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Acar M, Tatini D, Fidi A, Pacini L, Quagliata M, Nuti F, Papini AM, Lo Nostro P. A Promising Compound for Green Multiresponsive Materials Based on Acyl Carrier Protein. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2024; 40:12381-12393. [PMID: 38836557 DOI: 10.1021/acs.langmuir.4c00476] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2024]
Abstract
A gel that exhibits intrinsically multiple-responsive behavior was prepared from an oligopeptide and studied. ACP(65-74) is an active decapeptide fragment of acyl carrier protein. We investigated 3% w/v ACP(65-74)-NH2 self-healing physical gels in water, glycerol carbonate (GC), and their mixtures. The morphology was investigated by optical, birefringence, and confocal laser scanning microscopy, circular dichroism, Fourier transform infrared, and fluorescence spectroscopy experiments. We found that all samples possess pH responsiveness with fully reversible sol-to-gel transitions. The rheological properties depend on the temperature and solvent composition. The temperature dependence of the gels in water shows a peculiar behavior that is similar to that of thermoresponsive polymer solutions. The results reveal the presence of several β-sheet structures and amyloid aggregates, offering valuable insights into the fibrillation mechanism of amyloids in different solvent media.
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Affiliation(s)
- Mert Acar
- Department of Chemistry "Ugo Schiff", University of Florence, 50019 Sesto Fiorentino (FI), Italy
| | - Duccio Tatini
- Department of Biotechnologies, Chemistry and Pharmacy, University of Siena, 53100 Siena, Italy
| | - Alberto Fidi
- Department of Chemistry "Ugo Schiff", University of Florence, 50019 Sesto Fiorentino (FI), Italy
| | - Lorenzo Pacini
- Department of Chemistry "Ugo Schiff", University of Florence, 50019 Sesto Fiorentino (FI), Italy
- PeptLab, University of Florence, 50019 Sesto Fiorentino (FI), Italy
| | - Michael Quagliata
- Department of Chemistry "Ugo Schiff", University of Florence, 50019 Sesto Fiorentino (FI), Italy
- PeptLab, University of Florence, 50019 Sesto Fiorentino (FI), Italy
| | - Francesca Nuti
- Department of Chemistry "Ugo Schiff", University of Florence, 50019 Sesto Fiorentino (FI), Italy
- PeptLab, University of Florence, 50019 Sesto Fiorentino (FI), Italy
| | - Anna Maria Papini
- Department of Chemistry "Ugo Schiff", University of Florence, 50019 Sesto Fiorentino (FI), Italy
- PeptLab, University of Florence, 50019 Sesto Fiorentino (FI), Italy
| | - Pierandrea Lo Nostro
- Department of Chemistry "Ugo Schiff", University of Florence, 50019 Sesto Fiorentino (FI), Italy
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2
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Mukherjee S, Poudyal M, Dave K, Kadu P, Maji SK. Protein misfolding and amyloid nucleation through liquid-liquid phase separation. Chem Soc Rev 2024; 53:4976-5013. [PMID: 38597222 DOI: 10.1039/d3cs01065a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/11/2024]
Abstract
Liquid-liquid phase separation (LLPS) is an emerging phenomenon in cell physiology and diseases. The weak multivalent interaction prerequisite for LLPS is believed to be facilitated through intrinsically disordered regions, which are prevalent in neurodegenerative disease-associated proteins. These aggregation-prone proteins also exhibit an inherent property for phase separation, resulting in protein-rich liquid-like droplets. The very high local protein concentration in the water-deficient confined microenvironment not only drives the viscoelastic transition from the liquid to solid-like state but also most often nucleate amyloid fibril formation. Indeed, protein misfolding, oligomerization, and amyloid aggregation are observed to be initiated from the LLPS of various neurodegeneration-related proteins. Moreover, in these cases, neurodegeneration-promoting genetic and environmental factors play a direct role in amyloid aggregation preceded by the phase separation. These cumulative recent observations ignite the possibility of LLPS being a prominent nucleation mechanism associated with aberrant protein aggregation. The present review elaborates on the nucleation mechanism of the amyloid aggregation pathway and the possible early molecular events associated with amyloid-related protein phase separation. It also summarizes the recent advancement in understanding the aberrant phase transition of major proteins contributing to neurodegeneration focusing on the common disease-associated factors. Overall, this review proposes a generic LLPS-mediated multistep nucleation mechanism for amyloid aggregation and its implication in neurodegeneration.
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Affiliation(s)
- Semanti Mukherjee
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India.
| | - Manisha Poudyal
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India.
| | - Kritika Dave
- Sunita Sanghi Centre of Aging and Neurodegenerative Diseases, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Pradeep Kadu
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India.
| | - Samir K Maji
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India.
- Sunita Sanghi Centre of Aging and Neurodegenerative Diseases, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
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3
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Ruttenberg SM, Nowick JS. A turn for the worse: Aβ β-hairpins in Alzheimer's disease. Bioorg Med Chem 2024; 105:117715. [PMID: 38615460 DOI: 10.1016/j.bmc.2024.117715] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2024] [Revised: 04/04/2024] [Accepted: 04/05/2024] [Indexed: 04/16/2024]
Abstract
Amyloid-β (Aβ) oligomers are a cause of neurodegeneration in Alzheimer's disease (AD). These soluble aggregates of the Aβ peptide have proven difficult to study due to their inherent metastability and heterogeneity. Strategies to isolate and stabilize homogenous Aβ oligomer populations have emerged such as mutations, covalent cross-linking, and protein fusions. These strategies along with molecular dynamics simulations have provided a variety of proposed structures of Aβ oligomers, many of which consist of molecules of Aβ in β-hairpin conformations. β-Hairpins are intramolecular antiparallel β-sheets composed of two β-strands connected by a loop or turn. Three decades of research suggests that Aβ peptides form several different β-hairpin conformations, some of which are building blocks of toxic Aβ oligomers. The insights from these studies are currently being used to design anti-Aβ antibodies and vaccines to treat AD. Research suggests that antibody therapies designed to target oligomeric Aβ may be more successful at treating AD than antibodies designed to target linear epitopes of Aβ or fibrillar Aβ. Aβ β-hairpins are good epitopes to use in antibody development to selectively target oligomeric Aβ. This review summarizes the research on β-hairpins in Aβ peptides and discusses the relevance of this conformation in AD pathogenesis and drug development.
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Affiliation(s)
- Sarah M Ruttenberg
- Department of Chemistry, University of California, Irvine, Irvine, CA 92697-2025, United States
| | - James S Nowick
- Department of Chemistry, University of California, Irvine, Irvine, CA 92697-2025, United States.
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4
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Sari L, Bali S, Joachimiak LA, Lin MM. Hairpin trimer transition state of amyloid fibril. Nat Commun 2024; 15:2756. [PMID: 38553453 PMCID: PMC10980705 DOI: 10.1038/s41467-024-46446-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Accepted: 02/28/2024] [Indexed: 04/02/2024] Open
Abstract
Protein fibril self-assembly is a universal transition implicated in neurodegenerative diseases. Although fibril structure/growth are well characterized, fibril nucleation is poorly understood. Here, we use a computational-experimental approach to resolve fibril nucleation. We show that monomer hairpin content quantified from molecular dynamics simulations is predictive of experimental fibril formation kinetics across a tau motif mutant library. Hairpin trimers are predicted to be fibril transition states; one hairpin spontaneously converts into the cross-beta conformation, templating subsequent fibril growth. We designed a disulfide-linked dimer mimicking the transition state that catalyzes fibril formation, measured by ThT fluorescence and TEM, of wild-type motif - which does not normally fibrillize. A dimer compatible with extended conformations but not the transition-state fails to nucleate fibril at any concentration. Tau repeat domain simulations show how long-range interactions sequester this motif in a mutation-dependent manner. This work implies that different fibril morphologies could arise from disease-dependent hairpin seeding from different loci.
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Affiliation(s)
- Levent Sari
- Green Center for Systems Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Lyda Hill Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Sofia Bali
- Molecular Biophysics Graduate Program, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Center for Alzheimer's and Neurodegenerative Diseases, Peter O'Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Lukasz A Joachimiak
- Center for Alzheimer's and Neurodegenerative Diseases, Peter O'Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Milo M Lin
- Green Center for Systems Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA.
- Lyda Hill Department of Bioinformatics, University of Texas Southwestern Medical Center, Dallas, TX, USA.
- Center for Alzheimer's and Neurodegenerative Diseases, Peter O'Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA.
- Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, USA.
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5
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Rinauro DJ, Chiti F, Vendruscolo M, Limbocker R. Misfolded protein oligomers: mechanisms of formation, cytotoxic effects, and pharmacological approaches against protein misfolding diseases. Mol Neurodegener 2024; 19:20. [PMID: 38378578 PMCID: PMC10877934 DOI: 10.1186/s13024-023-00651-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Accepted: 08/17/2023] [Indexed: 02/22/2024] Open
Abstract
The conversion of native peptides and proteins into amyloid aggregates is a hallmark of over 50 human disorders, including Alzheimer's and Parkinson's diseases. Increasing evidence implicates misfolded protein oligomers produced during the amyloid formation process as the primary cytotoxic agents in many of these devastating conditions. In this review, we analyze the processes by which oligomers are formed, their structures, physicochemical properties, population dynamics, and the mechanisms of their cytotoxicity. We then focus on drug discovery strategies that target the formation of oligomers and their ability to disrupt cell physiology and trigger degenerative processes.
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Affiliation(s)
- Dillon J Rinauro
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, CB2 1EW, UK
| | - Fabrizio Chiti
- Section of Biochemistry, Department of Experimental and Clinical Biomedical Sciences, University of Florence, 50134, Florence, Italy
| | - Michele Vendruscolo
- Centre for Misfolding Diseases, Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, CB2 1EW, UK.
| | - Ryan Limbocker
- Department of Chemistry and Life Science, United States Military Academy, West Point, NY, 10996, USA.
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6
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Bhopatkar AA, Kayed R. Flanking regions, amyloid cores, and polymorphism: the potential interplay underlying structural diversity. J Biol Chem 2023; 299:105122. [PMID: 37536631 PMCID: PMC10482755 DOI: 10.1016/j.jbc.2023.105122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 07/10/2023] [Accepted: 07/28/2023] [Indexed: 08/05/2023] Open
Abstract
The β-sheet-rich amyloid core is the defining feature of protein aggregates associated with neurodegenerative disorders. Recent investigations have revealed that there exist multiple examples of the same protein, with the same sequence, forming a variety of amyloid cores with distinct structural characteristics. These structural variants, termed as polymorphs, are hypothesized to influence the pathological profile and the progression of different neurodegenerative diseases, giving rise to unique phenotypic differences. Thus, identifying the origin and properties of these structural variants remain a focus of studies, as a preliminary step in the development of therapeutic strategies. Here, we review the potential role of the flanking regions of amyloid cores in inducing polymorphism. These regions, adjacent to the amyloid cores, show a preponderance for being structurally disordered, imbuing them with functional promiscuity. The dynamic nature of the flanking regions can then manifest in the form of conformational polymorphism of the aggregates. We take a closer look at the sequences flanking the amyloid cores, followed by a review of the polymorphic aggregates of the well-characterized proteins amyloid-β, α-synuclein, Tau, and TDP-43. We also consider different factors that can potentially influence aggregate structure and how these regions can be viewed as novel targets for therapeutic strategies by utilizing their unique structural properties.
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Affiliation(s)
- Anukool A Bhopatkar
- Mitchell Center for Neurodegenerative Diseases, University of Texas Medical Branch, Galveston, Texas, USA; Departments of Neurology, Neuroscience and Cell Biology, University of Texas Medical Branch, Galveston, Texas, USA
| | - Rakez Kayed
- Mitchell Center for Neurodegenerative Diseases, University of Texas Medical Branch, Galveston, Texas, USA; Departments of Neurology, Neuroscience and Cell Biology, University of Texas Medical Branch, Galveston, Texas, USA.
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7
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Khaled M, Rönnbäck I, Ilag LL, Gräslund A, Strodel B, Österlund N. A Hairpin Motif in the Amyloid-β Peptide Is Important for Formation of Disease-Related Oligomers. J Am Chem Soc 2023; 145:18340-18354. [PMID: 37555670 PMCID: PMC10450692 DOI: 10.1021/jacs.3c03980] [Citation(s) in RCA: 15] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Indexed: 08/10/2023]
Abstract
The amyloid-β (Aβ) peptide is associated with the development of Alzheimer's disease and is known to form highly neurotoxic prefibrillar oligomeric aggregates, which are difficult to study due to their transient, low-abundance, and heterogeneous nature. To obtain high-resolution information about oligomer structure and dynamics as well as relative populations of assembly states, we here employ a combination of native ion mobility mass spectrometry and molecular dynamics simulations. We find that the formation of Aβ oligomers is dependent on the presence of a specific β-hairpin motif in the peptide sequence. Oligomers initially grow spherically but start to form extended linear aggregates at oligomeric states larger than those of the tetramer. The population of the extended oligomers could be notably increased by introducing an intramolecular disulfide bond, which prearranges the peptide in the hairpin conformation, thereby promoting oligomeric structures but preventing conversion into mature fibrils. Conversely, truncating one of the β-strand-forming segments of Aβ decreased the hairpin propensity of the peptide and thus decreased the oligomer population, removed the formation of extended oligomers entirely, and decreased the aggregation propensity of the peptide. We thus propose that the observed extended oligomer state is related to the formation of an antiparallel sheet state, which then nucleates into the amyloid state. These studies provide increased mechanistic understanding of the earliest steps in Aβ aggregation and suggest that inhibition of Aβ folding into the hairpin conformation could be a viable strategy for reducing the amount of toxic oligomers.
