1
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Dasari AK, Sengupta U, Viverette E, Borgnia MJ, Kayed R, Lim KH. Characterization of α-synuclein oligomers formed in the presence of lipid vesicles. Biochem Biophys Rep 2024; 38:101687. [PMID: 38545462 PMCID: PMC10965497 DOI: 10.1016/j.bbrep.2024.101687] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Revised: 03/11/2024] [Accepted: 03/14/2024] [Indexed: 05/23/2024] Open
Abstract
Aggregation of α-synuclein into oligomers and fibrils is associated with numerous neurodegenerative diseases such as Parkinson's disease (PD). Although the identity of the pathogenic species formed during the aggregation process is still under active debate, mounting evidence suggests that small oligomeric species rather than fibrillar aggregates are real toxic species. Isolation and characterization of small oligomers is essential to developing therapeutic strategies to prevent oligomer formation. Preparation of misfolded oligomeric species for biophysical characterization is, however, a great challenge due to their heterogenous, transient nature. Here we report the preparation of toxic and non-toxic α-synuclein oligomeric species formed at different pH values in the presence of lipid vesicles that mimic mitochondria membranes containing cardiolipin. Biophysical characterization of the lipid-induced α-synuclein oligomeric assemblies revealed that α-synuclein oligomers formed at pH 7.4 have higher surface hydrophobicity than the aggregates formed at pH 6.0. In addition, the high-pH oligomers were shown to exhibit higher toxicity than the low-pH aggregates. Structural, dynamic properties of the oligomers were also investigated by using circular dichroism (CD) and NMR spectroscopy. Our CD analyses revealed that the two oligomeric species have distinct molecular conformations, and 2D 1H/15N HSQC NMR experiments suggested that the high-pH oligomers have more extended dynamic regions than the low-pH aggregates. The distinct structural and dynamic properties of the oligomers might be associated with their different cytotoxic properties.
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Affiliation(s)
- Anvesh K.R. Dasari
- Department of Chemistry, East Carolina University, Greenville, NC, 27858, USA
| | - Urmi Sengupta
- Departments of Neurology, Neuroscience and Cell Biology, University of Texas Medical Branch, Galveston, TX, 77555, USA
| | - Elizabeth Viverette
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, NC, 27709, USA
| | - Mario J. Borgnia
- Genome Integrity and Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, NC, 27709, USA
| | - Rakez Kayed
- Departments of Neurology, Neuroscience and Cell Biology, University of Texas Medical Branch, Galveston, TX, 77555, USA
| | - Kwang Hun Lim
- Department of Chemistry, East Carolina University, Greenville, NC, 27858, USA
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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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Juković M, Ratkaj I, Kalafatovic D, Bradshaw NJ. Amyloids, amorphous aggregates and assemblies of peptides - Assessing aggregation. Biophys Chem 2024; 308:107202. [PMID: 38382283 DOI: 10.1016/j.bpc.2024.107202] [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: 11/29/2023] [Revised: 01/31/2024] [Accepted: 02/14/2024] [Indexed: 02/23/2024]
Abstract
Amyloid and amorphous aggregates represent the two major categories of aggregates associated with diseases, and although exhibiting distinct features, researchers often treat them as equivalent, which demonstrates the need for more thorough characterization. Here, we compare amyloid and amorphous aggregates based on their biochemical properties, kinetics, and morphological features. To further decipher this issue, we propose the use of peptide self-assemblies as minimalistic models for understanding the aggregation process. Peptide building blocks are significantly smaller than proteins that participate in aggregation, however, they make a plausible means to bridge the gap in discerning the aggregation process at the more complex, protein level. Additionally, we explore the potential use of peptide-inspired models to research the liquid-liquid phase separation as a feasible mechanism preceding amyloid formation. Connecting these concepts can help clarify our understanding of aggregation-related disorders and potentially provide novel drug targets to impede and reverse these serious illnesses.
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Affiliation(s)
- Maja Juković
- Faculty of Biotechnology and Drug Development, University of Rijeka, 51000 Rijeka, Croatia
| | - Ivana Ratkaj
- Faculty of Biotechnology and Drug Development, University of Rijeka, 51000 Rijeka, Croatia
| | - Daniela Kalafatovic
- Faculty of Biotechnology and Drug Development, University of Rijeka, 51000 Rijeka, Croatia.
| | - Nicholas J Bradshaw
- Faculty of Biotechnology and Drug Development, University of Rijeka, 51000 Rijeka, Croatia.
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4
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Matassa R, Gatti M, Crociati M, Brunelli R, Battaglione E, Papi M, De Spirito M, Nottola SA, Familiari G. Self-assembly of glycoprotein nanostructured filaments for modulating extracellular networks at long range. NANOSCALE 2023; 15:17972-17986. [PMID: 37905731 DOI: 10.1039/d3nr02644b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/02/2023]
Abstract
The intriguing capability of branched glycoprotein filaments to change their hierarchical organization, mediated by external biophysical stimuli, continues to expand understanding of self-assembling strategies that can dynamically rearrange networks at long range. Previous research has explored the corresponding biological, physiological and genetic mechanisms, focusing on protein assemblies within a limited range of nanometric units. Using direct microscopy bio-imaging, we have determined the morpho-structural changes of self-assembled filament networks of the zona pellucida, revealing controlled levels of structured organizations to join distinct evolved stages of the oocyte (Immature, Mature, and Fertilized). This natural soft network reorganizes its corresponding hierarchical network to generate symmetric, asymmetric, and ultimately a state with the lowest asymmetry of the outer surface roughness, and internal pores reversibly changed from elliptical to circular configurations at the corresponding stages. These elusive morpho-structural changes are regulated by the nanostructured polymorphisms of the branched filaments by self-extension/-contraction/-bending processes, modulated by determinate theoretical angles among repetitive filament units. Controlling the nanoscale self-assembling properties by delivering a minimum number of activation bio-signals may be triggered by these specific nanostructured polymorphic organizations. Finally, this research aims to guide this soft biomaterial into a desired state to protect oocytes, eggs, and embryos during development, to favour/prevent the fertilization/polyspermy processes and eventually to impact interactions with bacteria/virus at multiscale levels.
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Affiliation(s)
- Roberto Matassa
- Department of Anatomical, Histological, Forensic and Orthopaedic Sciences, Section of Human Anatomy, Sapienza University of Rome, Via A. Borelli 50, 00161, Rome, Italy.
| | - Marta Gatti
- Department of Anatomical, Histological, Forensic and Orthopaedic Sciences, Section of Human Anatomy, Sapienza University of Rome, Via A. Borelli 50, 00161, Rome, Italy.
| | - Martina Crociati
- Department of Veterinary Medicine, University of Perugia, Via San Costanzo, 4, Perugia, 06126, Italy
- Centre for Perinatal and Reproductive Medicine, University of Perugia, 06129 Perugia, Italy
| | - Roberto Brunelli
- Department of Gynecological-Obstetric and Urologic Sciences, Sapienza University of Rome, Rome, Italy
| | - Ezio Battaglione
- Department of Anatomical, Histological, Forensic and Orthopaedic Sciences, Section of Human Anatomy, Sapienza University of Rome, Via A. Borelli 50, 00161, Rome, Italy.
| | - Massimiliano Papi
- Dipartimento di Neuroscienze, Università Cattolica del Sacro Cuore, Largo Francesco Vito 1, 00168 Rome, Italy
- Fondazione Policlinico Universitario A. Gemelli IRCSS, 00168 Rome, Italy
| | - Marco De Spirito
- Dipartimento di Neuroscienze, Università Cattolica del Sacro Cuore, Largo Francesco Vito 1, 00168 Rome, Italy
- Fondazione Policlinico Universitario A. Gemelli IRCSS, 00168 Rome, Italy
| | - Stefania Annarita Nottola
- Department of Anatomical, Histological, Forensic and Orthopaedic Sciences, Section of Human Anatomy, Sapienza University of Rome, Via A. Borelli 50, 00161, Rome, Italy.
| | - Giuseppe Familiari
- Department of Anatomical, Histological, Forensic and Orthopaedic Sciences, Section of Human Anatomy, Sapienza University of Rome, Via A. Borelli 50, 00161, Rome, Italy.
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5
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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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6
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Grover S, Pham T, Jones A, Sinobas-Pereira C, Villoch Diaz Maurino M, Garrad EC, Makoni NJ, Parks A, Domalewski RJ, Riggio G, An H, Chen K, Nichols MR. A new class of monoclonal Aβ antibodies selectively targets and triggers deposition of Aβ protofibrils. J Neurochem 2023; 165:860-873. [PMID: 37002186 DOI: 10.1111/jnc.15817] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2023] [Revised: 03/10/2023] [Accepted: 03/23/2023] [Indexed: 04/03/2023]
Abstract
Aggregation and accumulation of amyloid-β peptide (Aβ) are a critical trigger for the onset of Alzheimer's disease (AD). While the plaques are the most outstanding Aβ pathological feature, much of the recent research emphasis has been on soluble Aβ species because of their diffusible, proinflammatory, and toxic properties. The focus on soluble aggregated Aβ species has also increased the interest in antibodies that are selective for different Aβ conformations. In the current study, we developed and characterized a new class of monoclonal antibodies (referred to as mAbSL) that are selective for Aβ protofibrils. Cloning and sequencing of the heavy and light chain variable regions for multiple antibodies identified sequence characteristics that may impart the conformational selectivity by the antibodies. Transfection of FreeStyle 293F cells with the plasmids permitted in-house expression and purification of mAbSL antibodies along with non-conformation-selective Aβ monoclonal antibodies (Aβ mAbs). Several of the purified mAbSL antibodies demonstrated significant affinity and selectivity for Aβ42 protofibrils compared with Aβ42 monomers and Aβ42 fibrils. Competition ELISA assays assessing the best overall antibody, mAbSL 113, yielded affinity constants of 7 nM for the antibody-Aβ42 protofibril interaction, while the affinity for either Aβ42 monomers or Aβ42 fibrils was roughly 80 times higher. mAbSL 113 significantly inhibited Aβ42 monomer aggregation by a unique mechanism compared with the inhibition displayed by Aβ mAb 513. Aβ42 protofibril dynamics were also markedly altered in the presence of mAbSL 113, whereby insoluble complex formation and protofibril deposition were stimulated by the antibody at low substoichiometric molar ratios. As the field contemplates the therapeutic effectiveness of Aβ conformation-selective antibodies, the findings presented here demonstrate new information on a monoclonal antibody that selectively targets Aβ protofibrils and impacts Aβ dynamics.
