93106, United States.,Department of Neurology, David Geffen School of Medicine, §Brain Research Institute, and Molecular Biology Institute, University of California at Los Angeles , Los Angeles, California 90095, United States
| | - Michael T Bowers
- Department of Chemistry and Biochemistry and ∥Department of Physics, University of California , Santa Barbara, California 93106, United States.,Department of Neurology, David Geffen School of Medicine, §Brain Research Institute, and Molecular Biology Institute, University of California at Los Angeles , Los Angeles, California 90095, United States
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Pujol-Pina R, Vilaprinyó-Pascual S, Mazzucato R, Arcella A, Vilaseca M, Orozco M, Carulla N. SDS-PAGE analysis of Aβ oligomers is disserving research into Alzheimer´s disease: appealing for ESI-IM-MS. Sci Rep 2015; 5:14809. [PMID: 26450154 PMCID: PMC4598734 DOI: 10.1038/srep14809] [Citation(s) in RCA: 85] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2015] [Accepted: 09/09/2015] [Indexed: 12/20/2022] Open
Abstract
The characterization of amyloid-beta peptide (Aβ) oligomer forms and structures is crucial to the advancement in the field of Alzheimer´s disease (AD). Here we report a critical evaluation of two methods used for this purpose, namely sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE), extensively used in the field, and ion mobility coupled to electrospray ionization mass spectrometry (ESI-IM-MS), an emerging technique with great potential for oligomer characterization. To evaluate their performance, we first obtained pure cross-linked Aβ40 and Aβ42 oligomers of well-defined order. Analysis of these samples by SDS-PAGE revealed that SDS affects the oligomerization state of Aβ42 oligomers, thus providing flawed information on their order and distribution. In contrast, ESI-IM-MS provided accurate information, while also reported on the chemical nature and on the structure of the oligomers. Our findings have important implications as they challenge scientific paradigms in the AD field built upon SDS-PAGE characterization of Aβ oligomer samples.
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Affiliation(s)
- Rosa Pujol-Pina
- Institute for Research in Biomedicine (IRB Barcelona), Baldiri Reixac 10, Barcelona 08028, Spain
| | | | - Roberta Mazzucato
- Institute for Research in Biomedicine (IRB Barcelona), Baldiri Reixac 10, Barcelona 08028, Spain
| | - Annalisa Arcella
- Joint IRB-BSC Research Program in Computational Biology, Institute for Research in Biomedicine (IRB Barcelona), Baldiri Reixac 10, Barcelona 08028, Spain
| | - Marta Vilaseca
- Mass Spectrometry Core Facility, Institute for Research in Biomedicine (IRB Barcelona), Baldiri Reixac 10, Barcelona 08028, Spain
| | - Modesto Orozco
- Joint IRB-BSC Research Program in Computational Biology, Institute for Research in Biomedicine (IRB Barcelona), Baldiri Reixac 10, Barcelona 08028, Spain.,Department of Biochemistry and Molecular Biology, University of Barcelona, Diagonal 647, Barcelona 08028, Spain
| | - Natàlia Carulla
- Institute for Research in Biomedicine (IRB Barcelona), Baldiri Reixac 10, Barcelona 08028, Spain
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Radko SP, Khmeleva SA, Suprun EV, Kozin SA, Bodoev NV, Makarov AA, Archakov AI, Shumyantseva VV. Physico-chemical methods for studying amyloid-β aggregation. BIOCHEMISTRY MOSCOW-SUPPLEMENT SERIES B-BIOMEDICAL CHEMISTRY 2015. [DOI: 10.1134/s1990750815030075] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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