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Affiliation(s)
- Mohammed Khaled
- Institute
of Biological Information Processing: Structural Biochemistry (IBI-7), Forschungszentrum Jülich, 52428 Jülich, Germany
| | - Isabel Rönnbäck
- Department
of Biochemistry and Biophysics, Stockholm
University, 106 91 Stockholm, Sweden
| | - Leopold L. Ilag
- Department
of Materials and Environmental Chemistry, Stockholm University, 106 91 Stockholm, Sweden
| | - Astrid Gräslund
- Department
of Biochemistry and Biophysics, Stockholm
University, 106 91 Stockholm, Sweden
| | - Birgit Strodel
- Institute
of Biological Information Processing: Structural Biochemistry (IBI-7), Forschungszentrum Jülich, 52428 Jülich, Germany
- Institute
of Theoretical and Computational Chemistry, Heinrich Heine University Düsseldorf, 40225 Düsseldorf, Germany
| | - Nicklas Österlund
- Department
of Biochemistry and Biophysics, Stockholm
University, 106 91 Stockholm, Sweden
- Department
of Materials and Environmental Chemistry, Stockholm University, 106 91 Stockholm, Sweden
- Department
of Microbiology, Tumor and Cell Biology, Karolinska Institutet − Biomedicum, 171 65 Solna, Sweden
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8
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Muschol M, Hoyer W. Amyloid oligomers as on-pathway precursors or off-pathway competitors of fibrils. Front Mol Biosci 2023; 10:1120416. [PMID: 36845541 PMCID: PMC9947291 DOI: 10.3389/fmolb.2023.1120416] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Accepted: 01/27/2023] [Indexed: 02/11/2023] Open
Abstract
Amyloid Diseases involve the growth of disease specific proteins into amyloid fibrils and their deposition in protein plaques. Amyloid fibril formation is typically preceded by oligomeric intermediates. Despite significant efforts, the specific role fibrils or oligomers play in the etiology of any given amyloid disease remains controversial. In neurodegenerative disease, though, amyloid oligomers are widely considered critical contributors to disease symptoms. Aside from oligomers as inevitable on-pathway precursors of fibril formation, there is significant evidence for off-pathway oligomer formation competing with fibril growth. The distinct mechanisms and pathways of oligomer formation directly affect our understanding under which conditions oligomers emerge in vivo, and whether their formation is directly coupled to, or distinct from, amyloid fibril formation. In this review, we will discuss the basic energy landscapes underlying the formation of on-pathway vs. off-pathway oligomers, their relation to the related amyloid aggregation kinetics, and their resulting implications for disease etiology. We will review evidence on how differences in the local environment of amyloid assembly can dramatically shift the relative preponderance of oligomers vs. fibrils. Finally, we will comment on gaps in our knowledge of oligomer assembly, of their structure, and on how to assess their relevance to disease etiology.
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Affiliation(s)
- Martin Muschol
- Department of Physics, University of South Florida, Tampa, FL, United States,*Correspondence: Martin Muschol, ; Wolfgang Hoyer,
| | - Wolfgang Hoyer
- Institut für Physikalische Biologie, Heinrich-Heine-Universität, Düsseldorf, Germany,Institute of Biological Information Processing (IBI-7) and JuStruct, Jülich Center for Structural Biology, Forschungszentrum Jülich, Jülich, Germany,*Correspondence: Martin Muschol, ; Wolfgang Hoyer,
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9
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Chen EW, Guo Z. Preparation and Fractionation of Heterogeneous Aβ42 Oligomers with Different Aggregation Properties. Methods Mol Biol 2023; 2551:29-39. [PMID: 36310194 DOI: 10.1007/978-1-0716-2597-2_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Deposition of amyloid-β (Aβ) aggregates in the form of amyloid plaques is a central feature of Alzheimer's disease. The end products of Aβ aggregation are amyloid fibrils. Soluble Aβ aggregates called oligomers are also formed either on or off the pathway of fibril formation. The amyloid fibrils from different clinical subtypes of Alzheimer's disease have been found to adopt different structures, a phenomenon called fibril polymorphism. Meanwhile, different types of Aβ oligomers have also been found. Recently, it has been shown that different types of Aβ42 oligomers may form fibrils of different structures, linking oligomer heterogeneity to fibril polymorphism. In this chapter, we describe methods to prepare heterogeneous Aβ42 oligomers and to quantify the concentration of these oligomers at a low micromolar range using a fluorescamine method. Fractionation of these oligomers by size using ultrafiltration filters allows for the formation of Aβ42 fibrils with different structural properties.
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Affiliation(s)
- Erica W Chen
- Department of Neurology, Brain Research Institute, Molecular Biology Institute, University of California, Los Angeles, CA, USA
| | - Zhefeng Guo
- Department of Neurology, Brain Research Institute, Molecular Biology Institute, University of California, Los Angeles, CA, USA.
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10
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Effects of zinc and carnosine on aggregation kinetics of Amyloid-β40 peptide. Biochem Biophys Rep 2022; 32:101333. [PMID: 36105613 PMCID: PMC9464885 DOI: 10.1016/j.bbrep.2022.101333] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 07/15/2022] [Accepted: 08/21/2022] [Indexed: 11/24/2022] Open
Abstract
The accumulation and amyloid formation of amyloid-β (Aβ) peptides is closely associated with the pathology of Alzheimer's disease. The physiological environment wherein Aβ aggregation happens is crowded with a large variety of metal ions including Zn2+. In this study, we investigated the role of Zn2+ in regulating the aggregation kinetics of Aβ40 peptide. Our results show that Zn2+ can shift a typical single sigmoidal aggregation kinetics of Aβ40 to a biphasic aggregation process. Zn2+ aids in initiating the rapid self-assembly of monomers to form oligomeric intermediates, which further grow into amyloid fibrils in the first aggregation phase. The presence of Zn2+ also retards the appearance of the second aggregation phase in a concentration dependent manner. In addition, our results show that a natural dipeptide, carnosine, can greatly alleviate the effect of Zn2+ on Aβ aggregation kinetics, most likely by coordinating with the metal ion to form chelates. These results suggest a potential in vivo protective effect of carnosine against the cytotoxicity of Aβ by suppressing Zn2+-induced rapid formation of Aβ oligomers. Zn2+ shifts a typical single sigmoidal aggregation kinetics of Aβ40 to a biphasic process. Zn2+ facilitates the rapid formation oligomers in the first aggregation phase. Zn2+ retards the second aggregation phase in a concentration dependent manner. Carnosine greatly reduces the effect of Zn2+ on Aβ aggregation by coordinating with Zn2+.
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11
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Kuhn AJ, Raskatov JA. A robust preparation method for the amyloidogenic and intrinsically disordered amyloid-α peptide. J Pept Sci 2022; 28:e3414. [PMID: 35484922 PMCID: PMC9452447 DOI: 10.1002/psc.3414] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Accepted: 04/26/2022] [Indexed: 11/10/2022]
Abstract
Recent findings suggest that amyloid-β (Aβ) may not be the only peptidic culprit for the cognitive decline observed in patients with Alzheimer's disease. A C-terminal fragment of Aβ, amyloid-α (Aα), also known as p3, has been shown to form amyloidogenic oligomers and fibrils more rapidly than Aβ. However, the insolubility and aggregation propensity of this 24-26-residue peptide make it exceptionally difficult to produce, purify, and subsequently study. This paper reports a reproducible, multi-step method for the purification and pre-treatment of Aα and related analogues, yielding 95%-99% pure peptides. We anticipate that the methods described herein will permit previously inaccessible biophysical and biological experiments that may be critical to understanding the role of this too long overlooked peptide in AD disease pathology.
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Affiliation(s)
- Ariel J. Kuhn
- Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Jevgenij A. Raskatov
- Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, CA, USA
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12
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Rajpoot J, Crooks EJ, Irizarry BA, Amundson A, Van Nostrand WE, Smith SO. Insights into Cerebral Amyloid Angiopathy Type 1 and Type 2 from Comparisons of the Fibrillar Assembly and Stability of the Aβ40-Iowa and Aβ40-Dutch Peptides. Biochemistry 2022; 61:1181-1198. [PMID: 35666749 PMCID: PMC9219409 DOI: 10.1021/acs.biochem.1c00781] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Two distinct diseases are associated with the deposition of fibrillar amyloid-β (Aβ) peptides in the human brain in an age-dependent fashion. Alzheimer's disease is primarily associated with parenchymal plaque deposition of Aβ42, while cerebral amyloid angiopathy (CAA) is associated with amyloid formation of predominantly Aβ40 in the cerebral vasculature. In addition, familial mutations at positions 22 and 23 of the Aβ sequence can enhance vascular deposition in the two major subtypes of CAA. The E22Q (Dutch) mutation is associated with CAA type 2, while the D23N (Iowa) mutation is associated with CAA type 1. Here we investigate differences in the formation and structure of fibrils of these mutant Aβ peptides in vitro to gain insights into their biochemical and physiological differences in the brain. Using Fourier transform infrared and nuclear magnetic resonance spectroscopy, we measure the relative propensities of Aβ40-Dutch and Aβ40-Iowa to form antiparallel structure and compare these propensities to those of the wild-type Aβ40 and Aβ42 isoforms. We find that both Aβ40-Dutch and Aβ40-Iowa have strong propensities to form antiparallel β-hairpins in the first step of the fibrillization process. However, there is a marked difference in the ability of these peptides to form elongated antiparallel structures. Importantly, we find marked differences in the stability of the protofibril or fibril states formed by the four Aβ peptides. We discuss these differences with respect to the mechanisms of Aβ fibril formation in CAA.
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Affiliation(s)
- Jitika Rajpoot
- Department of Biochemistry and Cell Biology, Center for Structural Biology, Stony Brook University, Stony Brook, New York 11794-5215, United States
| | - Elliot J Crooks
- Department of Biochemistry and Cell Biology, Center for Structural Biology, Stony Brook University, Stony Brook, New York 11794-5215, United States
| | - Brandon A Irizarry
- Department of Biochemistry and Cell Biology, Center for Structural Biology, Stony Brook University, Stony Brook, New York 11794-5215, United States
| | - Ashley Amundson
- Department of Biochemistry and Cell Biology, Center for Structural Biology, Stony Brook University, Stony Brook, New York 11794-5215, United States
| | | | - Steven O Smith
- Department of Biochemistry and Cell Biology, Center for Structural Biology, Stony Brook University, Stony Brook, New York 11794-5215, United States
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13
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Sevcuka A, White K, Terry C. Factors That Contribute to hIAPP Amyloidosis in Type 2 Diabetes Mellitus. Life (Basel) 2022; 12:life12040583. [PMID: 35455074 PMCID: PMC9025880 DOI: 10.3390/life12040583] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 04/01/2022] [Accepted: 04/12/2022] [Indexed: 12/24/2022] Open
Abstract
Cases of Type 2 Diabetes Mellitus (T2DM) are increasing at an alarming rate due to the rise in obesity, sedentary lifestyles, glucose-rich diets and other factors. Numerous studies have increasingly illustrated the pivotal role that human islet amyloid polypeptide (hIAPP) plays in the pathology of T2DM through damage and subsequent loss of pancreatic β-cell mass. HIAPP can misfold and form amyloid fibrils which are preceded by pre-fibrillar oligomers and monomers, all of which have been linked, to a certain extent, to β-cell cytotoxicity through a range of proposed mechanisms. This review provides an up-to-date summary of recent progress in the field, highlighting factors that contribute to hIAPP misfolding and aggregation such as hIAPP protein concentration, cell stress, molecular chaperones, the immune system response and cross-seeding with other amyloidogenic proteins. Understanding the structure of hIAPP and how these factors affect amyloid formation will help us better understand how hIAPP misfolds and aggregates and, importantly, help identify potential therapeutic targets for inhibiting amyloidosis so alternate and more effective treatments for T2DM can be developed.