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Affiliation(s)
- Shikha Grover
- Department of Chemistry & Biochemistry, University of Missouri-St. Louis, St. Louis, Missouri, USA
| | - Thao Pham
- Department of Chemistry & Biochemistry, University of Missouri-St. Louis, St. Louis, Missouri, USA
| | - Anna Jones
- Department of Chemistry & Biochemistry, University of Missouri-St. Louis, St. Louis, Missouri, USA
| | - Cristina Sinobas-Pereira
- Department of Chemistry & Biochemistry, University of Missouri-St. Louis, St. Louis, Missouri, USA
| | | | - Evan C Garrad
- Department of Chemistry & Biochemistry, University of Missouri-St. Louis, St. Louis, Missouri, USA
| | - Nyasha J Makoni
- Department of Chemistry & Biochemistry, University of Missouri-St. Louis, St. Louis, Missouri, USA
| | - Antanisha Parks
- Department of Chemistry & Biochemistry, University of Missouri-St. Louis, St. Louis, Missouri, USA
| | - Ryan J Domalewski
- Department of Chemistry & Biochemistry, University of Missouri-St. Louis, St. Louis, Missouri, USA
| | - Gabriel Riggio
- Department of Chemistry & Biochemistry, University of Missouri-St. Louis, St. Louis, Missouri, USA
| | - Hannah An
- Department of Chemistry & Biochemistry, University of Missouri-St. Louis, St. Louis, Missouri, USA
| | | | - Michael R Nichols
- Department of Chemistry & Biochemistry, University of Missouri-St. Louis, St. Louis, Missouri, USA
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7
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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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8
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Natarajan A, Rangan K, Vadrevu R. Self-assembly of a peptide sequence, EKKE, composed of exclusively charged amino acids: Role of charge in morphology and lead binding. J Pept Sci 2023; 29:e3451. [PMID: 36098076 DOI: 10.1002/psc.3451] [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: 04/25/2022] [Revised: 08/14/2022] [Accepted: 09/08/2022] [Indexed: 01/12/2023]
Abstract
The self-assembly of peptides is influenced by their amino acid sequence and other factors including pH, charge, temperature, and solvent. Herein, we explore whether a four-residue sequence, EKKE, consisting of exclusively charged amino acids shows the propensity to form self-assembled ordered nanostructures and whether the overall charge plays any role in morphological and functional properties. From a combination of experimental data provided by Thioflavin T fluorescence, Congo red absorbance, circular dichroism spectroscopy, dynamic light scattering, field emission-scanning electron microscopy, atomic force microscopy, and confocal microscopy, it is clear that the all-polar peptide and charged EKKE sequence shows a pH-dependent tendency to form amyloid-like structures, and the self-assembled entities under acidic, basic and neutral conditions exhibit morphological variation. Additionally, the ability of the self-assembled amyloid nanostructures to bind to the toxic metal, lead (Pb2+ ), was demonstrated from the analysis of the ultraviolet absorbance and X-ray photoelectron spectroscopy data. The modulation at the sequence level for the amyloid-forming EKKE scaffold can further extend its potential role not only in the remediation of other toxic metals but also towards biomedical applications.
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Affiliation(s)
- Aishwarya Natarajan
- Department of Biological Sciences, Birla Institute of Technology and Science Pilani, Hyderabad Campus, Hyderabad, India
| | - Krishnan Rangan
- Department of Chemistry, Birla Institute of Technology and Science Pilani, Hyderabad Campus, Hyderabad, India
| | - Ramakrishna Vadrevu
- Department of Biological Sciences, Birla Institute of Technology and Science Pilani, Hyderabad Campus, Hyderabad, India
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9
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Saha G, Ghosh S, Dubey VK, Saudagar P. Gene Alterations Induced by Glutamine (Q) Encoding CAG Repeats Associated with Neurodegeneration. Methods Mol Biol 2023; 2575:3-23. [PMID: 36301468 DOI: 10.1007/978-1-0716-2716-7_1] [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
Several studies have been reported linking the role of polyglutamine (polyQ) disease-associated proteins with altered gene regulation induced by an unstable trinucleotide (CAG) repeat. Owing to their dynamic nature of expansion, these DNA repeats form secondary structures interfering with the normal cellular mechanisms like replication and transcription and, thereby, have become the underlying cause of numerous neurodegenerative disorders involving mental retardation and/or muscular or neuronal degeneration. Despite the widespread expression of the disease-causing protein, specific subsets of neurons are susceptible to specific patterns of inheritance and clinical symptoms. Although this cell-type selectivity is still elusive and less understood, it has been found that aberrant transcriptional regulation is one of the primary causes of polyQ diseases where the functions of histone-modifying complexes are disrupted. Besides, epigenetic modifications play a critical role in the pathogenesis of these diseases. In this chapter, we will be delving into how these polyQ repeats induce the self-assembly and aggregation of altered carrier proteins based on gene alterations, causing neuronal toxicity and cellular deaths. Besides, genomic instability in CAG repeats due to altered chromatin-related enzymes will be highlighted, along with epigenetic changes present in many polyQ disorders. Understanding the underlying molecular mechanisms in the root cause of these disorders will culminate in identifying therapeutic approaches for the treatment of these neurodegenerative disorders.
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Affiliation(s)
- Gundappa Saha
- Department of Basic & Translational Sciences, Penn Dental Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Sukanya Ghosh
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, New Delhi, India
| | - Vikash Kumar Dubey
- School of Biochemical Engineering, Indian Institute of Technology BHU, Varanasi, Uttar Pradesh, India
| | - Prakash Saudagar
- Department of Biotechnology, National Institute of Technology, Warangal, Telangana, India.
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10
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Saha D, Jana B. Identifying the Template for Oligomer to Fibril Conversion for Amyloid-β (1-42) Oligomers using Hamiltonian Replica Exchange Molecular Dynamics. Chemphyschem 2022; 23:e202200393. [PMID: 36052514 DOI: 10.1002/cphc.202200393] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Revised: 08/26/2022] [Indexed: 01/04/2023]
Abstract
The toxicity of amyloid-β (Aβ) oligomers has been known to be higher compared to mature fibrils. Yet the presence of plaques in Alzheimer's disease patients indicates the significance of oligomer to fibril conversion for Aβ aggregates. In this study, we investigate Aβ13-42 oligomers having two to five peptide chains using extensive all-atom molecular dynamics simulations to identify the on- or off-pathway intermediates in fibril formation pathway. Hamiltonian replica exchange method through solute tempering (REST2) has been employed to explore the different structures attained by these aggregates. Using intra-chain and inter-chain contacts as reaction coordinates, we obtain the free energy surface for the Aβ13-42 oligomers. Consequently, their stable conformations and structural features have been identified. The found conformations belonging to most probable structures possess both parallel and anti-parallel β-sheets, characteristic of on- and off-pathway intermediates, respectively. Further, we have measured the tendency to form fibril like interactions among the β-sheet forming residues. Our analysis finds that residues 30-36 possess higher tendency to form fibril like contacts among all the residues. While we find stronger interaction among residues 30-36, these amino acids are also found to be more shielded from water compared to others. With previous experimental studies finding these residues to be more crucial for the stability of Aβ42 oligomers, we propose that interactions within this patch could trigger seed formation that leads to conversion of on-pathway oligomers into disease relevant fibrils.
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Affiliation(s)
- Debasis Saha
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Kolkata, Jadavpur, Kolkata, 700032, West Bengal, India
| | - Biman Jana
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Kolkata, Jadavpur, Kolkata, 700032, West Bengal, India
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11
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Krzek M, Stroobants S, Gelin P, De Malsche W, Maes D. Influence of Centrifugation and Shaking on the Self-Assembly of Lysozyme Fibrils. Biomolecules 2022; 12:biom12121746. [PMID: 36551175 PMCID: PMC9775142 DOI: 10.3390/biom12121746] [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: 10/25/2022] [Revised: 11/15/2022] [Accepted: 11/19/2022] [Indexed: 11/25/2022] Open
Abstract
Protein self-assembly into fibrils and oligomers plays a key role in the etiology of degenerative diseases. Several pathways for this self-assembly process have been described and shown to result in different types and ratios of final assemblies, therewith defining the effective physiological response. Known factors that influence assembly pathways are chemical conditions and the presence or lack of agitation. However, in natural and industrial systems, proteins are exposed to a sequence of different and often complex mass transfers. In this paper, we compare the effect of two fundamentally different mass transfer processes on the fibrilization process. Aggregation-prone solutions of hen egg white lysozyme were subjected to predominantly non-advective mass transfer by employing centrifugation and to advective mass transport represented by orbital shaking. In both cases, fibrilization was triggered, while in quiescent only oligomers were formed. The fibrils obtained by shaking compared to fibrils obtained through centrifugation were shorter, thicker, and more rigid. They had rod-like protofibrils as building blocks and a significantly higher β-sheet content was observed. In contrast, fibrils from centrifugation were more flexible and braided. They consisted of intertwined filaments and had low β-sheet content at the expense of random coil. To the best of our knowledge, this is the first evidence of a fibrilization pathway selectivity, with the fibrilization route determined by the mass transfer and mixing configuration (shaking versus centrifugation). This selectivity can be potentially employed for directed protein fibrilization.