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14
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Mrdenovic D, Pieta IS, Nowakowski R, Kutner W, Lipkowski J, Pieta P. Amyloid β interaction with model cell membranes - What are the toxicity-defining properties of amyloid β? Int J Biol Macromol 2022; 200:520-531. [PMID: 35074328 DOI: 10.1016/j.ijbiomac.2022.01.117] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 01/10/2022] [Accepted: 01/18/2022] [Indexed: 01/26/2023]
Abstract
Disruption of the neuronal membrane by toxic amyloid β oligomers is hypothesized to be the major event associated with Alzheimer's disease's neurotoxicity. Misfolding of amyloid β is followed by aggregation via different pathways in which structurally different amyloid β oligomers can be formed. The respective toxic actions of these structurally diverse oligomers can vary significantly. Linking a particular toxic action to a structurally unique kind of amyloid β oligomers and resolving their toxicity-determining feature remains challenging because of their transient stability and heterogeneity. Moreover, the lipids that make up the membrane affect amyloid β oligomers' behavior, thus adding to the problem's complexity. The present review compares and analyzes the latest results to improve understanding of amyloid β oligomers' interaction with lipid bilayers.
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Affiliation(s)
- Dusan Mrdenovic
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland; Department of Chemistry, University of Guelph, 50 Stone Road East, Guelph, Ontario N1G 2W1, Canada
| | - Izabela S Pieta
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland
| | - Robert Nowakowski
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland
| | - Wlodzimierz Kutner
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland; Faculty of Mathematics and Natural Sciences, School of Sciences, Cardinal Stefan Wyszynski University in Warsaw, Wóycickiego 1/3, 01-815 Warsaw, Poland
| | - Jacek Lipkowski
- Department of Chemistry, University of Guelph, 50 Stone Road East, Guelph, Ontario N1G 2W1, Canada
| | - Piotr Pieta
- Institute of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland.
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15
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Lye YS, Chen YR. TAR DNA-binding protein 43 oligomers in physiology and pathology. IUBMB Life 2022; 74:794-811. [PMID: 35229461 DOI: 10.1002/iub.2603] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 01/19/2022] [Accepted: 01/28/2022] [Indexed: 11/08/2022]
Abstract
TAR DNA-binding protein 43 (TDP-43) is an RNA/DNA-binding protein involved in RNA regulation and diseases. In 2006, TDP-43 inclusions were found in the disease lesions of several neurodegenerative diseases. It is the pathological hallmark in both amyotrophic lateral sclerosis and frontotemporal lobar dementia. It also presents in a large portion of patients with Alzheimer's disease. TDP-43 is prone to aggregate; however, the role of TDP-43 oligomers remains poorly understood in both physiological and pathological conditions. In this review, we emphasize the role of oligomeric TDP-43 in both physiological and pathological conditions and discuss the potential mechanisms of oligomer formation. Finally, we suggest therapeutic strategies against the TDP-43 oligomers in neurodegenerative diseases.
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Affiliation(s)
- Yuh Shen Lye
- Genomics Research Center, Academia Sinica, Taipei, Taiwan.,Taiwan International Graduate Program in Interdisciplinary Neuroscience, National Cheng Kung University and Academia Sinica, Taipei, Taiwan
| | - Yun-Ru Chen
- Genomics Research Center, Academia Sinica, Taipei, Taiwan.,Taiwan International Graduate Program in Interdisciplinary Neuroscience, National Cheng Kung University and Academia Sinica, Taipei, Taiwan
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16
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Irizarry BA, Davis J, Zhu X, Boon BDC, Rozemuller AJM, Van Nostrand WE, Smith SO. Human cerebral vascular amyloid contains both antiparallel and parallel in-register Aβ40 fibrils. J Biol Chem 2021; 297:101259. [PMID: 34599967 PMCID: PMC8528725 DOI: 10.1016/j.jbc.2021.101259] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2021] [Revised: 09/19/2021] [Accepted: 09/27/2021] [Indexed: 01/02/2023] Open
Abstract
The accumulation of fibrillar amyloid-β (Aβ) peptides alongside or within the cerebral vasculature is the hallmark of cerebral amyloid angiopathy (CAA). This condition commonly co-occurs with Alzheimer's disease (AD) and leads to cerebral microbleeds, intracranial hemorrhages, and stroke. CAA also occurs sporadically in an age-dependent fashion and can be accelerated by the presence of familial Aβ mutant peptides. Recent studies using Fourier transform infrared (FTIR) spectroscopy of vascular Aβ fibrils derived from rodents containing the double E22Q/D23N mutations indicated the presence of a novel antiparallel β-sheet structure. To address whether this structure is associated solely with the familial mutations or is a common feature of CAA, we propagated Aβ fibrils from human brain vascular tissue of patients diagnosed with nonfamilial CAA. Aβ fibrils were isolated from cerebral blood vessels using laser capture microdissection in which specific amyloid deposits were removed from thin slices of the brain tissue. Transmission electron microscopy revealed that these deposits were organized into a tight meshwork of fibrils, which FTIR measurements showed could serve as seeds to propagate the growth of Aβ40 fibrils for structural studies. Solid-state NMR measurements of the fibrils propagated from vascular amyloid showed they contained a mixture of parallel, in-register, and antiparallel β-sheet structures. The presence of fibrils with antiparallel structure derived from vascular amyloid is distinct from the typical parallel, in-register β-sheet structure that appears in fibrils derived from parenchymal amyloid in AD. These observations reveal that different microenvironments influence the structures of Aβ fibrils in the human brain.
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Affiliation(s)
- Brandon A Irizarry
- Center for Structural Biology, Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, New York, USA
| | - Judianne Davis
- George and Anne Ryan Institute for Neuroscience, Department of Biomedical and Pharmaceutical Sciences, University of Rhode Island, Kingston, Rhode Island, USA
| | - Xiaoyue Zhu
- George and Anne Ryan Institute for Neuroscience, Department of Biomedical and Pharmaceutical Sciences, University of Rhode Island, Kingston, Rhode Island, USA
| | - Baayla D C Boon
- Department of Neurology, Alzheimer Center Amsterdam, Amsterdam Neuroscience, Amsterdam UMC - VUmc, Amsterdam, the Netherlands; Department of Pathology, Alzheimer Center Amsterdam, Amsterdam Neuroscience, Amsterdam UMC - VUmc, Amsterdam, the Netherlands
| | - Annemieke J M Rozemuller
- Department of Pathology, Alzheimer Center Amsterdam, Amsterdam Neuroscience, Amsterdam UMC - VUmc, Amsterdam, the Netherlands
| | - William E Van Nostrand
- George and Anne Ryan Institute for Neuroscience, Department of Biomedical and Pharmaceutical Sciences, University of Rhode Island, Kingston, Rhode Island, USA
| | - Steven O Smith
- Center for Structural Biology, Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, New York, USA.
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17
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Schützmann MP, Hasecke F, Bachmann S, Zielinski M, Hänsch S, Schröder GF, Zempel H, Hoyer W. Endo-lysosomal Aβ concentration and pH trigger formation of Aβ oligomers that potently induce Tau missorting. Nat Commun 2021; 12:4634. [PMID: 34330900 PMCID: PMC8324842 DOI: 10.1038/s41467-021-24900-4] [Citation(s) in RCA: 52] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Accepted: 07/14/2021] [Indexed: 02/08/2023] Open
Abstract
Amyloid-β peptide (Aβ) forms metastable oligomers >50 kDa, termed AβOs, that are more effective than Aβ amyloid fibrils at triggering Alzheimer’s disease-related processes such as synaptic dysfunction and Tau pathology, including Tau mislocalization. In neurons, Aβ accumulates in endo-lysosomal vesicles at low pH. Here, we show that the rate of AβO assembly is accelerated 8,000-fold upon pH reduction from extracellular to endo-lysosomal pH, at the expense of amyloid fibril formation. The pH-induced promotion of AβO formation and the high endo-lysosomal Aβ concentration together enable extensive AβO formation of Aβ42 under physiological conditions. Exploiting the enhanced AβO formation of the dimeric Aβ variant dimAβ we furthermore demonstrate targeting of AβOs to dendritic spines, potent induction of Tau missorting, a key factor in tauopathies, and impaired neuronal activity. The results suggest that the endosomal/lysosomal system is a major site for the assembly of pathomechanistically relevant AβOs. Aβ oligomers (AβO) are thought to represent the main toxic species in Alzheimer’s disease but very high Aβ concentrations are required to study them in vitro and it remains unknown what role these off-pathway oligomers play in vivo. Here, the authors use a dimeric variant of Aβ termed dimAβ, where two Aβ40 units are linked, which facilitates to study AβO formation kinetics and they observe that Aβ off-pathway oligomer formation is strongly accelerated at endo-lysosomal pH, while amyloid fibril formation is delayed. Furthermore, the authors demonstrate that dimAβ is a disease-relevant model construct for pathogenic AβO formation by showing that dimAβ AβOs target dendritic spines and induce AD-like somatodendritic Tau missorting.
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Affiliation(s)
- Marie P Schützmann
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany
| | - Filip Hasecke
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany
| | - Sarah Bachmann
- Institute of Human Genetics and Center for Molecular Medicine Cologne (CMMC), University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany
| | - Mara Zielinski
- Institute of Biological Information Processing (IBI-7) and JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich, Jülich, Germany
| | - Sebastian Hänsch
- Department of Biology, Center for Advanced Imaging (CAi), Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany
| | - Gunnar F Schröder
- Institute of Biological Information Processing (IBI-7) and JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich, Jülich, Germany.,Physics Department, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany
| | - Hans Zempel
- Institute of Human Genetics and Center for Molecular Medicine Cologne (CMMC), University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany.
| | - Wolfgang Hoyer
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, Düsseldorf, Germany. .,Institute of Biological Information Processing (IBI-7) and JuStruct: Jülich Center for Structural Biology, Forschungszentrum Jülich, Jülich, Germany.
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18
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Deleanu M, Hernandez JF, Cipelletti L, Biron JP, Rossi E, Taverna M, Cottet H, Chamieh J. Unraveling the Speciation of β-Amyloid Peptides during the Aggregation Process by Taylor Dispersion Analysis. Anal Chem 2021; 93:6523-6533. [PMID: 33852281 DOI: 10.1021/acs.analchem.1c00527] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Aggregation mechanisms of amyloid β peptides depend on multiple intrinsic and extrinsic physicochemical factors (e.g., peptide chain length, truncation, peptide concentration, pH, ionic strength, temperature, metal concentration, etc.). Due to this high number of parameters, the formation of oligomers and their propensity to aggregate make the elucidation of this physiopathological mechanism a challenging task. From the analytical point of view, up to our knowledge, few techniques are able to quantify, in real time, the proportion and the size of the different soluble species during the aggregation process. This work aims at demonstrating the efficacy of the modern Taylor dispersion analysis (TDA) performed in capillaries (50 μm i.d.) to unravel the speciation of β-amyloid peptides in low-volume peptide samples (∼100 μL) with an analysis time of ∼3 min per run. TDA was applied to study the aggregation process of Aβ(1-40) and Aβ(1-42) peptides at physiological pH and temperature, where more than 140 data points were generated with a total volume of ∼1 μL over the whole aggregation study (about 0.5 μg of peptides). TDA was able to give a complete and quantitative picture of the Aβ speciation during the aggregation process, including the sizing of the oligomers and protofibrils, the consumption of the monomer, and the quantification of different early- and late-formed aggregated species.
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Affiliation(s)
- Mihai Deleanu
- IBMM, ENSCM, Université Montpellier, CNRS, 34095 Montpellier, France
| | | | - Luca Cipelletti
- Laboratoire Charles Coulomb (L2C), Université Montpellier, CNRS, 34095 Montpellier, France.,Institut Universitaire de France (IUF), France
| | | | - Emilie Rossi
- , Université Paris-Saclay, CNRS, Institut Galien Paris-Saclay, 92296 Châtenay-Malabry, France
| | - Myriam Taverna
- Institut Universitaire de France (IUF), France.,, Université Paris-Saclay, CNRS, Institut Galien Paris-Saclay, 92296 Châtenay-Malabry, France
| | - Hervé Cottet
- IBMM, ENSCM, Université Montpellier, CNRS, 34095 Montpellier, France
| | - Joseph Chamieh
- IBMM, ENSCM, Université Montpellier, CNRS, 34095 Montpellier, France
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19
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Wu T, Lai R, Yao C, Juang J, Lin S. Supramolecular Bait to Trigger Non-Equilibrium Co-Assembly and Clearance of Aβ42. Angew Chem Int Ed Engl 2021; 60:4014-4017. [PMID: 33191624 PMCID: PMC7898541 DOI: 10.1002/anie.202013754] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Indexed: 12/20/2022]
Abstract
In living systems, non-equilibrium states that control the assembly-disassembly of cellular components underlie the gradual complexification of life, whereas in nonliving systems, most molecules follow the laws of thermodynamic equilibrium to sustain dynamic consistency. Little is known about the roles of non-equilibrium states of interactions between supramolecules in living systems. Here, a non-equilibrium state of interaction between supramolecular lipopolysaccharide (LPS) and Aβ42, an aggregate-prone protein that causes Alzheimer's disease (AD), was identified. Structurally, Aβ42 presents a specific groove that is recognized by the amphiphilicity of LPS bait in a non-equilibrium manner. Functionally, the transient complex elicits a cellular response to clear extracellular Aβ42 deposits in neuronal cells. Since the impaired clearance of toxic Aβ42 deposits correlates with AD pathology, the non-equilibrium LPS and Aβ42 could represent a useful target for developing AD therapeutics.
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Affiliation(s)
- Te‐Haw Wu
- Institute of Biomedical Engineering and NanomedicineNational Health Research Institutes (NHRI)Miaoli County35053Taiwan
| | - Rai‐Hua Lai
- Institute of Molecular and Genomic MedicineNHRITaiwan
| | - Chun‐Nien Yao
- Institute of Biomedical Engineering and NanomedicineNational Health Research Institutes (NHRI)Miaoli County35053Taiwan
| | - Jyh‐Lyh Juang
- Institute of Molecular and Genomic MedicineNHRITaiwan
| | - Shu‐Yi Lin
- Institute of Biomedical Engineering and NanomedicineNational Health Research Institutes (NHRI)Miaoli County35053Taiwan
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20
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Protofibril–Fibril Interactions Inhibit Amyloid Fibril Assembly by Obstructing Secondary Nucleation. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202010098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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21
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Hasecke F, Niyangoda C, Borjas G, Pan J, Matthews G, Muschol M, Hoyer W. Protofibril-Fibril Interactions Inhibit Amyloid Fibril Assembly by Obstructing Secondary Nucleation. Angew Chem Int Ed Engl 2021; 60:3016-3021. [PMID: 33095508 PMCID: PMC7898819 DOI: 10.1002/anie.202010098] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Revised: 10/16/2020] [Indexed: 12/29/2022]
Abstract
Amyloid-β peptides (Aβ) assemble into both rigid amyloid fibrils and metastable oligomers termed AβO or protofibrils. In Alzheimer's disease, Aβ fibrils constitute the core of senile plaques, but Aβ protofibrils may represent the main toxic species. Aβ protofibrils accumulate at the exterior of senile plaques, yet the protofibril-fibril interplay is not well understood. Applying chemical kinetics and atomic force microscopy to the assembly of Aβ and lysozyme, protofibrils are observed to bind to the lateral surfaces of amyloid fibrils. When utilizing Aβ variants with different critical oligomer concentrations, the interaction inhibits the autocatalytic proliferation of amyloid fibrils by secondary nucleation on the fibril surface. Thus, metastable oligomers antagonize their replacement by amyloid fibrils both by competing for monomers and blocking secondary nucleation sites. The protofibril-fibril interaction governs their temporal evolution and potential to exert specific toxic activities.
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Affiliation(s)
- Filip Hasecke
- Institut für Physikalische BiologieHeinrich-Heine-Universität Düsseldorf40204DüsseldorfGermany
| | | | - Gustavo Borjas
- Department of PhysicsUniversity of South FloridaTampaFL33620USA
| | - Jianjun Pan
- Department of PhysicsUniversity of South FloridaTampaFL33620USA
| | | | - Martin Muschol
- Department of PhysicsUniversity of South FloridaTampaFL33620USA
| | - Wolfgang Hoyer
- Institut für Physikalische BiologieHeinrich-Heine-Universität Düsseldorf40204DüsseldorfGermany
- Strukturbiochemie (IBI-7)Forschungszentrum Jülich52425JülichGermany
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22
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Vosough F, Barth A. Characterization of Homogeneous and Heterogeneous Amyloid-β42 Oligomer Preparations with Biochemical Methods and Infrared Spectroscopy Reveals a Correlation between Infrared Spectrum and Oligomer Size. ACS Chem Neurosci 2021; 12:473-488. [PMID: 33455165 PMCID: PMC8023574 DOI: 10.1021/acschemneuro.0c00642] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
![]()
Soluble oligomers of the amyloid-β(1-42)
(Aβ42) peptide,
widely considered to be among the relevant neurotoxic species involved
in Alzheimer’s disease, were characterized with a combination
of biochemical and biophysical methods. Homogeneous and stable Aβ42
oligomers were prepared by treating monomeric solutions of the peptide
with detergents. The prepared oligomeric solutions were analyzed with
blue native and sodium dodecyl sulfate polyacrylamide gel electrophoresis,
as well as with infrared (IR) spectroscopy. The IR spectra indicated
a well-defined β-sheet structure of the prepared oligomers.
We also found a relationship between the size/molecular weight of
the Aβ42 oligomers and their IR spectra: The position of the
main amide I′ band of the peptide backbone correlated with
oligomer size, with larger oligomers being associated with lower wavenumbers.
This relationship explained the time-dependent band shift observed
in time-resolved IR studies of Aβ42 aggregation in the absence
of detergents, during which the oligomer size increased. In addition,
the bandwidth of the main IR band in the amide I′ region was
found to become narrower with time in our time-resolved aggregation
experiments, indicating a more homogeneous absorption of the β-sheets
of the oligomers after several hours of aggregation. This is predominantly
due to the consumption of smaller oligomers in the aggregation process.
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Affiliation(s)
- Faraz Vosough
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm SE-106 91, Sweden
| | - Andreas Barth
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm SE-106 91, Sweden
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23
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Mrdenovic D, Zarzycki P, Majewska M, Pieta IS, Nowakowski R, Kutner W, Lipkowski J, Pieta P. Inhibition of Amyloid β-Induced Lipid Membrane Permeation and Amyloid β Aggregation by K162. ACS Chem Neurosci 2021; 12:531-541. [PMID: 33478212 PMCID: PMC7877724 DOI: 10.1021/acschemneuro.0c00754] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Accepted: 01/07/2021] [Indexed: 01/17/2023] Open
Abstract
Alzheimer's disease (AD) is characterized by progressive neurodegeneration associated with amyloid β (Aβ) peptide aggregation. The aggregation of Aβ monomers (AβMs) leads to the formation of Aβ oligomers (AβOs), the neurotoxic Aβ form, capable of permeating the cell membrane. Here, we investigated the effect of a fluorene-based active drug candidate, named K162, on both Aβ aggregation and AβO toxicity toward the bilayer lipid membrane (BLM). Electrochemical impedance spectroscopy (EIS), atomic force microscopy (AFM), and molecular dynamics (MD) were employed to show that K162 inhibits AβOs-induced BLM permeation, thus preserving BLM integrity. In the presence of K162, only shallow defects on the BLM surface were formed. Apparently, K162 modifies Aβ aggregation by bypassing the formation of toxic AβOs, and only nontoxic AβMs, dimers (AβDs), and fibrils (AβFs) are produced. Unlike other Aβ toxicity inhibitors, K162 preserves neurologically beneficial AβMs. This unique K162 inhibition mechanism provides an alternative AD therapeutic strategy that could be explored in the future.
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Affiliation(s)
- Dusan Mrdenovic
- Institute
of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland
- Department
of Chemistry, University of Guelph, 50 Stone Road East, Guelph, Ontario N1G 2W1, Canada
| | - Piotr Zarzycki
- Energy Geosciences
Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road, Berkeley, California 94720, United States
| | - Marta Majewska
- Institute
of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland
| | - Izabela S. Pieta
- Institute
of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland
| | - Robert Nowakowski
- Institute
of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland
| | - Wlodzimierz Kutner
- Institute
of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland
- Faculty
of Mathematics and Natural Sciences, School of Sciences, Cardinal Stefan Wyszynski University in Warsaw, Wóycickiego 1/3, 01-815 Warsaw, Poland
| | - Jacek Lipkowski
- Department
of Chemistry, University of Guelph, 50 Stone Road East, Guelph, Ontario N1G 2W1, Canada
| | - Piotr Pieta
- Institute
of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland
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24
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Fu Z, Van Nostrand WE, Smith SO. Anti-Parallel β-Hairpin Structure in Soluble Aβ Oligomers of Aβ40-Dutch and Aβ40-Iowa. Int J Mol Sci 2021; 22:ijms22031225. [PMID: 33513738 PMCID: PMC7865275 DOI: 10.3390/ijms22031225] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 01/20/2021] [Accepted: 01/24/2021] [Indexed: 11/16/2022] Open
Abstract
The amyloid-β (Aβ) peptides are associated with two prominent diseases in the brain, Alzheimer’s disease (AD) and cerebral amyloid angiopathy (CAA). Aβ42 is the dominant component of cored parenchymal plaques associated with AD, while Aβ40 is the predominant component of vascular amyloid associated with CAA. There are familial CAA mutations at positions Glu22 and Asp23 that lead to aggressive Aβ aggregation, drive vascular amyloid deposition and result in degradation of vascular membranes. In this study, we compared the transition of the monomeric Aβ40-WT peptide into soluble oligomers and fibrils with the corresponding transitions of the Aβ40-Dutch (E22Q), Aβ40-Iowa (D23N) and Aβ40-Dutch, Iowa (E22Q, D23N) mutants. FTIR measurements show that in a fashion similar to Aβ40-WT, the familial CAA mutants form transient intermediates with anti-parallel β-structure. This structure appears before the formation of cross-β-sheet fibrils as determined by thioflavin T fluorescence and circular dichroism spectroscopy and occurs when AFM images reveal the presence of soluble oligomers and protofibrils. Although the anti-parallel β-hairpin is a common intermediate on the pathway to Aβ fibrils for the four peptides studied, the rate of conversion to cross-β-sheet fibril structure differs for each.
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Affiliation(s)
- Ziao Fu
- Center for Structural Biology, Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794, USA;
| | - William E. Van Nostrand
- George and Anne Ryan Institute for Neuroscience, University of Rhode Island, Kingston, RI 02881, USA;
- Department of Biomedical and Pharmaceutical Sciences, University of Rhode Island, Kingston, RI 02881, USA
| | - Steven O. Smith
- Center for Structural Biology, Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794, USA;
- Correspondence: ; Tel.: +1-631-632-1210
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25
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Wu T, Lai R, Yao C, Juang J, Lin S. Supramolecular Bait to Trigger Non‐Equilibrium Co‐Assembly and Clearance of Aβ42. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202013754] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Te‐Haw Wu
- Institute of Biomedical Engineering and Nanomedicine National Health Research Institutes (NHRI) Miaoli County 35053 Taiwan
| | - Rai‐Hua Lai
- Institute of Molecular and Genomic Medicine NHRI Taiwan
| | - Chun‐Nien Yao
- Institute of Biomedical Engineering and Nanomedicine National Health Research Institutes (NHRI) Miaoli County 35053 Taiwan
| | - Jyh‐Lyh Juang
- Institute of Molecular and Genomic Medicine NHRI Taiwan
| | - Shu‐Yi Lin
- Institute of Biomedical Engineering and Nanomedicine National Health Research Institutes (NHRI) Miaoli County 35053 Taiwan
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26
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Noda K, Tachi Y, Okamoto Y. Structural Characteristics of Monomeric Aβ42 on Fibril in the Early Stage of Secondary Nucleation Process. ACS Chem Neurosci 2020; 11:2989-2998. [PMID: 32794732 DOI: 10.1021/acschemneuro.0c00163] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Amyloid-β (Aβ) aggregates are believed to be one of the main causes of Alzheimer's disease. Aβ peptides form fibrils having cross β-sheet structures mainly through primary nucleation, secondary nucleation, and elongation. In particular, self-catalyzed secondary nucleation is of great interest. Here, we investigate the adsorption of Aβ42 peptides to the Aβ42 fibril to reveal a role of adsorption as a part of secondary nucleation. We performed extensive molecular dynamics simulations based on replica exchange with solute tempering 2 (REST2) to two systems: a monomeric Aβ42 in solution and a complex of an Aβ42 peptide and Aβ42 fibril. Results of our simulations show that the Aβ42 monomer is extended on the fibril. Furthermore, we find that the hairpin structure of the Aβ42 monomer decreases but the helix structure increases by adsorption to the fibril surface. These structural changes are preferable for forming fibril-like aggregates, suggesting that the fibril surface serves as a catalyst in the secondary nucleation process. In addition, the stabilization of the helix structure of the Aβ42 monomer on the fibril indicates that the strategy of a secondary nucleation inhibitor design for Aβ40 can also be used for Aβ42.
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Affiliation(s)
- Kohei Noda
- Department of Physics, Graduate School of Science, Nagoya University, Nagoya, Aichi 464-8602, Japan
| | - Yuhei Tachi
- Department of Physics, Graduate School of Science, Nagoya University, Nagoya, Aichi 464-8602, Japan
| | - Yuko Okamoto
- Department of Physics, Graduate School of Science, Nagoya University, Nagoya, Aichi 464-8602, Japan
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27
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Ghosh P, De P. Modulation of Amyloid Protein Fibrillation by Synthetic Polymers: Recent Advances in the Context of Neurodegenerative Diseases. ACS APPLIED BIO MATERIALS 2020; 3:6598-6625. [DOI: 10.1021/acsabm.0c01021] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Pooja Ghosh
- Polymer Research Centre and Centre for Advanced Functional Materials, Department of Chemical Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur, 741246 Nadia, West Bengal, India
| | - Priyadarsi De
- Polymer Research Centre and Centre for Advanced Functional Materials, Department of Chemical Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur, 741246 Nadia, West Bengal, India
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28
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López-Laguna H, Sánchez J, Unzueta U, Mangues R, Vázquez E, Villaverde A. Divalent Cations: A Molecular Glue for Protein Materials. Trends Biochem Sci 2020; 45:992-1003. [PMID: 32891514 DOI: 10.1016/j.tibs.2020.08.003] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Revised: 07/30/2020] [Accepted: 08/06/2020] [Indexed: 02/06/2023]
Abstract
Among inorganic materials, divalent cations modulate thousands of physiological processes that support life. Their roles in protein assembly and aggregation are less known, although they are progressively being brought to light. We review the structural roles of divalent cations here, as well as the novel protein materials that are under development, in which they are used as glue-like agents. More specifically, we discuss how mechanically stable nanoparticles, fibers, matrices, and hydrogels are generated through their coordination with histidine-rich proteins. We also describe how the rational use of divalent cations combined with simple protein engineering offers unexpected and very simple biochemical approaches to biomaterial design that might address unmet clinical needs in precision medicine.