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Affiliation(s)
- Marzena Krzek
- Structural Biology Brussels, Vrije Universiteit Brussel, 1050 Brussels, Belgium
| | - Sander Stroobants
- Structural Biology Brussels, Vrije Universiteit Brussel, 1050 Brussels, Belgium
| | - Pierre Gelin
- μFlow Group, Department of Chemical Engineering, Vrije Universiteit Brussel, 1050 Brussels, Belgium
| | - Wim De Malsche
- μFlow Group, Department of Chemical Engineering, Vrije Universiteit Brussel, 1050 Brussels, Belgium
| | - Dominique Maes
- Structural Biology Brussels, Vrije Universiteit Brussel, 1050 Brussels, Belgium
- Correspondence:
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12
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Romano A, Engelberg Y, Landau M, Lesmes U. Alpha-lactalbumin amyloid-like fibrils for intestinal delivery: Formation, physiochemical characterization, and digestion fate of capsaicin-loaded fibrils. Food Hydrocoll 2022. [DOI: 10.1016/j.foodhyd.2022.108248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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13
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Windheim J, Colombo L, Battajni NC, Russo L, Cagnotto A, Diomede L, Bigini P, Vismara E, Fiumara F, Gabbrielli S, Gautieri A, Mazzuoli-Weber G, Salmona M, Colnaghi L. Micro- and Nanoplastics’ Effects on Protein Folding and Amyloidosis. Int J Mol Sci 2022; 23:ijms231810329. [PMID: 36142234 PMCID: PMC9499421 DOI: 10.3390/ijms231810329] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 09/02/2022] [Accepted: 09/03/2022] [Indexed: 11/30/2022] Open
Abstract
A significant portion of the world’s plastic is not properly disposed of and, through various processes, is degraded into microscopic particles termed micro- and nanoplastics. Marine and terrestrial faunae, including humans, inevitably get in contact and may inhale and ingest these microscopic plastics which can deposit throughout the body, potentially altering cellular and molecular functions in the nervous and other systems. For instance, at the cellular level, studies in animal models have shown that plastic particles can cross the blood–brain barrier and interact with neurons, and thus affect cognition. At the molecular level, plastics may specifically influence the folding of proteins, induce the formation of aberrant amyloid proteins, and therefore potentially trigger the development of systemic and local amyloidosis. In this review, we discuss the general issue of plastic micro- and nanoparticle generation, with a focus on their effects on protein folding, misfolding, and their possible clinical implications.
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Affiliation(s)
- Joseph Windheim
- Department of Medicine, NYU Grossman School of Medicine, New York, NY 10016, USA
| | - Laura Colombo
- Department of Molecular Biochemistry and Pharmacology, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, 20156 Milan, Italy
| | - Nora C. Battajni
- Department of Molecular Biochemistry and Pharmacology, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, 20156 Milan, Italy
| | - Luca Russo
- Department of Molecular Biochemistry and Pharmacology, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, 20156 Milan, Italy
| | - Alfredo Cagnotto
- Department of Molecular Biochemistry and Pharmacology, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, 20156 Milan, Italy
| | - Luisa Diomede
- Department of Molecular Biochemistry and Pharmacology, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, 20156 Milan, Italy
| | - Paolo Bigini
- Department of Molecular Biochemistry and Pharmacology, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, 20156 Milan, Italy
| | - Elena Vismara
- Department of Chemistry, Materials and Chemical Engineering “G. Natta”, Politecnico di Milano, 20156 Milan, Italy
| | - Ferdinando Fiumara
- Rita Levi Montalcini Department of Neuroscience, University of Torino, Corso Raffaello 30, 10125 Torino, Italy
- National Institute of Neuroscience (INN), University of Torino, Corso Raffaello 30, 10125 Torino, Italy
| | - Silvia Gabbrielli
- Biomolecular Engineering Lab, Dipartimento di Elettronica, Informazione e Bioingegneria, Politecnico di Milano, Piazza Leonardo da Vinci 32, 20133 Milano, Italy
| | - Alfonso Gautieri
- Biomolecular Engineering Lab, Dipartimento di Elettronica, Informazione e Bioingegneria, Politecnico di Milano, Piazza Leonardo da Vinci 32, 20133 Milano, Italy
| | - Gemma Mazzuoli-Weber
- Center for Systems Neuroscience (ZSN), 30559 Hannover, Germany
- Institute for Physiology and Cell Biology, University of Veterinary Medicine Hannover, 30559 Hannover, Germany
| | - Mario Salmona
- Department of Molecular Biochemistry and Pharmacology, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, 20156 Milan, Italy
| | - Luca Colnaghi
- Department of Molecular Biochemistry and Pharmacology, Istituto di Ricerche Farmacologiche Mario Negri IRCCS, 20156 Milan, Italy
- Correspondence: ; Tel.: +39-02-2643-4818
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Deol HK, Broom HR, Sienbeneichler B, Lee B, Leonenko Z, Meiering EM. Immature ALS-associated mutant superoxide dismutases form variable aggregate structures through distinct oligomerization processes. Biophys Chem 2022; 288:106844. [DOI: 10.1016/j.bpc.2022.106844] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 05/31/2022] [Accepted: 06/02/2022] [Indexed: 11/15/2022]
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15
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Paul R, Bera S, Devi M, Paul S. Inhibition of Aβ 16–22 Peptide Aggregation by Small Molecules and Their Permeation through POPC Lipid Bilayer: Insight from Molecular Dynamics Simulation Study. J Chem Inf Model 2022; 62:5193-5207. [DOI: 10.1021/acs.jcim.1c01366] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Rabindranath Paul
- Department of Chemistry, Indian Institute of Technology, Guwahati, Assam, India 781039
| | - Siddhartha Bera
- Department of Chemistry, Indian Institute of Technology, Guwahati, Assam, India 781039
| | - Madhusmita Devi
- Department of Chemistry, Indian Institute of Technology, Guwahati, Assam, India 781039
| | - Sandip Paul
- Department of Chemistry, Indian Institute of Technology, Guwahati, Assam, India 781039
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16
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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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17
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Rahman MU, Song K, Da LT, Chen HF. Early aggregation mechanism of Aβ 16-22 revealed by Markov state models. Int J Biol Macromol 2022; 204:606-616. [PMID: 35134456 DOI: 10.1016/j.ijbiomac.2022.02.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 01/24/2022] [Accepted: 02/01/2022] [Indexed: 12/19/2022]
Abstract
Aβ16-22 is believed to have critical role in early aggregation of full length amyloids that are associated with the Alzheimer's disease and can aggregate to form amyloid fibrils. However, the early aggregation mechanism is still unsolved. Here, multiple long-term molecular dynamics simulations combining with Markov state model were used to probe the early oligomerization mechanism of Aβ16-22 peptides. The identified dimeric form adopted either globular random-coil or extended β-strand like conformations. The observed dimers of these variants shared many overall conformational characteristics but differed in several aspects at detailed level. In all cases, the most common type of secondary structure was intermolecular antiparallel β-sheets. The inter-state transitions were very frequent ranges from few to hundred nanoseconds. More strikingly, those states which contain fraction of β secondary structure and significant amount of extended coiled structures, therefore exposed to the solvent, were majorly participated in aggregation. The assembly of low-energy dimers, in which the peptides form antiparallel β sheets, occurred by multiple pathways with the formation of an obligatory intermediates. We proposed that these states might facilitate the Aβ16-22 aggregation through a significant component of the conformational selection mechanism, because they might increase the aggregates population by promoting the inter-chain hydrophobic and the hydrogen bond contacts. The formation of early stage antiparallel β sheet structures is critical for oligomerization, and at the same time provided a flat geometry to seed the ordered β-strand packing of the fibrils. Our findings hint at reorganization of this part of the molecule as a potentially critical step in Aβ aggregation and will insight into early oligomerization for large β amyloids.
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Affiliation(s)
- Mueed Ur Rahman
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, Department of Bioinformatics and Biostatistics, National Experimental Teaching Center for Life Sciences and Biotechnology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Kaiyuan Song
- Key Laboratory of System Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Lin-Tai Da
- Key Laboratory of System Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Hai-Feng Chen
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences, Department of Bioinformatics and Biostatistics, National Experimental Teaching Center for Life Sciences and Biotechnology, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China; Shanghai Center for Bioinformation Technology, Shanghai, 200235, China.
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18
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Effect of 1-Ethyl-3-methylimidazolium Tetrafluoroborate and Acetate Ionic Liquids on Stability and Amyloid Aggregation of Lysozyme. Int J Mol Sci 2022; 23:ijms23020783. [PMID: 35054967 PMCID: PMC8775716 DOI: 10.3390/ijms23020783] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Revised: 01/08/2022] [Accepted: 01/08/2022] [Indexed: 02/01/2023] Open
Abstract
Amyloid fibrils draw attention as potential novel biomaterials due to their high stability, strength, elasticity or resistance against degradation. Therefore, the controlled and fast fibrillization process is of great interest, which raises the demand for effective tools capable of regulating amyloid fibrillization. Ionic liquids (ILs) were identified as effective modulators of amyloid aggregation. The present work is focused on the study of the effect of 1-ethyl-3-methyl imidazolium-based ILs with kosmotropic anion acetate (EMIM-ac) and chaotropic cation tetrafluoroborate (EMIM-BF4) on the kinetics of lysozyme amyloid aggregation and morphology of formed fibrils using fluorescence and CD spectroscopy, differential scanning calorimetry, AFM with statistical image analysis and docking calculations. We have found that both ILs decrease the thermal stability of lysozyme and significantly accelerate amyloid fibrillization in a dose-dependent manner at concentrations of 0.5%, 1% and 5% (v/v) in conditions and time-frames when no fibrils are formed in ILs-free solvent. The effect of EMIM-BF4 is more prominent than EMIM-ac due to the different specific interactions of the anionic part with the protein surface. Although both ILs induced formation of amyloid fibrils with typical needle-like morphology, a higher variability of fibril morphology consisting of a different number of intertwining protofilaments was identified for EMIM-BF4.
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19
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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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20
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Bandyopadhyay A, Sannigrahi A, Chattopadhyay K. Membrane composition and lipid to protein ratio modulate amyloid kinetics of yeast prion protein. RSC Chem Biol 2021; 2:592-605. [PMID: 34458802 PMCID: PMC8341755 DOI: 10.1039/d0cb00203h] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Accepted: 01/15/2021] [Indexed: 12/22/2022] Open
Abstract
Understanding of prion aggregation in a membrane environment may help to ameliorate neurodegenerative complications caused by the amyloid forms of prions. Here, we investigated the membrane binding-induced aggregation of yeast prion protein Sup35. Using the combination of fluorescence correlation spectroscopy (FCS) at single molecule resolution and other biophysical studies, we establish that lipid composition and lipid/protein ratio are key modulators of the aggregation kinetics of Sup35. In the presence of a zwitterionic membrane (DMPC), Sup35 exhibited novel biphasic aggregation kinetics at lipid/protein ratios ranging between 20 : 1 and 70 : 1 (termed here as the optimum lipid concentration, OLC). In ratios below (low lipid concentration, LLC) and above (ELC, excess lipid concentration) that range, the aggregation was found to be monophasic. In contrast, in the presence of negatively charged membranes, we did not observe any bi-phasic aggregation kinetics in the entire range of protein to lipid ratios. Our results provide a mechanistic description of the role that membrane concentration/composition-modulated aggregation may play in neurodegenerative diseases.