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Affiliation(s)
- Hèctor López-Laguna
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, Bellaterra, 08193, Barcelona, Spain; Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, Bellaterra, 08193, Barcelona, Spain; CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Madrid, Spain
| | - Julieta Sánchez
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, Bellaterra, 08193, Barcelona, Spain; Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, Bellaterra, 08193, Barcelona, Spain; Instituto de Investigaciones Biológicas y Tecnológicas (IIBYT) (CONICET-Universidad Nacional de Córdoba), ICTA & Cátedra de Química Biológica, Departamento de Química, FCEFyN, X 5016GCA, Córdoba, Argentina
| | - Ugutz Unzueta
- Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, Bellaterra, 08193, Barcelona, Spain; CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Madrid, Spain; Biomedical Research Institute Sant Pau (IIB-Sant Pau), Hospital de la Santa Creu i Sant Pau, 08041 Barcelona, Spain; Josep Carreras Research Institute, 08041 Barcelona, Spain.
| | - Ramón Mangues
- CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Madrid, Spain; Biomedical Research Institute Sant Pau (IIB-Sant Pau), Hospital de la Santa Creu i Sant Pau, 08041 Barcelona, Spain; Josep Carreras Research Institute, 08041 Barcelona, Spain
| | - Esther Vázquez
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, Bellaterra, 08193, Barcelona, Spain; Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, Bellaterra, 08193, Barcelona, Spain; CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Madrid, Spain
| | - Antonio Villaverde
- Institut de Biotecnologia i de Biomedicina, Universitat Autònoma de Barcelona, Bellaterra, 08193, Barcelona, Spain; Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, Bellaterra, 08193, Barcelona, Spain; CIBER de Bioingeniería, Biomateriales y Nanomedicina (CIBER-BBN), Madrid, Spain.
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29
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Crooks EJ, Irizarry BA, Ziliox M, Kawakami T, Victor T, Xu F, Hojo H, Chiu K, Simmerling C, Van Nostrand WE, Smith SO, Miller LM. Copper stabilizes antiparallel β-sheet fibrils of the amyloid β40 (Aβ40)-Iowa variant. J Biol Chem 2020; 295:8914-8927. [PMID: 32376688 PMCID: PMC7335782 DOI: 10.1074/jbc.ra119.011955] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2019] [Revised: 04/25/2020] [Indexed: 01/05/2023] Open
Abstract
Cerebral amyloid angiopathy (CAA) is a vascular disorder that primarily involves deposition of the 40-residue-long β-amyloid peptide (Aβ40) in and along small blood vessels of the brain. CAA is often associated with Alzheimer's disease (AD), which is characterized by amyloid plaques in the brain parenchyma enriched in the Aβ42 peptide. Several recent studies have suggested a structural origin that underlies the differences between the vascular amyloid deposits in CAA and the parenchymal plaques in AD. We previously have found that amyloid fibrils in vascular amyloid contain antiparallel β-sheet, whereas previous studies by other researchers have reported parallel β-sheet in fibrils from parenchymal amyloid. Using X-ray fluorescence microscopy, here we found that copper strongly co-localizes with vascular amyloid in human sporadic CAA and familial Iowa-type CAA brains compared with control brain blood vessels lacking amyloid deposits. We show that binding of Cu(II) ions to antiparallel fibrils can block the conversion of these fibrils to the more stable parallel, in-register conformation and enhances their ability to serve as templates for seeded growth. These results provide an explanation for how thermodynamically less stable antiparallel fibrils may form amyloid in or on cerebral vessels by using Cu(II) as a structural cofactor.
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Affiliation(s)
- Elliot J Crooks
- Department of Biochemistry and Cell Biology, Center for Structural Biology, Stony Brook University, Stony Brook, New York, USA
| | - Brandon A Irizarry
- Department of Biochemistry and Cell Biology, Center for Structural Biology, Stony Brook University, Stony Brook, New York, USA
| | - Martine Ziliox
- Department of Biochemistry and Cell Biology, Center for Structural Biology, Stony Brook University, Stony Brook, New York, USA
| | - Toru Kawakami
- Institute for Protein Research, Osaka University, Suita, Osaka, Japan
| | - Tiffany Victor
- National Synchrotron Light Source II, Brookhaven National Laboratory, Upton, New York, USA
| | - Feng Xu
- George & Anne Ryan Institute for Neuroscience and Department of Biomedical and Pharmaceutical Sciences, University of Rhode Island, Kingston, Rhode Island, USA
| | - Hironobu Hojo
- Institute for Protein Research, Osaka University, Suita, Osaka, Japan
| | - Kelley Chiu
- Department of Chemistry, Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, New York, USA
| | - Carlos Simmerling
- Department of Chemistry, Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, New York, USA
| | - William E Van Nostrand
- George & Anne Ryan Institute for Neuroscience and Department of Biomedical and Pharmaceutical Sciences, University of Rhode Island, Kingston, Rhode Island, USA
| | - Steven O Smith
- Department of Biochemistry and Cell Biology, Center for Structural Biology, Stony Brook University, Stony Brook, New York, USA.
| | - Lisa M Miller
- National Synchrotron Light Source II, Brookhaven National Laboratory, Upton, New York, USA; Department of Chemistry, Laufer Center for Physical and Quantitative Biology, Stony Brook University, Stony Brook, New York, USA
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30
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Brunello CA, Merezhko M, Uronen RL, Huttunen HJ. Mechanisms of secretion and spreading of pathological tau protein. Cell Mol Life Sci 2020; 77:1721-1744. [PMID: 31667556 PMCID: PMC7190606 DOI: 10.1007/s00018-019-03349-1] [Citation(s) in RCA: 163] [Impact Index Per Article: 40.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Revised: 10/10/2019] [Accepted: 10/16/2019] [Indexed: 12/12/2022]
Abstract
Accumulation of misfolded and aggregated forms of tau protein in the brain is a neuropathological hallmark of tauopathies, such as Alzheimer's disease and frontotemporal lobar degeneration. Tau aggregates have the ability to transfer from one cell to another and to induce templated misfolding and aggregation of healthy tau molecules in previously healthy cells, thereby propagating tau pathology across different brain areas in a prion-like manner. The molecular mechanisms involved in cell-to-cell transfer of tau aggregates are diverse, not mutually exclusive and only partially understood. Intracellular accumulation of misfolded tau induces several mechanisms that aim to reduce the cellular burden of aggregated proteins and also promote secretion of tau aggregates. However, tau may also be released from cells physiologically unrelated to protein aggregation. Tau secretion involves multiple vesicular and non-vesicle-mediated pathways, including secretion directly through the plasma membrane. Consequently, extracellular tau can be found in various forms, both as a free protein and in vesicles, such as exosomes and ectosomes. Once in the extracellular space, tau aggregates can be internalized by neighboring cells, both neurons and glial cells, via endocytic, pinocytic and phagocytic mechanisms. Importantly, accumulating evidence suggests that prion-like propagation of misfolding protein pathology could provide a general mechanism for disease progression in tauopathies and other related neurodegenerative diseases. Here, we review the recent literature on cellular mechanisms involved in cell-to-cell transfer of tau, with a particular focus in tau secretion.
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Affiliation(s)
- Cecilia A Brunello
- Neuroscience Center, HiLIFE, University of Helsinki, P.O. Box 63, Haartmaninkatu 8, 00014, Helsinki, Finland
| | - Maria Merezhko
- Neuroscience Center, HiLIFE, University of Helsinki, P.O. Box 63, Haartmaninkatu 8, 00014, Helsinki, Finland
| | - Riikka-Liisa Uronen
- Neuroscience Center, HiLIFE, University of Helsinki, P.O. Box 63, Haartmaninkatu 8, 00014, Helsinki, Finland
| | - Henri J Huttunen
- Neuroscience Center, HiLIFE, University of Helsinki, P.O. Box 63, Haartmaninkatu 8, 00014, Helsinki, Finland.
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31
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L. Almeida Z, M. M. Brito R. Structure and Aggregation Mechanisms in Amyloids. Molecules 2020; 25:molecules25051195. [PMID: 32155822 PMCID: PMC7179426 DOI: 10.3390/molecules25051195] [Citation(s) in RCA: 97] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Revised: 02/17/2020] [Accepted: 02/19/2020] [Indexed: 12/27/2022] Open
Abstract
The aggregation of a polypeptide chain into amyloid fibrils and their accumulation and deposition into insoluble plaques and intracellular inclusions is the hallmark of several misfolding diseases known as amyloidoses. Alzheimer′s, Parkinson′s and Huntington’s diseases are some of the approximately 50 amyloid diseases described to date. The identification and characterization of the molecular species critical for amyloid formation and disease development have been the focus of intense scrutiny. Methods such as X-ray and electron diffraction, solid-state nuclear magnetic resonance spectroscopy (ssNMR) and cryo-electron microscopy (cryo-EM) have been extensively used and they have contributed to shed a new light onto the structure of amyloid, revealing a multiplicity of polymorphic structures that generally fit the cross-β amyloid motif. The development of rational therapeutic approaches against these debilitating and increasingly frequent misfolding diseases requires a thorough understanding of the molecular mechanisms underlying the amyloid cascade. Here, we review the current knowledge on amyloid fibril formation for several proteins and peptides from a kinetic and thermodynamic point of view, the structure of the molecular species involved in the amyloidogenic process, and the origin of their cytotoxicity.
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32
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Xiao Y, Matsuda I, Inoue M, Sasahara T, Hoshi M, Ishii Y. NMR-based site-resolved profiling of β-amyloid misfolding reveals structural transitions from pathologically relevant spherical oligomer to fibril. J Biol Chem 2019; 295:458-467. [PMID: 31771980 DOI: 10.1074/jbc.ra119.008522] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Revised: 11/12/2019] [Indexed: 11/06/2022] Open
Abstract
Increasing evidence highlights the central role of neurotoxic oligomers of the 42-residue-long β-amyloid (Aβ42) in Alzheimer's disease (AD). However, very limited information is available on the structural transition from oligomer to fibril, particularly for pathologically relevant amyloids. To the best of our knowledge, we present here the first site-specific structural characterization of Aβ42 misfolding, from toxic oligomeric assembly yielding a similar conformation to an AD-associated Aβ42 oligomer, into a fibril. Transmission EM (TEM) analysis revealed that a spherical amyloid assembly (SPA) of Aβ42 with a 15.6 ± 2.1-nm diameter forms in a ∼30-μm Aβ42 solution after a ∼10-h incubation at 4 °C, followed by a slow conversion into fibril at ∼180 h. Immunological analysis suggested that the SPA has a surface structure similar to that of amylospheroid (ASPD), a patient-derived toxic Aβ oligomer, which had a diameter of 10-15 nm in negative-stain TEM. Solid-state NMR analyses indicated that the SPA structure involves a β-loop-β motif, which significantly differed from the triple-β motif observed for the Aβ42 fibril. The comparison of the 13C chemical shifts of SPA with those of the fibril prepared in the above conditions and interstrand distance measurements suggested a large conformational change involving rearrangements of intermolecular β-sheet into in-register parallel β-sheet during the misfolding. A comparison of the SPA and ASPD 13C chemical shifts indicated that SPA is structurally similar to the ASPD relevant to AD. These observations provide insights into the architecture and key structural transitions of amyloid oligomers relevant for AD pathology.