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Affiliation(s)
- Arnab Bandyopadhyay
- Structural Biology & Bio-Informatics Division, CSIR-Indian Institute of Chemical Biology 4, Raja S. C. Mullick Road Kolkata 700032 India
| | - Achinta Sannigrahi
- Structural Biology & Bio-Informatics Division, CSIR-Indian Institute of Chemical Biology 4, Raja S. C. Mullick Road Kolkata 700032 India
| | - Krishnananda Chattopadhyay
- Structural Biology & Bio-Informatics Division, CSIR-Indian Institute of Chemical Biology 4, Raja S. C. Mullick Road Kolkata 700032 India
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21
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Fraczyk A, Janczewski L, Wasko J, Rozniakowski K, Galecki K, Kaminski ZJ, Kolesinska B. Non-Aggregating Amylin Fragments as an Inhibitors of the Aggregation Process of Susceptible to Aggregation Fragments 18-22, 23-27, and 33-37 of Hormone. Chem Biodivers 2021; 18:e2100034. [PMID: 33687147 DOI: 10.1002/cbdv.202100034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2021] [Accepted: 02/18/2021] [Indexed: 11/10/2022]
Abstract
Amylin aggregation is one of the factors in the development of diabetes mellitus, which is classified as a civilization disease. The aim of this research was to find whether non-aggregating fragments 1-7, 8-12, 13-17 and 28-32 of amylin would inhibit the aggregation of the amyloidogenic cores 18-22, 23-27, 33-37 of hormone. In the study of the inhibitory potential of non-aggregating amylin fragments, a set of independent methods were used to study aggregation properties (spectroscopic and fluorescence studies with the use of indicators, microscopic studies, circular dichroism studies) and the method of prediction of aggregation properties. The performed research allowed to select the cyclic fragment (1-7) H-KCNTATC-OH with disulfide bond as an inhibitor capable of inhibiting the aggregation of all amyloidogenic cores 18-22, 23-27, 33-37 of the hormone. Additionally, it was found that this peptide inhibits insulin hot spot aggregation, which may indicate its universal utility in inhibiting the process of aggregation of hormones regulating carbohydrate metabolism directly related to the development of diabetes. Research on the possibility of the extensive use of the cyclic fragment (1-7) of H-KCNTATC-OH as a peptide inhibitor of the polypeptide/protein aggregation process is ongoing.
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Affiliation(s)
- Andrzej Fraczyk
- Institute of Applied Computer Science, Lodz University of Technology, Stefanowskiego Łódź, 18/22, 90-537, Lodz, Poland
| | - Lukasz Janczewski
- Institute of Organic Chemistry, Faculty of Chemistry, Lodz University of Technology, Zeromskiego 116, 90-924, Lodz, Poland
| | - Joanna Wasko
- Institute of Organic Chemistry, Faculty of Chemistry, Lodz University of Technology, Zeromskiego 116, 90-924, Lodz, Poland
| | - Kamil Rozniakowski
- Institute of Organic Chemistry, Faculty of Chemistry, Lodz University of Technology, Zeromskiego 116, 90-924, Lodz, Poland
| | - Krystian Galecki
- Institute of General Food Chemistry, Faculty of Biotechnology and Food Sciences, Lodz University of Technology, Stefanowskiego 4/10, 90-924, Lodz, Poland
| | - Zbigniew J Kaminski
- Institute of Organic Chemistry, Faculty of Chemistry, Lodz University of Technology, Zeromskiego 116, 90-924, Lodz, Poland
| | - Beata Kolesinska
- Institute of Organic Chemistry, Faculty of Chemistry, Lodz University of Technology, Zeromskiego 116, 90-924, Lodz, Poland
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22
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On the Protein Fibrillation Pathway: Oligomer Intermediates Detection Using ATR-FTIR Spectroscopy. Molecules 2021; 26:molecules26040970. [PMID: 33673072 PMCID: PMC7918411 DOI: 10.3390/molecules26040970] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2020] [Revised: 02/02/2021] [Accepted: 02/05/2021] [Indexed: 01/17/2023] Open
Abstract
Oligomeric intermediates on the pathway of amyloid fibrillation are suspected as the main cytotoxins responsible for amyloid-related pathogenicity. As they appear to be a part of the lag phase of amyloid fibrillation when analyzed using standard methods such as Thioflavin T (ThT) fluorescence, a more sensitive method is needed for their detection. Here we apply Fourier transform infrared spectroscopy (FTIR) in attenuated total reflectance (ATR) mode for fast and cheap analysis of destabilized hen-egg-white lysozyme solution and detection of oligomer intermediates of amyloid fibrillation. Standard methods of protein aggregation analysis— Thioflavin T (ThT) fluorescence, atomic force microscopy (AFM), and 8-anilinonaphthalene-1-sulphonic acid (ANS) fluorescence were applied and compared to FTIR spectroscopy data. Results show the great potential of FTIR for both, qualitative and quantitative monitoring of oligomer formation based on the secondary structure changes. While oligomer intermediates do not induce significant changes in ThT fluorescence, their secondary structure changes were very prominent. Normalization of specific Amide I region peak intensities by using Amide II peak intensity as an internal standard provides an opportunity to use FTIR spectroscopy for both qualitative and quantitative analysis of biological samples and detection of potentially toxic oligomers, as well as for screening of efficiency of fibrillation procedures.
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23
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Yang J, Agnihotri MV, Huseby CJ, Kuret J, Singer SJ. A theoretical study of polymorphism in VQIVYK fibrils. Biophys J 2021; 120:1396-1416. [PMID: 33571490 DOI: 10.1016/j.bpj.2021.01.032] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 01/07/2021] [Accepted: 01/11/2021] [Indexed: 02/06/2023] Open
Abstract
The VQIVYK fragment from the Tau protein, also known as PHF6, is essential for aggregation of Tau into neurofibrillary lesions associated with neurodegenerative diseases. VQIVYK itself forms amyloid fibrils composed of paired β-sheets. Therefore, the full Tau protein and VQIVYK fibrils have been intensively investigated. A central issue in these studies is polymorphism, the ability of a protein to fold into more than one structure. Using all-atom molecular simulations, we generate five stable polymorphs of VQIVYK fibrils, establish their relative free energy with umbrella sampling methods, and identify the side chain interactions that provide stability. The two most stable polymorphs, which have nearly equal free energy, are formed by interdigitation of the mostly hydrophobic VIY "face" sides of the β-sheets. Another stable polymorph is formed by interdigitation of the QVK "back" sides. When we turn to examine structures from cryo-electron microscopy experiments on Tau filaments taken from diseased patients or generated in vitro, we find that the pattern of side chain interactions found in the two most stable face-to-face as well as the back-to-back polymorphs are recapitulated in amyloid structures of the full protein. Thus, our studies suggest that the interactions stabilizing PHF6 fibrils explain the amyloidogenicity of the VQIVYK motif within the full Tau protein and provide justification for the use of VQIVYK fibrils as a test bed for the design of molecules that identify or inhibit amyloid structures.
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Affiliation(s)
- Jaehoon Yang
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio
| | - Mithila V Agnihotri
- Interdisciplinary Biophysics Graduate Program, The Ohio State University, Columbus, Ohio
| | - Carol J Huseby
- Interdisciplinary Biophysics Graduate Program, The Ohio State University, Columbus, Ohio
| | - Jeff Kuret
- Interdisciplinary Biophysics Graduate Program, The Ohio State University, Columbus, Ohio; Department of Biological Chemistry and Pharmacology, The Ohio State University, Columbus, Ohio.
| | - Sherwin J Singer
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio; Interdisciplinary Biophysics Graduate Program, The Ohio State University, Columbus, Ohio.
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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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25
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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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26
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Pathological ATX3 Expression Induces Cell Perturbations in E. coli as Revealed by Biochemical and Biophysical Investigations. Int J Mol Sci 2021; 22:ijms22020943. [PMID: 33477953 PMCID: PMC7835732 DOI: 10.3390/ijms22020943] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 01/15/2021] [Accepted: 01/16/2021] [Indexed: 02/06/2023] Open
Abstract
Amyloid aggregation of human ataxin-3 (ATX3) is responsible for spinocerebellar ataxia type 3, which belongs to the class of polyglutamine neurodegenerative disorders. It is widely accepted that the formation of toxic oligomeric species is primarily involved in the onset of the disease. For this reason, to understand the mechanisms underlying toxicity, we expressed both a physiological (ATX3-Q24) and a pathological ATX3 variant (ATX3-Q55) in a simplified cellular model, Escherichia coli. It has been observed that ATX3-Q55 expression induces a higher reduction of the cell growth compared to ATX3-Q24, due to the bacteriostatic effect of the toxic oligomeric species. Furthermore, the Fourier transform infrared microspectroscopy investigation, supported by multivariate analysis, made it possible to monitor protein aggregation and the induced cell perturbations in intact cells. In particular, it has been found that the toxic oligomeric species associated with the expression of ATX3-Q55 are responsible for the main spectral changes, ascribable mainly to the cell envelope modifications. A structural alteration of the membrane detected through electron microscopy analysis in the strain expressing the pathological form supports the spectroscopic results.
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Aggarwal L, Biswas P. Hydration Thermodynamics of the N-Terminal FAD Mutants of Amyloid-β. J Chem Inf Model 2021; 61:298-310. [PMID: 33440932 DOI: 10.1021/acs.jcim.0c01286] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The hydration thermodynamics of amyloid-β (Aβ) and its pathogenic familial Alzheimer's disease (FAD) mutants such as A2V, Taiwan (D7H), Tottori (D7N), and English (H6R) and the protective A2T mutant is investigated by a combination of all-atom, explicit water molecular dynamics (MD) simulations and the three-dimensional reference interaction site model (3D-RISM) theory. The change in the hydration free energy on mutation is decomposed into the energetic and entropic components, which comprise electrostatic and nonelectrostatic contributions. An increase in the hydration free energy is observed for A2V, D7H, D7N, and H6R mutations that increase the aggregation propensity of Aβ and lead to an early onset of Alzheimer's disease, while a reverse trend is noted for the protective A2T mutation. An antiphase correlation is found between the change in the hydration energy and the internal energy of Aβ upon mutation. A residue-wise decomposition analysis shows that the change in the hydration free energy of Aβ on mutation is primarily due to the hydration/dehydration of the side-chain atoms of the negatively charged residues. The decrease in the hydration of the negatively charged residues on mutation may decrease the solubility of the mutant, which increases the observed aggregation propensity of the FAD mutants. Results obtained from the theory show an excellent match with the experimentally reported data.