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Affiliation(s)
- Yiling Xiao
- Department of Chemistry, University of Illinois, Chicago, Illinois 60607
| | - Isamu Matsuda
- Department of Chemistry, University of Illinois, Chicago, Illinois 60607; School of Life Science and Technology, Tokyo Institute of Technology, 4259 Midori-ku, Yokohama, Kanagawa 226-8503, Japan
| | - Masafumi Inoue
- TAO Health Life Pharma Co. Ltd., Med-Pharma Collaboration Building, Kyoto University Graduate School of Medicine, Kyoto 606-8501, Japan; Department of System Pathology for Neurological Disorders, Center for Bioresources, Brain Research Institute, Niigata University, 1-757 Asahimachidori, Chuo-ku, Niigata 951-8585, Japan
| | - Tomoya Sasahara
- TAO Health Life Pharma Co. Ltd., Med-Pharma Collaboration Building, Kyoto University Graduate School of Medicine, Kyoto 606-8501, Japan; Department for Brain and Neurodegenerative Disease Research, Institute of Biomedical Research and Innovation, Foundation for Biomedical Research and Innovation at Kobe, Hyogo 650-0047, Japan
| | - Minako Hoshi
- Department for Brain and Neurodegenerative Disease Research, Institute of Biomedical Research and Innovation, Foundation for Biomedical Research and Innovation at Kobe, Hyogo 650-0047, Japan; Department of Anatomy and Developmental Biology, Graduate School of Medicine, Kyoto University, Kyoto 606-8501, Japan
| | - Yoshitaka Ishii
- Department of Chemistry, University of Illinois, Chicago, Illinois 60607; School of Life Science and Technology, Tokyo Institute of Technology, 4259 Midori-ku, Yokohama, Kanagawa 226-8503, Japan; NMR Science and Development Division, RIKEN SPring-8 Center (RSC), RIKEN, 1-7-22 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan.
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33
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Barton J, Arias DS, Niyangoda C, Borjas G, Le N, Mohamed S, Muschol M. Kinetic Transition in Amyloid Assembly as a Screening Assay for Oligomer-Selective Dyes. Biomolecules 2019; 9:biom9100539. [PMID: 31569739 PMCID: PMC6843685 DOI: 10.3390/biom9100539] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Revised: 09/24/2019] [Accepted: 09/25/2019] [Indexed: 02/06/2023] Open
Abstract
Assembly of amyloid fibrils and small globular oligomers is associated with a significant number of human disorders that include Alzheimer’s disease, senile systemic amyloidosis, and type II diabetes. Recent findings implicate small amyloid oligomers as the dominant aggregate species mediating the toxic effects in these disorders. However, validation of this hypothesis has been hampered by the dearth of experimental techniques to detect, quantify, and discriminate oligomeric intermediates from late-stage fibrils, in vitro and in vivo. We have shown that the onset of significant oligomer formation is associated with a transition in thioflavin T kinetics from sigmoidal to biphasic kinetics. Here we showed that this transition can be exploited for screening fluorophores for preferential responses to oligomer over fibril formation. This assay identified crystal violet as a strongly selective oligomer-indicator dye for lysozyme. Simultaneous recordings of amyloid kinetics with thioflavin T and crystal violet enabled us to separate the combined signals into their underlying oligomeric and fibrillar components. We provided further evidence that this screening assay could be extended to amyloid-β peptides under physiological conditions. Identification of oligomer-selective dyes not only holds the promise of biomedical applications but provides new approaches for unraveling the mechanisms underlying oligomer versus fibril formation in amyloid assembly.
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Affiliation(s)
- Jeremy Barton
- Department of Physics, University of South Florida, Tampa, FL 33620, USA.
| | - D Sebastian Arias
- Department of Physics, University of South Florida, Tampa, FL 33620, USA.
| | - Chamani Niyangoda
- Department of Physics, University of South Florida, Tampa, FL 33620, USA.
| | - Gustavo Borjas
- Department of Physics, University of South Florida, Tampa, FL 33620, USA.
| | - Nathan Le
- Department of Physics, University of South Florida, Tampa, FL 33620, USA.
| | - Saefallah Mohamed
- Department of Physics, University of South Florida, Tampa, FL 33620, USA.
| | - Martin Muschol
- Department of Physics, University of South Florida, Tampa, FL 33620, USA.
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34
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Mrdenovic D, Majewska M, Pieta IS, Bernatowicz P, Nowakowski R, Kutner W, Lipkowski J, Pieta P. Size-Dependent Interaction of Amyloid β Oligomers with Brain Total Lipid Extract Bilayer-Fibrillation Versus Membrane Destruction. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2019; 35:11940-11949. [PMID: 31328526 DOI: 10.1021/acs.langmuir.9b01645] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Amyloid β, Aβ(1-42), is a component of senile plaques present in the brain of Alzheimer's disease patients and one of the main suspects responsible for pathological consequences of the disease. Herein, we directly visualize the Aβ activity toward a brain-like model membrane and demonstrate that this activity strongly depends on the Aβ oligomer size. PeakForce quantitative nanomechanical mapping mode of atomic force microscopy imaging revealed that the interaction of large-size (LS) Aβ oligomers, corresponding to high-molecular-weight Aβ oligomers, with the brain total lipid extract (BTLE) membrane resulted in accelerated Aβ fibrillogenesis on the membrane surface. Importantly, the fibrillogenesis did not affect integrity of the membrane. In contrast, small-size (SS) Aβ oligomers, corresponding to low-molecular-weight Aβ oligomers, created pores and then disintegrated the BTLE membrane. Both forms of the Aβ oligomers changed nanomechanical properties of the membrane by decreasing its Young's modulus by ∼45%. Our results demonstrated that both forms of Aβ oligomers induce the neurotoxic effect on the brain cells but their action toward the membrane differs significantly.
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Affiliation(s)
- Dusan Mrdenovic
- Institute of Physical Chemistry , Polish Academy of Sciences , Kasprzaka 44/52 , 01-224 Warsaw , Poland
- Department of Chemistry , University of Guelph , 50 Stone Road East , Guelph , Ontario N1G 2W1 , Canada
| | - Marta Majewska
- Institute of Physical Chemistry , Polish Academy of Sciences , Kasprzaka 44/52 , 01-224 Warsaw , Poland
| | - Izabela S Pieta
- Institute of Physical Chemistry , Polish Academy of Sciences , Kasprzaka 44/52 , 01-224 Warsaw , Poland
| | - Piotr Bernatowicz
- Institute of Physical Chemistry , Polish Academy of Sciences , Kasprzaka 44/52 , 01-224 Warsaw , Poland
| | - Robert Nowakowski
- Institute of Physical Chemistry , Polish Academy of Sciences , Kasprzaka 44/52 , 01-224 Warsaw , Poland
| | - Wlodzimierz Kutner
- Institute of Physical Chemistry , Polish Academy of Sciences , Kasprzaka 44/52 , 01-224 Warsaw , Poland
- Faculty of Mathematics and Natural Sciences, School of Sciences , Cardinal Stefan Wyszynski University in Warsaw , Wóycickiego 1/3 , 01-815 Warsaw , Poland
| | - Jacek Lipkowski
- Department of Chemistry , University of Guelph , 50 Stone Road East , Guelph , Ontario N1G 2W1 , Canada
| | - Piotr Pieta
- Institute of Physical Chemistry , Polish Academy of Sciences , Kasprzaka 44/52 , 01-224 Warsaw , Poland
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35
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Morel B, Conejero-Lara F. Early mechanisms of amyloid fibril nucleation in model and disease-related proteins. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2019; 1867:140264. [PMID: 31437584 DOI: 10.1016/j.bbapap.2019.140264] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Revised: 07/18/2019] [Accepted: 08/12/2019] [Indexed: 02/06/2023]
Abstract
Protein amyloid aggregation is a hallmark in neuropathologies and other diseases of tremendous impact such as Alzheimer's or Parkinson's diseases. During the last decade, it has become increasingly evident that neuronal death is mainly induced by proteinaceous oligomers rather than the mature amyloid fibrils. Therefore, the earliest molecular events occurring during the amyloid aggregation cascade represent a growing interest of study. Important breakthroughs have been achieved using experimental data from different proteins, used as models, as well as systems related to diseases. Here, we summarize the structural properties of amyloid oligomeric and fibrillar aggregates and review the recent advances on how biophysical techniques can be combined with quantitative kinetic analysis and theoretical models to study the detailed mechanism of oligomer formation and nucleation of fibrils. These insights into the mechanism of early oligomerization and amyloid nucleation are of relevant interest in drug discovery and in the design of preventive strategies against neurodegenerative diseases.
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Affiliation(s)
- Bertrand Morel
- Departamento de Química Física e Instituto de Biotecnología, Universidad de Granada, 18071 Granada, Spain.
| | - Francisco Conejero-Lara
- Departamento de Química Física e Instituto de Biotecnología, Universidad de Granada, 18071 Granada, Spain
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36
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Trumbore CN. Shear-Induced Amyloid Formation in the Brain: III. The Roles of Shear Energy and Seeding in a Proposed Shear Model. J Alzheimers Dis 2019; 65:47-70. [PMID: 30040710 PMCID: PMC6087447 DOI: 10.3233/jad-171003] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
If cerebrospinal and interstitial fluids move through very narrow brain flow channels, these restrictive surroundings generate varying levels of fluid shear and different shear rates, and dissolved amyloid monomers absorb different shear energies. It is proposed that dissolved amyloid-β protein (Aβ) and other amyloid monomers undergo shear-induced conformational changes that ultimately lead to amyloid monomer aggregation even at very low brain flow and shear rates. Soluble Aβ oligomers taken from diseased brains initiate in vivo amyloid formation in non-diseased brains. The brain environment is apparently responsible for this result. A mechanism involving extensional shear is proposed for the formation of a seed Aβ monomer molecule that ultimately promotes templated conformational change of other Aβ molecules. Under non-quiescent, non-equilibrium conditions, gentle extensional shear within the brain parenchyma, and perhaps even during laboratory preparation of Aβ samples, may be sufficient to cause subtle conformational changes in these monomers. These result from brain processes that significantly lower the high activation energy predicted for the quiescent Aβ dimerization process. It is further suggested that changes in brain location and changes brought about by aging expose Aβ molecules to different shear rates, total shear, and types of shear, resulting in different conformational changes in these molecules. The consequences of such changes caused by variable shear energy are proposed to underlie formation of amyloid strains causing different amyloid diseases. Amyloid researchers are urged to undertake studies with amyloids, anti-amyloid drugs, and antibodies while all of these are under shear conditions similar to those in the brain.
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Affiliation(s)
- Conrad N Trumbore
- Department of Chemistry and Biochemistry, University of Delaware, Newark, DE, USA
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37
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Vivoli Vega M, Cascella R, Chen SW, Fusco G, De Simone A, Dobson CM, Cecchi C, Chiti F. The Toxicity of Misfolded Protein Oligomers Is Independent of Their Secondary Structure. ACS Chem Biol 2019; 14:1593-1600. [PMID: 31074957 DOI: 10.1021/acschembio.9b00324] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The self-assembly of proteins into structured fibrillar aggregates is associated with a range of neurodegenerative diseases, including Alzheimer's and Parkinson's diseases, in which an important cytotoxic role is thought to be played by small soluble oligomers accumulating during the aggregation process or released by mature fibrils. As the structural characteristics of such species and their links with toxicity are still not fully defined, we have compared six examples of preformed misfolded protein oligomers with different β-sheet content, as determined using Fourier transform infrared spectroscopy, and with different toxicity, as determined by three cellular readouts of cell viability. The results show the absence of any measurable correlation between the nature of their secondary structure and their cellular toxicity, both when comparing the six types of oligomers as a group and when comparing species in subgroups characterized by either the same size or the same exposure of hydrophobic moieties.
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Affiliation(s)
- Mirella Vivoli Vega
- Department of Experimental and Clinical Biomedical Sciences, Section of Biochemistry, University of Florence, 50134 Florence, Italy
| | - Roberta Cascella
- Department of Experimental and Clinical Biomedical Sciences, Section of Biochemistry, University of Florence, 50134 Florence, Italy
| | - Serene W Chen
- Department of Life Sciences, Imperial College London, London SW7 2AZ, U.K
| | - Giuliana Fusco
- Centre for Misfolding disease, Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, U.K
| | - Alfonso De Simone
- Department of Life Sciences, Imperial College London, London SW7 2AZ, U.K
| | - Christopher M. Dobson
- Centre for Misfolding disease, Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, U.K
| | - Cristina Cecchi
- Department of Experimental and Clinical Biomedical Sciences, Section of Biochemistry, University of Florence, 50134 Florence, Italy
| | - Fabrizio Chiti
- Department of Experimental and Clinical Biomedical Sciences, Section of Biochemistry, University of Florence, 50134 Florence, Italy
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38
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Xue C, Tran J, Wang H, Park G, Hsu F, Guo Z. Aβ42 fibril formation from predominantly oligomeric samples suggests a link between oligomer heterogeneity and fibril polymorphism. ROYAL SOCIETY OPEN SCIENCE 2019; 6:190179. [PMID: 31417723 PMCID: PMC6689619 DOI: 10.1098/rsos.190179] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Accepted: 06/10/2019] [Indexed: 05/27/2023]
Abstract
Amyloid-β (Aβ) oligomers play a central role in the pathogenesis of Alzheimer's disease. Oligomers of different sizes, morphology and structures have been reported in both in vivo and in vitro studies, but there is a general lack of understanding about where to place these oligomers in the overall process of Aβ aggregation and fibrillization. Here, we show that Aβ42 spontaneously forms oligomers with a wide range of sizes in the same sample. These Aβ42 samples contain predominantly oligomers, and they quickly form fibrils upon incubation at 37°C. When fractionated using ultrafiltration filters, the samples enriched with smaller oligomers form fibrils at a faster rate than the samples enriched with larger oligomers, with both a shorter lag time and faster fibril growth rate. This observation is independent of Aβ42 batches and hexafluoroisopropanol treatment. Furthermore, the fibrils formed by the samples enriched with larger oligomers are more readily solubilized by epigallocatechin gallate, a main catechin component of green tea. These results suggest that the fibrils formed by larger oligomers may adopt a different structure from fibrils formed by smaller oligomers, pointing to a link between oligomer heterogeneity and fibril polymorphism.