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Affiliation(s)
- Leena Aggarwal
- Department of Chemistry, University of Delhi, Delhi 110007, India
| | - Parbati Biswas
- Department of Chemistry, University of Delhi, Delhi 110007, India
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28
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Pal I, Roy M, Dey SG. Interaction of ApoMyoglobin with Heme-hIAPP complex. J Inorg Biochem 2020; 216:111348. [PMID: 33450674 DOI: 10.1016/j.jinorgbio.2020.111348] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Revised: 12/16/2020] [Accepted: 12/21/2020] [Indexed: 12/13/2022]
Abstract
Human Islet Amyloid Polypeptide (hIAPP) or amylin, can bind heme and the resultant complexes are prone to generate partially reduced oxygen species (PROS). The formation of PROS and the related oxidative stress highlight the importance of Heme-hIAPP in the onset and development of Type 2 Diabetes mellitus (T2Dm) in humans. In this study, the interaction of Heme-hIAPP with apomyoglobin (ApoMb) has been investigated using a combination of spectroscopic and electrophoresis techniques. Absorption, resonance Raman data and gel electrophoresis results confirm that ApoMb can uptake heme from Heme-hIAPP and constitute a six-coordinate high-spin ferric heme active site identical to that of myoglobin (Mb). The heme transfer reaction has two distinct kinetic steps. A possible mechanism of this reaction involves heme transfer to the apoprotein in the first step followed by a reorganisation of the protein chain to form the active site of native Mb. Increase in the pH of the reaction medium enhances the rate of the second step of heme transfer. This possibly corresponds to the deprotonation of a propionate side chain of the heme moiety at high pH which facilitates secondary interactions with the conserved distal Lys45 residue of horse heart Mb. Additionally, ApoMb sequesters ligand bound heme from Heme-hIAPP. After the heme transfer reaction, the amount of PROS formed by Heme-hIAPP complex diminishes significantly. This not only potentially diminishes heme-induced toxicity in the pancreatic β-cells but also produces Mb which has well-documented functions throughout the respiratory system and can thereby likely reduce the risks associated with T2Dm.
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Affiliation(s)
- Ishita Pal
- School of Chemical Sciences, Indian Association for the Cultivation of Science, 2A & 2B, Raja S. C. Mullick Road, Jadavpur, Kolkata 700032, India
| | - Madhuparna Roy
- School of Chemical Sciences, Indian Association for the Cultivation of Science, 2A & 2B, Raja S. C. Mullick Road, Jadavpur, Kolkata 700032, India
| | - Somdatta Ghosh Dey
- School of Chemical Sciences, Indian Association for the Cultivation of Science, 2A & 2B, Raja S. C. Mullick Road, Jadavpur, Kolkata 700032, India.
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29
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Martins PM, Navarro S, Silva A, Pinto MF, Sárkány Z, Figueiredo F, Pereira PJB, Pinheiro F, Bednarikova Z, Burdukiewicz M, Galzitskaya OV, Gazova Z, Gomes CM, Pastore A, Serpell LC, Skrabana R, Smirnovas V, Ziaunys M, Otzen DE, Ventura S, Macedo-Ribeiro S. MIRRAGGE - Minimum Information Required for Reproducible AGGregation Experiments. Front Mol Neurosci 2020; 13:582488. [PMID: 33328883 PMCID: PMC7729192 DOI: 10.3389/fnmol.2020.582488] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2020] [Accepted: 10/23/2020] [Indexed: 12/12/2022] Open
Abstract
Reports on phase separation and amyloid formation for multiple proteins and aggregation-prone peptides are recurrently used to explore the molecular mechanisms associated with several human diseases. The information conveyed by these reports can be used directly in translational investigation, e.g., for the design of better drug screening strategies, or be compiled in databases for benchmarking novel aggregation-predicting algorithms. Given that minute protocol variations determine different outcomes of protein aggregation assays, there is a strong urge for standardized descriptions of the different types of aggregates and the detailed methods used in their production. In an attempt to address this need, we assembled the Minimum Information Required for Reproducible Aggregation Experiments (MIRRAGGE) guidelines, considering first-principles and the established literature on protein self-assembly and aggregation. This consensus information aims to cover the major and subtle determinants of experimental reproducibility while avoiding excessive technical details that are of limited practical interest for non-specialized users. The MIRRAGGE table (template available in Supplementary Information) is useful as a guide for the design of new studies and as a checklist during submission of experimental reports for publication. Full disclosure of relevant information also enables other researchers to reproduce results correctly and facilitates systematic data deposition into curated databases.
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Affiliation(s)
- Pedro M Martins
- Instituto de Biologia Molecular e Celular and Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal.,Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, Porto, Portugal
| | - Susanna Navarro
- Institut de Biotecnologia i Biomedicina - Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Alexandra Silva
- Instituto de Biologia Molecular e Celular and Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
| | - Maria F Pinto
- Instituto de Biologia Molecular e Celular and Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
| | - Zsuzsa Sárkány
- Instituto de Biologia Molecular e Celular and Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
| | - Francisco Figueiredo
- Instituto de Biologia Molecular e Celular and Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal.,Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, Porto, Portugal.,International Iberian Nanotechnology Laboratory - Department of Atomic Structure - Composition of Materials, Braga, Portugal
| | - Pedro José Barbosa Pereira
- Instituto de Biologia Molecular e Celular and Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
| | - Francisca Pinheiro
- Institut de Biotecnologia i Biomedicina - Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Zuzana Bednarikova
- Department of Biophysics, Institute of Experimental Physics, Slovak Academy of Sciences, Kosice, Slovakia
| | - Michał Burdukiewicz
- Faculty of Mathematics and Information Science, Warsaw University of Technology, Warsaw, Poland
| | - Oxana V Galzitskaya
- Institute of Protein Research, Russian Academy of Sciences, Pushchino, Russia.,Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences, Pushchino, Russia
| | - Zuzana Gazova
- Department of Biophysics, Institute of Experimental Physics, Slovak Academy of Sciences, Kosice, Slovakia
| | - Cláudio M Gomes
- Biosystems and Integrative Sciences Institute and Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade de Lisboa, Lisbon, Portugal
| | - Annalisa Pastore
- UK-DRI Centre at King's College London, the Maurice Wohl Clinical Neuroscience Institute, London, United Kingdom
| | - Louise C Serpell
- Sussex Neuroscience, School of Life Sciences, University of Sussex, Brighton, United Kingdom
| | - Rostislav Skrabana
- Department of Neuroimmunology, Axon Neuroscience R&D Services SE, Bratislava, Slovakia.,Institute of Neuroimmunology, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Vytautas Smirnovas
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Mantas Ziaunys
- Institute of Biotechnology, Life Sciences Center, Vilnius University, Vilnius, Lithuania
| | - Daniel E Otzen
- Interdisciplinary Nanoscience Center (iNANO) and Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark
| | - Salvador Ventura
- Institut de Biotecnologia i Biomedicina - Departament de Bioquímica i Biologia Molecular, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Sandra Macedo-Ribeiro
- Instituto de Biologia Molecular e Celular and Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
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30
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Abdelrahman S, Alghrably M, Lachowicz JI, Emwas AH, Hauser CAE, Jaremko M. "What Doesn't Kill You Makes You Stronger": Future Applications of Amyloid Aggregates in Biomedicine. Molecules 2020; 25:E5245. [PMID: 33187056 PMCID: PMC7696280 DOI: 10.3390/molecules25225245] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Revised: 10/24/2020] [Accepted: 10/27/2020] [Indexed: 02/06/2023] Open
Abstract
Amyloid proteins are linked to the pathogenesis of several diseases including Alzheimer's disease, but at the same time a range of functional amyloids are physiologically important in humans. Although the disease pathogenies have been associated with protein aggregation, the mechanisms and factors that lead to protein aggregation are not completely understood. Paradoxically, unique characteristics of amyloids provide new opportunities for engineering innovative materials with biomedical applications. In this review, we discuss not only outstanding advances in biomedical applications of amyloid peptides, but also the mechanism of amyloid aggregation, factors affecting the process, and core sequences driving the aggregation. We aim with this review to provide a useful manual for those who engineer amyloids for innovative medicine solutions.
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Affiliation(s)
- Sherin Abdelrahman
- Laboratory for Nanomedicine, Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia;
| | - Mawadda Alghrably
- Division of Biological and Environmental Sciences and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia;
| | - Joanna Izabela Lachowicz
- Department of Medical Sciences and Public Health, University of Cagliari, Policlinico Universitario, I-09042 Monserrato, Italy
| | - Abdul-Hamid Emwas
- Core Labs, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia;
| | - Charlotte A. E. Hauser
- Laboratory for Nanomedicine, Division of Biological and Environmental Science and Engineering, King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia;
| | - Mariusz Jaremko
- Division of Biological and Environmental Sciences and Engineering (BESE), King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia;
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31
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Bristol AN, Saha J, George HE, Das PK, Kemp LK, Jarrett WL, Rangachari V, Morgan SE. Effects of Stereochemistry and Hydrogen Bonding on Glycopolymer-Amyloid-β Interactions. Biomacromolecules 2020; 21:4280-4293. [PMID: 32786526 PMCID: PMC7847044 DOI: 10.1021/acs.biomac.0c01077] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Saccharide stereochemistry plays an important role in carbohydrate functions such as biological recognition processes and protein binding. Synthetic glycopolymers with pendant saccharides of controlled stereochemistry provide an attractive approach for the design of polysaccharide-inspired biomaterials. Acrylamide-based polymers containing either β,d-glucose or β,d-galactose pendant groups, designed to mimic GM1 ganglioside saccharides, and their small-molecule analogues were used to evaluate the effect of stereochemistry on glycopolymer solution aggregation processes alone and in the presence of Aβ42 peptide using dynamic light scattering, gel permeation chromatography-multiangle laser light scattering, and fluorescence assays. Fourier transform infrared and nuclear magnetic resonance (NMR) were employed to determine hydrogen bonding patterns of the systems. The galactose-containing polymer displayed significant intramolecular hydrogen bonding and self-aggregation and minimal association with Aβ42, while the glucose-containing glycopolymers showed intermolecular interactions with the surrounding environment and association with Aβ42. Saturation transfer difference NMR spectroscopy demonstrated different binding affinities for the two glycopolymers to Aβ42 peptide.
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Affiliation(s)
- Ashleigh N Bristol
- School of Polymer Science and Engineering, The University of Southern Mississippi, Hattiesburg, Mississippi 39406-5050, United States
| | - Jhinuk Saha
- Department of Chemistry and Biochemistry, The University of Southern Mississippi, Hattiesburg, Mississippi 39406-5050, United States
| | - Hannah E George
- School of Polymer Science and Engineering, The University of Southern Mississippi, Hattiesburg, Mississippi 39406-5050, United States
| | - Pradipta K Das
- School of Polymer Science and Engineering, The University of Southern Mississippi, Hattiesburg, Mississippi 39406-5050, United States
| | - Lisa K Kemp
- School of Polymer Science and Engineering, The University of Southern Mississippi, Hattiesburg, Mississippi 39406-5050, United States
| | - William L Jarrett
- School of Polymer Science and Engineering, The University of Southern Mississippi, Hattiesburg, Mississippi 39406-5050, United States
| | - Vijayaraghavan Rangachari
- Department of Chemistry and Biochemistry, The University of Southern Mississippi, Hattiesburg, Mississippi 39406-5050, United States
| | - Sarah E Morgan
- School of Polymer Science and Engineering, The University of Southern Mississippi, Hattiesburg, Mississippi 39406-5050, United States
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32
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Rozniakowski K, Fraczyk A, Galecki K, Wietrzyk J, Filip-Psurska B, Fraczyk J, Kaminski ZJ, Kolesinska B. New Human Islet Amyloid Polypeptide Fragments Susceptible to Aggregation. Chem Biodivers 2020; 17:e2000501. [PMID: 32876375 DOI: 10.1002/cbdv.202000501] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Accepted: 07/28/2020] [Indexed: 12/21/2022]
Abstract
Human Islet Amyloid Polypeptide (hIAPP) plays a key role in the pathogenesis of type II diabetes. The aim of this research was to search for new amyloidogenic fragments of hIAPP. An initial attempt to predict the amyloidogenic cores of polypeptides/proteins using five different computer programs did not provide conclusive results. Therefore, we synthesized hIAPP fragments covering the entire hormone. The fragments were assessed for their aggregation ability, using recommended methods to search for the amyloidogenic fragments of the polypeptides/proteins. It was found that fragments (18-22) H-HSSNN-OH and (33-37) H-GSNTY-NH2 aggregate and form stable amyloid-like structures. Both of these fragments have a much higher antiproliferative activity relative to the RIN-5F cell compared to the (23-27) H-FGAIL-OH fragment widely regarded as the amyloidogenic core of amylin. The analog of (33-37) H-GSNTY-NH2 containing a free carboxy group on the C-terminal amino acid (H-GSNTY-OH) does not have amyloidogenic properties and can therefore be considered as a potential inhibitor of amylin aggregation. Research on the use of non-aggregating amylin fragments as potential hormone aggregation inhibitors is ongoing.
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Affiliation(s)
- Kamil Rozniakowski
- Institute of Organic Chemistry, Faculty of Chemistry, Lodz University of Technology, Zeromskiego 116, Lodz, 90-924, Poland
| | - Andrzej Fraczyk
- Institute of Applied Computer Science, Lodz University of Technology, Stefanowskiego Łódź, 18/22, Lodz, 90-537, Poland
| | - Krystian Galecki
- Institute of General Food Chemistry, Faculty of Biotechnology and Food Sciences, Lodz University of Technology, Stefanowskiego 4/10, Lodz, 90-924, Poland
| | - Joanna Wietrzyk
- Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, 12 Rudolfa Weigla St., 53-114, Wroclaw, Poland
| | - Beata Filip-Psurska
- Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, 12 Rudolfa Weigla St., 53-114, Wroclaw, Poland
| | - Justyna Fraczyk
- Institute of Organic Chemistry, Faculty of Chemistry, Lodz University of Technology, Zeromskiego 116, Lodz, 90-924, Poland
| | - Zbigniew J Kaminski
- Institute of Organic Chemistry, Faculty of Chemistry, Lodz University of Technology, Zeromskiego 116, Lodz, 90-924, Poland
| | - Beata Kolesinska
- Institute of Organic Chemistry, Faculty of Chemistry, Lodz University of Technology, Zeromskiego 116, Lodz, 90-924, Poland
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33
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Taylor AIP, Gahan LD, Chakrabarti B, Staniforth RA. A two-step biopolymer nucleation model shows a nonequilibrium critical point. J Chem Phys 2020; 153:025102. [PMID: 32668930 DOI: 10.1063/5.0009394] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Biopolymer self-assembly pathways are complicated by the ability of their monomeric subunits to adopt different conformational states. This means nucleation often involves a two-step mechanism where the monomers first condense to form a metastable intermediate, which then converts to a stable polymer by conformational rearrangement of constituent monomers. Nucleation intermediates play a causative role in amyloid diseases such as Alzheimer's and Parkinson's. While existing mathematical models neglect the conversion dynamics, experiments show that conversion events frequently occur on comparable timescales to the condensation of intermediates and growth of mature polymers and thus cannot be ignored. We present a model that explicitly accounts for simultaneous assembly and conversion. To describe conversion, we propose an experimentally motivated initiation-propagation mechanism in which the stable phase arises locally within the intermediate and then spreads by nearest-neighbor interactions, in a manner analogous to one-dimensional Glauber dynamics. Our analysis shows that the competing timescales of assembly and conversion result in a nonequilibrium critical point, separating a regime where intermediates are kinetically unstable from one where conformationally mixed intermediates accumulate. This strongly affects the accumulation rate of the stable biopolymer phase. Our model is uniquely able to explain experimental phenomena such as the formation of mixed intermediates and abrupt changes in the scaling exponent γ, which relates the total monomer concentration to the accumulation rate of the stable phase. This provides a first step toward a general model of two-step biopolymer nucleation, which can quantitatively predict the concentration and composition of biologically crucial intermediates.
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Affiliation(s)
- Alexander I P Taylor
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield S10 2TN, United Kingdom
| | - Lianne D Gahan
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield S10 2TN, United Kingdom
| | - Buddhapriya Chakrabarti
- Department of Physics and Astronomy, University of Sheffield, Sheffield S3 7RH, United Kingdom
| | - Rosemary A Staniforth
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield S10 2TN, United Kingdom
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34
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Boatz JC, Piretra T, Lasorsa A, Matlahov I, Conway JF, van der Wel PCA. Protofilament Structure and Supramolecular Polymorphism of Aggregated Mutant Huntingtin Exon 1. J Mol Biol 2020; 432:4722-4744. [PMID: 32598938 DOI: 10.1016/j.jmb.2020.06.021] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2020] [Revised: 06/01/2020] [Accepted: 06/18/2020] [Indexed: 12/11/2022]
Abstract
Huntington's disease is a progressive neurodegenerative disease caused by expansion of the polyglutamine domain in the first exon of huntingtin (HttEx1). The extent of expansion correlates with disease progression and formation of amyloid-like protein deposits within the brain. The latter display polymorphism at the microscopic level, both in cerebral tissue and in vitro. Such polymorphism can dramatically influence cytotoxicity, leading to much interest in the conditions and mechanisms that dictate the formation of polymorphs. We examine conditions that govern HttEx1 polymorphism in vitro, including concentration and the role of the non-polyglutamine flanking domains. Using electron microscopy, we observe polymorphs that differ in width and tendency for higher-order bundling. Strikingly, aggregation yields different polymorphs at low and high concentrations. Narrow filaments dominate at low concentrations that may be more relevant in vivo. We dissect the role of N- and C-terminal flanking domains using protein with the former (httNT or N17) largely removed. The truncated protein is generated by trypsin cleavage of soluble HttEx1 fusion protein, which we analyze in some detail. Dye binding and solid-state NMR studies reveal changes in fibril surface characteristics and flanking domain mobility. Higher-order interactions appear facilitated by the C-terminal tail, while the polyglutamine forms an amyloid core resembling those of other polyglutamine deposits. Fibril-surface-mediated branching, previously attributed to secondary nucleation, is reduced in absence of httNT. A new model for the architecture of the HttEx1 filaments is presented and discussed in context of the assembly mechanism and biological activity.
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Affiliation(s)
- Jennifer C Boatz
- Department of Structural Biology, School of Medicine, University of Pittsburgh, 3501 5th Ave, Biomedical Science Tower 3, Pittsburgh, PA 15213, USA.
| | - Talia Piretra
- Department of Structural Biology, School of Medicine, University of Pittsburgh, 3501 5th Ave, Biomedical Science Tower 3, Pittsburgh, PA 15213, USA.
| | - Alessia Lasorsa
- Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747, AG, Groningen, the Netherlands.
| | - Irina Matlahov
- Department of Structural Biology, School of Medicine, University of Pittsburgh, 3501 5th Ave, Biomedical Science Tower 3, Pittsburgh, PA 15213, USA; Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747, AG, Groningen, the Netherlands.
| | - James F Conway
- Department of Structural Biology, School of Medicine, University of Pittsburgh, 3501 5th Ave, Biomedical Science Tower 3, Pittsburgh, PA 15213, USA.
| | - Patrick C A van der Wel
- Department of Structural Biology, School of Medicine, University of Pittsburgh, 3501 5th Ave, Biomedical Science Tower 3, Pittsburgh, PA 15213, USA; Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 4, 9747, AG, Groningen, the Netherlands.
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35
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Pansieri J, Iashchishyn IA, Fakhouri H, Ostojić L, Malisauskas M, Musteikyte G, Smirnovas V, Schneider MM, Scheidt T, Xu CK, Meisl G, Knowles TPJ, Gazit E, Antoine R, Morozova-Roche LA. Templating S100A9 amyloids on Aβ fibrillar surfaces revealed by charge detection mass spectrometry, microscopy, kinetic and microfluidic analyses. Chem Sci 2020; 11:7031-7039. [PMID: 34122996 PMCID: PMC8159403 DOI: 10.1039/c9sc05905a] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Accepted: 06/16/2020] [Indexed: 12/16/2022] Open
Abstract
The mechanism of amyloid co-aggregation and its nucleation process are not fully understood in spite of extensive studies. Deciphering the interactions between proinflammatory S100A9 protein and Aβ42 peptide in Alzheimer's disease is fundamental since inflammation plays a central role in the disease onset. Here we use innovative charge detection mass spectrometry (CDMS) together with biophysical techniques to provide mechanistic insight into the co-aggregation process and differentiate amyloid complexes at a single particle level. Combination of mass and charge distributions of amyloids together with reconstruction of the differences between them and detailed microscopy reveals that co-aggregation involves templating of S100A9 fibrils on the surface of Aβ42 amyloids. Kinetic analysis further corroborates that the surfaces available for the Aβ42 secondary nucleation are diminished due to the coating by S100A9 amyloids, while the binding of S100A9 to Aβ42 fibrils is validated by a microfluidic assay. We demonstrate that synergy between CDMS, microscopy, kinetic and microfluidic analyses opens new directions in interdisciplinary research.