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Affiliation(s)
| | | | | | | | | | - Zhefeng Guo
- Department of Neurology, Brain Research Institute, Molecular Biology Institute, University of California, 710 Westwood Plaza, Los Angeles, CA 90095, USA
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39
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Zhang T, Loschwitz J, Strodel B, Nagel-Steger L, Willbold D. Interference with Amyloid-β Nucleation by Transient Ligand Interaction. Molecules 2019; 24:E2129. [PMID: 31195746 PMCID: PMC6600523 DOI: 10.3390/molecules24112129] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Revised: 06/02/2019] [Accepted: 06/04/2019] [Indexed: 12/20/2022] Open
Abstract
Amyloid-β peptide (Aβ) is an intrinsically disordered protein (IDP) associated with Alzheimer's disease. The structural flexibility and aggregation propensity of Aβ pose major challenges for elucidating the interaction between Aβ monomers and ligands. All-D-peptides consisting solely of D-enantiomeric amino acid residues are interesting drug candidates that combine high binding specificity with high metabolic stability. Here we characterized the interaction between the 12-residue all-D-peptide D3 and Aβ42 monomers, and how the interaction influences Aβ42 aggregation. We demonstrate for the first time that D3 binds to Aβ42 monomers with submicromolar affinities. These two highly unstructured molecules are able to form complexes with 1:1 and other stoichiometries. Further, D3 at substoichiometric concentrations effectively slows down the β-sheet formation and Aβ42 fibrillation by modulating the nucleation process. The study provides new insights into the molecular mechanism of how D3 affects Aβ assemblies and contributes to our knowledge on the interaction between two IDPs.
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Affiliation(s)
- Tao Zhang
- Institute of Complex Systems, Structural Biochemistry (ICS-6), Forschungszentrum Jülich, 52425 Jülich, Germany.
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, 40225 Düsseldorf, Germany.
| | - Jennifer Loschwitz
- Institute of Complex Systems, Structural Biochemistry (ICS-6), Forschungszentrum Jülich, 52425 Jülich, Germany.
- Institute of Theoretical and Computational Chemistry, Heinrich-Heine-Universität Düsseldorf, 40225 Düsseldorf, Germany.
| | - Birgit Strodel
- Institute of Complex Systems, Structural Biochemistry (ICS-6), Forschungszentrum Jülich, 52425 Jülich, Germany.
- Institute of Theoretical and Computational Chemistry, Heinrich-Heine-Universität Düsseldorf, 40225 Düsseldorf, Germany.
| | - Luitgard Nagel-Steger
- Institute of Complex Systems, Structural Biochemistry (ICS-6), Forschungszentrum Jülich, 52425 Jülich, Germany.
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, 40225 Düsseldorf, Germany.
| | - Dieter Willbold
- Institute of Complex Systems, Structural Biochemistry (ICS-6), Forschungszentrum Jülich, 52425 Jülich, Germany.
- Institut für Physikalische Biologie, Heinrich-Heine-Universität Düsseldorf, 40225 Düsseldorf, Germany.
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Cieplak AS. Tau Inclusions in Alzheimer's, Chronic Traumatic Encephalopathy and Pick's Disease. A Speculation on How Differences in Backbone Polarization Underlie Divergent Pathways of Tau Aggregation. Front Neurosci 2019; 13:488. [PMID: 31156372 PMCID: PMC6530265 DOI: 10.3389/fnins.2019.00488] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Accepted: 04/29/2019] [Indexed: 12/13/2022] Open
Abstract
Tau-related dementias appear to involve specific to each disease aggregation pathways and morphologies of filamentous tau assemblies. To understand etiology of these differences, here we elucidate molecular mechanism of formation of tau PHFs based on the PMO theory of misfolding and aggregation of pleiomorphic proteins associated with neurodegenerative diseases. In this model, fibrillization of tau is initiated by the coupled binding and folding of the MTB domains that yields antiparallel homodimers, in analogy to folding of split inteins. The free energy of binding is minimized when the antiparallel alignment brings about backbone-backbone H-bonding between the MTBD segments of similar "strand" propensities. To assess these propensities, a function of the NMR shielding tensors of the Cα atoms is introduced as the folding potential function FP i ; the Cα tensors are obtained by the quantum mechanical modeling of protein secondary structure (GIAO//B3LYP/D95**). The calculated FP i plots show that the "strand" propensities of the MBTD segments, and hence the homodimer's register, can be affected by the relatively small changes in the environment's pH, as a result of protonation of MBTD's conserved histidines. The assembly of the antiparallel tau dimers into granular aggregates and their subsequent conversion into the parallel cross-β structure of paired helical filaments is expected to follow the same path as the previously described fibrillization of Aβ. Consequently, the core structure of the nascent tau fibril is determined by the register of the tau homodimer. This model accounts for the reported differences in (i) fibril-core structure of in vivo and in vitro filaments, (ii) cross-seeding of isoforms, (iii) effects of reducing/non-reducing conditions, (iv) effects of PHF6 mutations, and (v) homologs' aggregation properties. The proposed model also suggests that in contrast to Alzheimer's and chronic traumatic encephalopathy disease, the assembly of tau prions in Pick's disease would be facilitated by a moderate drop in pH that accompanies e.g., transit in the endosomal system, inflammation response or an ischemic injury.
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Affiliation(s)
- Andrzej Stanisław Cieplak
- Department of Chemistry, Bilkent University, Ankara, Turkey
- Department of Chemistry, Yale University, New Haven, CT, United States
- Department of Chemistry, Brandeis University, Waltham, MA, United States
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41
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Influence of crowding and surfaces on protein amyloidogenesis: A thermo-kinetic perspective. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2019; 1867:941-953. [PMID: 30928692 DOI: 10.1016/j.bbapap.2019.03.009] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Revised: 03/22/2019] [Accepted: 03/23/2019] [Indexed: 01/24/2023]
Abstract
The last few decades have irreversibly implicated protein self-assembly and aggregation leading to amyloid fibril formation in proteopathies that include several neurodegenerative diseases. Emerging studies recognize the importance of eliciting the pathways leading to protein aggregation in the context of the crowded intracellular environment rather than in conventional in vitro conditions. It is found that crowded environments can have acceleratory as well as inhibitory effects on protein aggregation, depending on the interplay of underlying factors on the crucial rate limiting steps. The aggregation mechanism and transient species formed along the pathway are further altered when they interface with natural and artificial surfaces in the cellular milieu. An increasing number of studies probe the autocatalytic nature of amyloid surfaces as well as membrane bilayer effects on amyloidogenesis. Moreover, exposure to modern nanosurfaces via nanomedicines and other sources potentially invokes beneficial or deleterious biological response that needs rigorous investigation. Mounting evidences indicate that nanoparticles can either promote or impede amyloid aggregation, spurring efforts to tune their interactions for developing effective anti-amyloid strategies. Mechanistic insights into nanoparticle mediated aggregation pathways are therefore crucial for engineering anti-amyloid nanoparticle strategies that are biocompatible and sustainable. This review is a compilation of studies that contribute to the current understanding of the altering effects of molecular crowding as well as natural and artificial surfaces on protein amyloidogenesis.
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42
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Xi W, Dean DN, Stockmal KA, Morgan SE, Hansmann UHE, Rangachari V. Large fatty acid-derived Aβ42 oligomers form ring-like assemblies. J Chem Phys 2019; 150:075101. [PMID: 30795679 DOI: 10.1063/1.5082659] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
As the primary toxic species in the etiology of Alzheimer disease (AD) are low molecular weight oligomers of Aβ, it is crucial to understand the structure of Aβ oligomers for gaining molecular insights into AD pathology. We have earlier demonstrated that in the presence of fatty acids, Aβ42 peptides assemble as 12-24mer oligomers. These Large Fatty Acid-derived Oligomers (LFAOs) exist predominantly as 12mers at low and as 24mers at high concentrations. The 12mers are more neurotoxic than the 24mers and undergo self-replication, while the latter propagate to morphologically distinct fibrils with succinct pathological consequences. In order to glean into their functional differences and similarities, we have determined their structures in greater detail by combining molecular dynamic simulations with biophysical measurements. We conjecture that the LFAO are made of Aβ units in an S-shaped conformation, with the 12mers forming a double-layered hexamer ring (6 × 2) while the structure of 24mers is a double-layered dodecamer ring (12 × 2). A closer inspection of the (6 × 2) and (12 × 2) structures reveals a concentration and pH dependent molecular reorganization in the assembly of 12 to 24mers, which seems to be the underlying mechanism for the observed biophysical and cellular properties of LFAOs.
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Affiliation(s)
- Wenhui Xi
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73019, USA
| | - Dexter N Dean
- Department of Chemistry and Biochemistry, University of Southern Mississippi, Hattiesburg, Mississippi 39406, USA
| | - Kelli A Stockmal
- School of Polymer Science and Engineering, University of Southern Mississippi, Hattiesburg, Mississippi 39406, USA
| | - Sarah E Morgan
- School of Polymer Science and Engineering, University of Southern Mississippi, Hattiesburg, Mississippi 39406, USA
| | - Ulrich H E Hansmann
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, Oklahoma 73019, USA
| | - Vijayaraghavan Rangachari
- Department of Chemistry and Biochemistry, University of Southern Mississippi, Hattiesburg, Mississippi 39406, USA
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43
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Ahmed I, Jones EM. Importance of micelle‐like multimers in the atypical aggregation kinetics of N‐terminal serum amyloid A peptides. FEBS Lett 2019; 593:518-526. [DOI: 10.1002/1873-3468.13334] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Revised: 02/06/2019] [Accepted: 02/07/2019] [Indexed: 11/06/2022]
Affiliation(s)
- Ikhlaus Ahmed
- Department of Chemistry and Biochemistry California Polytechnic State University San Luis Obispo CA USA
| | - Eric M. Jones
- Department of Chemistry and Biochemistry California Polytechnic State University San Luis Obispo CA USA
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44
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Menadione sodium bisulfite inhibits the toxic aggregation of amyloid-β(1–42). Biochim Biophys Acta Gen Subj 2018; 1862:2226-2235. [DOI: 10.1016/j.bbagen.2018.07.019] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2018] [Revised: 06/22/2018] [Accepted: 07/17/2018] [Indexed: 12/16/2022]
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45
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Przygońska K, Poznański J, Mistarz UH, Rand KD, Dadlez M. Side-chain moieties from the N-terminal region of Aβ are Involved in an oligomer-stabilizing network of interactions. PLoS One 2018; 13:e0201761. [PMID: 30080867 PMCID: PMC6078298 DOI: 10.1371/journal.pone.0201761] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Accepted: 07/20/2018] [Indexed: 12/31/2022] Open
Abstract
Oligomeric forms of the Aβ peptide represent the most probable neurotoxic agent in Alzheimer’s disease. The dynamic and heterogeneous character of these oligomers makes their structural characterization by classic methods difficult. Native mass spectrometry, when supported by additional gas phase techniques, like ion mobility separation and hydrogen-deuterium exchange (IM-HDX-MS), enable analysis of different oligomers coexisting in the sample and may provide species-specific structural information for each oligomeric form populated in the gas phase. Here, we have combined these three techniques to obtain insight into the structural properties of oligomers of Aβ1–40 and two variants with scrambled sequences. Gas-phase HDX-MS revealed a sequence-specific engagement of the side-chains of residues located at the N-terminal part of the peptide in a network of oligomer-stabilizing interactions. Oligomer-specific interactions were no longer observed in the case of the fully scrambled sequence. Also, the ability to form alternative structures, observed for WT Aβ peptide, was lost upon scrambling. Our data underscore a role for the N-terminal residues in shaping the equilibria of oligomeric forms. Although the peptide lacking the N-terminal 1–16 residues (p3 peptide) is thought to be benign, the role of the N-terminus has not been sufficiently characterized yet. We speculate that the interaction networks revealed here may be crucial for enabling structural transitions necessary to obtain mature parallel cross-β structures from smaller antiparallel oligomers. We provide a hypothetical molecular model of the trajectory that allows a gradual conversion from antiparallel to parallel oligomers without decomposition of oligomers. Oligomer-defining interactions involving the Aβ peptide N-terminus may be important in production of the neurotoxic forms and thus should not be neglected.