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Affiliation(s)
- Jonathan Pansieri
- Department of Medical Biochemistry and Biophysics, Umeå University SE-90187 Umeå Sweden
| | - Igor A Iashchishyn
- Department of Medical Biochemistry and Biophysics, Umeå University SE-90187 Umeå Sweden
| | - Hussein Fakhouri
- Institut Lumière Matière, UMR 5306, Université Claude Bernard Lyon 1, CNRS, Univ Lyon F-69100 Villeurbanne France
| | - Lucija Ostojić
- Department of Medical Biochemistry and Biophysics, Umeå University SE-90187 Umeå Sweden
| | - Mantas Malisauskas
- Department of Medical Biochemistry and Biophysics, Umeå University SE-90187 Umeå Sweden
| | - Greta Musteikyte
- Institute of Biotechnology, Life Sciences Center, Vilnius University Vilnius Lithuania
| | - Vytautas Smirnovas
- Institute of Biotechnology, Life Sciences Center, Vilnius University Vilnius Lithuania
| | - Matthias M Schneider
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge Lensfield Road Cambridge CB2 1EW UK
| | - Tom Scheidt
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge Lensfield Road Cambridge CB2 1EW UK
| | - Catherine K Xu
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge Lensfield Road Cambridge CB2 1EW UK
| | - Georg Meisl
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge Lensfield Road Cambridge CB2 1EW UK
| | - Tuomas P J Knowles
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge Lensfield Road Cambridge CB2 1EW UK
- Cavendish Laboratory, Department of Physics, University of Cambridge JJ Thompson Ave CB3 0HE Cambridge UK
| | - Ehud Gazit
- Department of Medical Biochemistry and Biophysics, Umeå University SE-90187 Umeå Sweden
- School of Molecular Cell Biology and Biotechnology, Tel Aviv University Tel Aviv 69978 Israel
| | - Rodolphe Antoine
- Institut Lumière Matière, UMR 5306, Université Claude Bernard Lyon 1, CNRS, Univ Lyon F-69100 Villeurbanne France
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36
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Tian M, Shen L. Self-Coiling of Single-Stranded Protofibrils into Rings: A Pathway of Alzheimer's β-Peptide Amyloidosis on Lipid Membranes. ACS Macro Lett 2020; 9:813-818. [PMID: 35648531 DOI: 10.1021/acsmacrolett.0c00262] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
An amyloidosis pathway of Alzheimer's β-peptide Aβ40 on lipid membranes, the self-coiling of single-stranded protofibrils into thermodynamically stable ring structures, is uncovered. Distinct from Aβ amyloid structures reported previously, the coiled rings observed here exhibit a narrow distribution of diameters centered at ∼170 nm and their circumference thicknesses increase as a longer single-stranded protofibril wraps around the ring, indicating the coaxial loop-by-loop winding of individual protofibrils. Such self-coiling is dominated by elastic properties of the flexible protofibrils subject to thermal fluctuations and surface interactions, as supported by an entropic elasticity model from polymer physics concepts. This work not only provides insights into the fundamental physics of Alzheimer's β-peptide amyloidosis but also is useful for designing amyloid filament materials.
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Affiliation(s)
- Mengting Tian
- School of Chemistry, Chemical Engineering and Life Science, Wuhan University of Technology, Wuhan 430070, China
| | - Lei Shen
- School of Chemistry, Chemical Engineering and Life Science, Wuhan University of Technology, Wuhan 430070, China
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37
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Louros N, Konstantoulea K, De Vleeschouwer M, Ramakers M, Schymkowitz J, Rousseau F. WALTZ-DB 2.0: an updated database containing structural information of experimentally determined amyloid-forming peptides. Nucleic Acids Res 2020; 48:D389-D393. [PMID: 31504823 PMCID: PMC6943037 DOI: 10.1093/nar/gkz758] [Citation(s) in RCA: 66] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2019] [Revised: 08/13/2019] [Accepted: 08/30/2019] [Indexed: 02/06/2023] Open
Abstract
Transition of soluble proteins into insoluble amyloid fibrils is driven by self-propagating short sequence stretches. However, accurate prediction of aggregation determinants remains challenging. Here, we describe WALTZ-DB 2.0, an updated and significantly expanded open-access database providing information on experimentally determined amyloid-forming hexapeptide sequences (http://waltzdb.switchlab.org/). We have updated WALTZ-DB 2.0 with new entries, including: (i) experimental validation of an in-house developed dataset of 229 hexapeptides, using electron microscopy and Thioflavin-T binding assays; (ii) manual curation of 98 amyloid-forming peptides isolated from literature. Furthermore, the content has been expanded by adding novel structural information for peptide entries, including sequences of the previous version. Using a computational methodology developed in the Switch lab, we have generated 3D-models of the putative amyloid fibril cores of WALTZ-DB 2.0 entries. Structural models, coupled with information on the energetic contributions and fibril core stabilities, can be accessed through individual peptide entries. Customized filtering options for subset selections and new modelling graphical features were added to upgrade online accessibility, providing a user-friendly interface for browsing, downloading and updating. WALTZ-DB 2.0 remains the largest open-access repository for amyloid fibril formation determinants and will continue to enhance the development of new approaches focused on accurate prediction of aggregation prone sequences.
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Affiliation(s)
- Nikolaos Louros
- VIB Center for Brain & Disease Research, Switch Laboratory, Leuven, 3000, Belgium.,KU Leuven, Department of Cellular and Molecular Medicine, Leuven, 3000, Belgium
| | - Katerina Konstantoulea
- VIB Center for Brain & Disease Research, Switch Laboratory, Leuven, 3000, Belgium.,KU Leuven, Department of Cellular and Molecular Medicine, Leuven, 3000, Belgium
| | - Matthias De Vleeschouwer
- VIB Center for Brain & Disease Research, Switch Laboratory, Leuven, 3000, Belgium.,KU Leuven, Department of Cellular and Molecular Medicine, Leuven, 3000, Belgium
| | - Meine Ramakers
- VIB Center for Brain & Disease Research, Switch Laboratory, Leuven, 3000, Belgium.,KU Leuven, Department of Cellular and Molecular Medicine, Leuven, 3000, Belgium
| | - Joost Schymkowitz
- VIB Center for Brain & Disease Research, Switch Laboratory, Leuven, 3000, Belgium.,KU Leuven, Department of Cellular and Molecular Medicine, Leuven, 3000, Belgium
| | - Frederic Rousseau
- VIB Center for Brain & Disease Research, Switch Laboratory, Leuven, 3000, Belgium.,KU Leuven, Department of Cellular and Molecular Medicine, Leuven, 3000, Belgium
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38
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Abstract
Amyloid fibrils represent one of the defining features of Alzheimer's disease (AD). They are made up of protofilaments composed of amyloid β (Aβ) peptides that are held together with extraordinary stability by a network of tight steric zippers and axial hydrogen bonds. This review explores the hypothesis that the peptide conformation within a protofilament represents the physical embodiment of a "strain" of AD. Evidence suggests that within a single strain the fold of individual peptides is invariant. However, the fibrils are capable of structural polymorphism that includes variation in the arrangement of protofilaments into fibrils, the pitch of the resultant fibrils, and the higher-order organization of the plaques into which they aggregate. These intrastrain polymorphisms are separated by low energy barriers, allowing multiple configurations to coexist within a single preparation or tissue. Clinical presentation of different strains may be determined by variation in the way different protofilament structures generate the relevant toxic species, be they monomers, oligomers, or higher-order structures. Evidence reviewed here is consistent with a model in which disease progression is concomitant with a gradual, progressive annealing of amyloid fibrils from benign, loosely packed structures into dense neurotoxic aggregates. This model challenges the commonly held hypothesis that oligomers of Aβ peptides are the only active proximate species in neurodegeneration. However, the data do not implicate fibrils themselves. Rather, they cast suspicion on larger-scale supramolecular aggregates as toxic agents. Electron tomography of amyloid plaques in situ strongly suggests that the formation of amyloid aggregates results in perturbation of the cellular membrane integrity, warranting further investigation of this as a potential mode of neurotoxicity. If dense supramolecular amyloid aggregates prove to be important agents of neurodegeneration in AD, this model may also have relevance to other forms of amyloidoses.
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Affiliation(s)
- Lee Makowski
- Departments of Bioengineering and Chemistry and Chemical Biology, Northeastern University, Boston, Massachusetts 02115, United States
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39
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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: 93] [Impact Index Per Article: 23.3] [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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40
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Krupová M, Kessler J, Bouř P. Recent Trends in Chiroptical Spectroscopy: Theory and Applications of Vibrational Circular Dichroism and Raman Optical Activity. Chempluschem 2020; 85:561-575. [DOI: 10.1002/cplu.202000014] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Revised: 02/18/2020] [Indexed: 12/13/2022]
Affiliation(s)
- Monika Krupová
- Institute of Organic Chemistry and Biochemistry Academy of Sciences Flemingovo náměstí 2 16610 Prague Czech Republic
- Faculty of Mathematics and PhysicsCharles University Ke Karlovu 3 12116 Prague 2 Czech Republic
| | - Jiří Kessler
- Institute of Organic Chemistry and Biochemistry Academy of Sciences Flemingovo náměstí 2 16610 Prague Czech Republic
| | - Petr Bouř
- Institute of Organic Chemistry and Biochemistry Academy of Sciences Flemingovo náměstí 2 16610 Prague Czech Republic
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41
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Ono K, Tsuji M. Protofibrils of Amyloid-β are Important Targets of a Disease-Modifying Approach for Alzheimer's Disease. Int J Mol Sci 2020; 21:ijms21030952. [PMID: 32023927 PMCID: PMC7037706 DOI: 10.3390/ijms21030952] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Revised: 01/20/2020] [Accepted: 01/29/2020] [Indexed: 12/20/2022] Open
Abstract
Worldwide, Alzheimer’s disease (AD) is the most common age-related neurodegenerative disease and is characterized by unique pathological hallmarks in the brain, including plaques composed of amyloid β-protein (Aβ) and neurofibrillary tangles of tau protein. Genetic studies, biochemical data, and animal models have suggested that Aβ is responsible for the pathogenesis of AD (i.e., the amyloid hypothesis). Indeed, Aβ molecules tend to aggregate, forming oligomers, protofibrils, and mature fibrils. However, while these Aβ species form amyloid plaques of the type implicated in AD neurodegeneration, recent clinical trials designed to reduce the production of Aβ and/or the plaque burden have not demonstrated clinical efficacy. In addition, recent studies using synthetic Aβ peptides, cell culture models, Arctic transgenic mice, and human samples of AD brain tissues have suggested that the pre-fibrillar forms of Aβ, particularly Aβ protofibrils, may be the most critical species, compared with extracellular fibrillar forms. We recently reported that protofibrils of Aβ1-42 disturbed membrane integrity by inducing reactive oxygen species generation and lipid peroxidation, resulting in decreased membrane fluidity, intracellular calcium dysregulation, depolarization, and synaptic toxicity. Therefore, the therapeutic reduction of protofibrils may prevent the progression of AD by ameliorating neuronal damage and cognitive dysfunction through multiple mechanisms.