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Affiliation(s)
- Kaja Przygońska
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Jarosław Poznański
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
| | - Ulrik H. Mistarz
- Department of Pharmacy, University of Copenhagen, Copenhagen, Denmark
| | - Kasper D. Rand
- Department of Pharmacy, University of Copenhagen, Copenhagen, Denmark
| | - Michał Dadlez
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Warsaw, Poland
- Institute of Genetics and Biotechnology, Department of Biology, University of Warsaw, Warsaw, Poland
- * E-mail:
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46
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Hsu F, Park G, Guo Z. Key Residues for the Formation of Aβ42 Amyloid Fibrils. ACS OMEGA 2018; 3:8401-8407. [PMID: 30087945 PMCID: PMC6068601 DOI: 10.1021/acsomega.8b00887] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Accepted: 07/17/2018] [Indexed: 05/27/2023]
Abstract
Formation of amyloid fibrils by Aβ42 protein is a pathological hallmark of Alzheimer's disease. Aβ42 fibrillization is a nucleation-dependent polymerization process, in which nucleation is the rate-limiting step. Structural knowledge of the fibril nucleus is important to understand the molecular mechanism of Aβ aggregation and is also critical for successful modulation of the fibrillization process. Here, we used a scanning mutagenesis approach to study the role of each residue position in Aβ42 fibrillization kinetics. The side chain we used to replace the native residue is a nitroxide spin label called R1, which was introduced using site-directed spin labeling. In this systematic study, all residue positions of Aβ42 sequence were studied, and we identified six key residues for the Aβ42 fibril formation: H14, E22, D23, G33, G37, and G38. Our results suggest that charges at positions 22 and 23 and backbone flexibilities at positions 33, 37, and 38 play key roles in Aβ42 fibrillization kinetics. Our results also suggest that the formation of a β-strand at residues 15-21 is an important feature in Aβ42 fibril nucleus. In overall evaluation of all of the mutational effects on fibrillization kinetics, we found that the thioflavin T fluorescence at the aggregation plateau is a poor indicator of aggregation rates.
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47
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Hasecke F, Miti T, Perez C, Barton J, Schölzel D, Gremer L, Grüning CSR, Matthews G, Meisl G, Knowles TPJ, Willbold D, Neudecker P, Heise H, Ullah G, Hoyer W, Muschol M. Origin of metastable oligomers and their effects on amyloid fibril self-assembly. Chem Sci 2018; 9:5937-5948. [PMID: 30079208 PMCID: PMC6050532 DOI: 10.1039/c8sc01479e] [Citation(s) in RCA: 70] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2018] [Accepted: 06/12/2018] [Indexed: 01/05/2023] Open
Abstract
Assembly of rigid amyloid fibrils with their characteristic cross-β sheet structure is a molecular signature of numerous neurodegenerative and non-neuropathic disorders. Frequently large populations of small globular amyloid oligomers (gOs) and curvilinear fibrils (CFs) precede the formation of late-stage rigid fibrils (RFs), and have been implicated in amyloid toxicity. Yet our understanding of the origin of these metastable oligomers, their role as on-pathway precursors or off-pathway competitors, and their effects on the self-assembly of amyloid fibrils remains incomplete. Using two unrelated amyloid proteins, amyloid-β and lysozyme, we find that gO/CF formation, analogous to micelle formation by surfactants, is delineated by a "critical oligomer concentration" (COC). Below this COC, fibril assembly replicates the sigmoidal kinetics of nucleated polymerization. Upon crossing the COC, assembly kinetics becomes biphasic with gO/CF formation responsible for the lag-free initial phase, followed by a second upswing dominated by RF nucleation and growth. RF lag periods below the COC, as expected, decrease as a power law in monomer concentration. Surprisingly, the build-up of gO/CFs above the COC causes a progressive increase in RF lag periods. Our results suggest that metastable gO/CFs are off-pathway from RF formation, confined by a condition-dependent COC that is distinct from RF solubility, underlie a transition from sigmoidal to biphasic assembly kinetics and, most importantly, not only compete with RFs for the shared monomeric growth substrate but actively inhibit their nucleation and growth.
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Affiliation(s)
- Filip Hasecke
- Institut für Physikalische Biologie , Heinrich-Heine-Universität , 40204 Düsseldorf , Germany .
| | - Tatiana Miti
- Department of Physics , University of South Florida , Tampa , FL 33620 , USA .
| | - Carlos Perez
- Department of Physics , University of South Florida , Tampa , FL 33620 , USA .
| | - Jeremy Barton
- Department of Physics , University of South Florida , Tampa , FL 33620 , USA .
| | - Daniel Schölzel
- Institut für Physikalische Biologie , Heinrich-Heine-Universität , 40204 Düsseldorf , Germany .
- Institute of Complex Systems (ICS-6) , Structural Biochemistry , Research Centre Jülich , Germany
| | - Lothar Gremer
- Institut für Physikalische Biologie , Heinrich-Heine-Universität , 40204 Düsseldorf , Germany .
- Institute of Complex Systems (ICS-6) , Structural Biochemistry , Research Centre Jülich , Germany
| | - Clara S R Grüning
- Institut für Physikalische Biologie , Heinrich-Heine-Universität , 40204 Düsseldorf , Germany .
| | - Garrett Matthews
- Department of Physics , University of South Florida , Tampa , FL 33620 , USA .
| | - Georg Meisl
- Department of Chemistry , University of Cambridge , Lensfield Road , Cambridge CB2 1EW , UK
| | - Tuomas P J Knowles
- Department of Chemistry , University of Cambridge , Lensfield Road , Cambridge CB2 1EW , UK
| | - Dieter Willbold
- Institut für Physikalische Biologie , Heinrich-Heine-Universität , 40204 Düsseldorf , Germany .
- Institute of Complex Systems (ICS-6) , Structural Biochemistry , Research Centre Jülich , Germany
| | - Philipp Neudecker
- Institut für Physikalische Biologie , Heinrich-Heine-Universität , 40204 Düsseldorf , Germany .
- Institute of Complex Systems (ICS-6) , Structural Biochemistry , Research Centre Jülich , Germany
| | - Henrike Heise
- Institut für Physikalische Biologie , Heinrich-Heine-Universität , 40204 Düsseldorf , Germany .
- Institute of Complex Systems (ICS-6) , Structural Biochemistry , Research Centre Jülich , Germany
| | - Ghanim Ullah
- Department of Physics , University of South Florida , Tampa , FL 33620 , USA .
| | - Wolfgang Hoyer
- Institut für Physikalische Biologie , Heinrich-Heine-Universität , 40204 Düsseldorf , Germany .
- Institute of Complex Systems (ICS-6) , Structural Biochemistry , Research Centre Jülich , Germany
| | - Martin Muschol
- Department of Physics , University of South Florida , Tampa , FL 33620 , USA .
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48
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Matsubara T, Yasumori H, Ito K, Shimoaka T, Hasegawa T, Sato T. Amyloid-β fibrils assembled on ganglioside-enriched membranes contain both parallel β-sheets and turns. J Biol Chem 2018; 293:14146-14154. [PMID: 30018137 DOI: 10.1074/jbc.ra118.002787] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Revised: 07/11/2018] [Indexed: 12/15/2022] Open
Abstract
Some protein and peptide aggregates, such as those of amyloid-β protein (Aβ), are neurotoxic and have been implicated in several neurodegenerative diseases. Aβ accumulates at nanoclusters enriched in neuronal lipids called gangliosides in the presynaptic neuronal membrane, and the resulting oligomeric and/or fibrous forms accelerate the development of Alzheimer's disease. Although the presence of Aβ deposits at such nanoclusters is known, the mechanism of their assembly and the relationship between Aβ secondary structure and topography are still unclear. Here, we first confirmed by atomic force microscopy that Aβ40 fibrils can be obtained by incubating seed-free Aβ40 monomers with a membrane composed of sphingomyelin, cholesterol, and the ganglioside GM1. Using Fourier transform infrared (FTIR) reflection-absorption spectroscopy, we then found that these lipid-associated fibrils contained parallel β-sheets, whereas self-assembled Aβ40 molecules formed antiparallel β-sheets. We also found that the fibrils obtained at GM1-rich nanoclusters were generated from turn Aβ40 Our findings indicate that Aβ generally self-assembles into antiparallel β-structures but can also form protofibrils with parallel β-sheets by interacting with ganglioside-bound Aβ. We concluded that by promoting the formation of parallel β-sheets, highly ganglioside-enriched nanoclusters help accelerate the elongation of Aβ fibrils. These results advance our understanding of ganglioside-induced Aβ fibril formation in neuronal membranes and may help inform the development of additional therapies for Alzheimer's disease.
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Affiliation(s)
- Teruhiko Matsubara
- From the Department of Biosciences and Informatics, Keio University, 3-14-1 Hiyoshi, Kouhoku-ku, Yokohama 223-8522, Japan and
| | - Hanaki Yasumori
- From the Department of Biosciences and Informatics, Keio University, 3-14-1 Hiyoshi, Kouhoku-ku, Yokohama 223-8522, Japan and
| | - Koichiro Ito
- From the Department of Biosciences and Informatics, Keio University, 3-14-1 Hiyoshi, Kouhoku-ku, Yokohama 223-8522, Japan and
| | - Takafumi Shimoaka
- the Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - Takeshi Hasegawa
- the Institute for Chemical Research, Kyoto University, Uji, Kyoto 611-0011, Japan
| | - Toshinori Sato
- From the Department of Biosciences and Informatics, Keio University, 3-14-1 Hiyoshi, Kouhoku-ku, Yokohama 223-8522, Japan and
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49
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Bellomo G, Bologna S, Gonnelli L, Ravera E, Fragai M, Lelli M, Luchinat C. Aggregation kinetics of the Aβ1-40 peptide monitored by NMR. Chem Commun (Camb) 2018; 54:7601-7604. [PMID: 29767190 DOI: 10.1039/c8cc01710g] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
The aggregation of Aβ1-40 was monitored by solution NMR, which showed a trend complementary to the one observed by ThT-fluorescence. The NMR data support a kinetic model where Aβ1-40 initially aggregates with the reversible formation of oligomeric species, which then irreversibly convert into fibrils.
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Affiliation(s)
- Giovanni Bellomo
- Magnetic Resonance Center (CERM), University of Florence, Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy.
| | - Sara Bologna
- Magnetic Resonance Center (CERM), University of Florence, Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy.
| | - Leonardo Gonnelli
- Magnetic Resonance Center (CERM), University of Florence, Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy.
| | - Enrico Ravera
- Magnetic Resonance Center (CERM), University of Florence, Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy. and Department of Chemistry "Ugo Schiff", University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy
| | - Marco Fragai
- Magnetic Resonance Center (CERM), University of Florence, Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy. and Department of Chemistry "Ugo Schiff", University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy
| | - Moreno Lelli
- Magnetic Resonance Center (CERM), University of Florence, Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy. and Department of Chemistry "Ugo Schiff", University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy
| | - Claudio Luchinat
- Magnetic Resonance Center (CERM), University of Florence, Via L. Sacconi 6, 50019 Sesto Fiorentino, Italy. and Department of Chemistry "Ugo Schiff", University of Florence, Via della Lastruccia 3, 50019 Sesto Fiorentino, Italy and Giotto Biotech S.R.L., Via Madonna del Piano 6, 50019 Sesto Fiorentino, Florence, Italy
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50
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Impact of membrane curvature on amyloid aggregation. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2018; 1860:1741-1764. [PMID: 29709613 DOI: 10.1016/j.bbamem.2018.04.012] [Citation(s) in RCA: 74] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/05/2018] [Revised: 04/23/2018] [Accepted: 04/25/2018] [Indexed: 12/11/2022]
Abstract
The misfolding, amyloid aggregation, and fibril formation of intrinsically disordered proteins/peptides (or amyloid proteins) have been shown to cause a number of disorders. The underlying mechanisms of amyloid fibrillation and structural properties of amyloidogenic precursors, intermediates, and amyloid fibrils have been elucidated in detail; however, in-depth examinations on physiologically relevant contributing factors that induce amyloidogenesis and lead to cell death remain challenging. A large number of studies have attempted to characterize the roles of biomembranes on protein aggregation and membrane-mediated cell death by designing various membrane components, such as gangliosides, cholesterol, and other lipid compositions, and by using various membrane mimetics, including liposomes, bicelles, and different types of lipid-nanodiscs. We herein review the dynamic effects of membrane curvature on amyloid generation and the inhibition of amyloidogenic proteins and peptides, and also discuss how amyloid formation affects membrane curvature and integrity, which are key for understanding relationships with cell death. Small unilamellar vesicles with high curvature and large unilamellar vesicles with low curvature have been demonstrated to exhibit different capabilities to induce the nucleation, amyloid formation, and inhibition of amyloid-β peptides and α-synuclein. Polymorphic amyloidogenesis in small unilamellar vesicles was revealed and may be viewed as one of the generic properties of interprotein interaction-dominated amyloid formation. Several mechanical models and phase diagrams are comprehensively shown to better explain experimental findings. The negative membrane curvature-mediated mechanisms responsible for the toxicity of pancreatic β cells by the amyloid aggregation of human islet amyloid polypeptide (IAPP) and binding of the precursors of the semen-derived enhancer of viral infection (SEVI) are also described. The curvature-dependent binding modes of several types of islet amyloid polypeptides with high-resolution NMR structures are also discussed.
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