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Affiliation(s)
- Kenjiro Ono
- Department of Internal Medicine, Division of Neurology, School of Medicine, Showa University, Tokyo 142-8666, Japan
- Correspondence: ; Tel.: +81-3-3784-8710
| | - Mayumi Tsuji
- Department of Pharmacology, School of Medicine, Showa University, Tokyo 142-8666, Japan;
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42
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Marcinko TM, Liang C, Savinov S, Chen J, Vachet RW. Structural Heterogeneity in the Preamyloid Oligomers of β-2-Microglobulin. J Mol Biol 2019; 432:396-409. [PMID: 31711963 DOI: 10.1016/j.jmb.2019.10.030] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Revised: 10/25/2019] [Accepted: 10/30/2019] [Indexed: 11/29/2022]
Abstract
In dialysis patients, the protein β2-microglobulin (β2m) forms amyloid fibrils in a condition known as dialysis-related amyloidosis. To understand the early stages of the amyloid assembly process, we have used native electrospray ionization (ESI) together with ion mobility mass spectrometry (IM-MS) to study soluble preamyloid oligomers. ESI-IM-MS reveals the presence of multiple conformers for the dimer, tetramer, and hexamer that precede the Cu(II)-induced amyloid assembly process, results which are distinct from β2m oligomers formed at low pH. Experimental and computational results indicate that the predominant dimer is a Cu(II)-bound structure with an antiparallel side-by-side configuration. In contrast, tetramers exist in solution in both Cu(II)-bound and Cu(II)-free forms. Selective depletion of Cu(II)-bound species results in two primary conformers-one that is compact and another that is more expanded. Molecular modeling and molecular dynamics simulations identify models for these two tetrameric conformers with unique interactions and interfaces that enthalpically compensate for the loss of Cu(II). Unlike with other amyloid systems in which conformational heterogeneity is often associated with different amyloid morphologies or off-pathway events, conformational heterogeneity in the tetramer seems to be a necessary aspect of Cu(II)-induced amyloid formation by β2m. Moreover, the Cu(II)-free models represent a new advance in our understanding of Cu(II) release in Cu(II)-induced amyloid formation, laying a foundation for further mechanistic studies as well as development of new inhibition strategies.
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Affiliation(s)
- Tyler M Marcinko
- Department of Chemistry, University of Massachusetts, Amherst, MA 01003, United States
| | - Chungwen Liang
- Computational and Modeling Core Facility, Institute for Applied Life Sciences, Amherst, MA 01003, United States
| | - Sergey Savinov
- Computational and Modeling Core Facility, Institute for Applied Life Sciences, Amherst, MA 01003, United States; Department of Biochemistry and Molecular Biology, University of Massachusetts, Amherst, MA 01003, United States
| | - Jianhen Chen
- Department of Chemistry, University of Massachusetts, Amherst, MA 01003, United States; Department of Biochemistry and Molecular Biology, University of Massachusetts, Amherst, MA 01003, United States
| | - Richard W Vachet
- Department of Chemistry, University of Massachusetts, Amherst, MA 01003, United States.
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43
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Zurlo E, Gorroño Bikandi I, Meeuwenoord NJ, Filippov DV, Huber M. Tracking amyloid oligomerization with monomer resolution using a 13-amino acid peptide with a backbone-fixed spin label. Phys Chem Chem Phys 2019; 21:25187-25195. [PMID: 31696167 DOI: 10.1039/c9cp01060b] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Amyloid oligomers are suspected as toxic agents in neurodegenerative disease, and are transient and often heterogeneous, making them difficult to detect. Here we show an approach to track the development of amyloid oligomers in situ by room temperature, continuous wave (cw) 9 and 95 GHz EPR. Three amyloid peptides with the 2,2,6,6-tetramethyl-N-oxyl-4-amino-4-carboxylic acid (TOAC) spin label were synthesized by solid phase peptide synthesis: T0EZ (TKVKVLGDVIEVGG) with TOAC (T) at the N-terminus, T5EZ with TOAC in the middle (KVKVTGDVIEVG) and T12EZ with TOAC at the C-terminus (KVKVLGDVIEVTG). These sequences are derived from the K11V (KVKVLGDVIEV) amyloid peptide, which self-aggregates to oligomers with a β-sheet configuration (A. Laganowsky, et al., Science, 2012, 335, 1228-1231). To monitor oligomerization, the rotational correlation time (τr) is measured by cw-EPR. For the backbone-fixed TOAC label that is devoid of local mobility τr should reflect the rotation and thereby the size of the peptide, resp. oligomer. For T5EZ a good match between the measured τr and the size of the peptide is obtained, showing the validity of the approach. One of the three peptides (T0EZ) aggregates (circular dichroism), whereas the other two do not. Since also the respective MTSL (S-(1-oxyl-2,2,5,5-tetramethyl-2,5-dihydro-1H-pyrrol-3-yl)methyl methanesulfonothioate) labelled peptides fail to aggregate, molecular crowding due to the label, rather than the helix-inducing properties of TOAC, seems to be responsible. Following in situ oligomer formation of T0EZ by the change in rotational correlation time, two oligomers are observed, a 5-6 mer and a 15-18 mer. The EPR approach, particularly 95 GHz EPR, enables following oligomerization of one monomer at a time, suggesting that the cw-EPR approach presented is a novel tool to follow amyloid oligomerization with high resolution.
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Affiliation(s)
- E Zurlo
- Department of Physics, Huygens-Kamerlingh Onnes Laboratory, Leiden University, 2300 RA Leiden, The Netherlands.
| | - I Gorroño Bikandi
- Department of Physics, Huygens-Kamerlingh Onnes Laboratory, Leiden University, 2300 RA Leiden, The Netherlands.
| | - N J Meeuwenoord
- Leiden Institute of Chemistry, Gorlaeus Laboratoria, Leiden University, 2300 RA Leiden, The Netherlands
| | - D V Filippov
- Leiden Institute of Chemistry, Gorlaeus Laboratoria, Leiden University, 2300 RA Leiden, The Netherlands
| | - M Huber
- Department of Physics, Huygens-Kamerlingh Onnes Laboratory, Leiden University, 2300 RA Leiden, The Netherlands.
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Pilkington AW, Donohoe GC, Akhmedov NG, Ferrebee T, Valentine SJ, Legleiter J. Hydrogen Peroxide Modifies Aβ-Membrane Interactions with Implications for Aβ 40 Aggregation. Biochemistry 2019; 58:2893-2905. [PMID: 31187978 DOI: 10.1021/acs.biochem.9b00233] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Alzheimer's disease (AD) is pathologically characterized by the formation of extracellular senile plaques, predominately comprised of aggregated β-amyloid (Aβ), deposited in the brain. Aβ aggregation can result in a myriad of distinct aggregate species, from soluble oligomers to insoluble fibrils. Aβ strongly interacts with membranes, which can be linked to a variety of potential toxic mechanisms associated with AD. Oxidative damage accompanies the formation of Aβ aggregates, with a 10-50% proportion of Aβ aggregates being oxidized in vivo. Hydrogen peroxide (H2O2) is a reactive oxygen species implicated in a number of neurodegenerative diseases. Recent evidence has demonstrated that the H2O2 concentration fluctuates rapidly in the brain, resulting in large concentration spikes, especially in the synaptic cleft. Here, the impact of environmental H2O2 on Aβ aggregation in the presence and absence of lipid membranes is investigated. Aβ40 was exposed to H2O2, resulting in the selective oxidation of methionine 35 (Met35) to produce Aβ40Met35[O]. While oxidation mildly reduced the rate of Aβ aggregation and produced a distinct fibril morphology at high H2O2 concentrations, H2O2 had a much more pronounced impact on Aβ aggregation in the presence of total brain lipid extract vesicles. The impact of H2O2 on Aβ aggregation in the presence of lipids was associated with a reduced affinity of Aβ for the vesicle surface. However, this reduced vesicle affinity was predominately associated with lipid peroxidation rather than Aβ oxidation.
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Affiliation(s)
- Albert W Pilkington
- The C. Eugene Bennett Department of Chemistry , West Virginia University , 217 Clark Hall , Morgantown , West Virginia 26506 , United States
| | - Gregory C Donohoe
- The C. Eugene Bennett Department of Chemistry , West Virginia University , 217 Clark Hall , Morgantown , West Virginia 26506 , United States
| | - Novruz G Akhmedov
- The C. Eugene Bennett Department of Chemistry , West Virginia University , 217 Clark Hall , Morgantown , West Virginia 26506 , United States
| | - Timothy Ferrebee
- The C. Eugene Bennett Department of Chemistry , West Virginia University , 217 Clark Hall , Morgantown , West Virginia 26506 , United States
| | - Stephen J Valentine
- The C. Eugene Bennett Department of Chemistry , West Virginia University , 217 Clark Hall , Morgantown , West Virginia 26506 , United States
| | - Justin Legleiter
- The C. Eugene Bennett Department of Chemistry , West Virginia University , 217 Clark Hall , Morgantown , West Virginia 26506 , United States.,Blanchette Rockefeller Neurosciences Institutes , West Virginia University , 1 Medical Center Drive , P.O. Box 9303, Morgantown , West Virginia 26505 , United States.,Department of Neuroscience , West Virginia University , 1 Medical Center Drive , P.O. Box 9303, Morgantown , West Virginia 26505 , United States
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45
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W. Pilkington IV A, Legleiter J. Challenges in understanding the structure/activity relationship of Aβ oligomers. AIMS BIOPHYSICS 2019. [DOI: 10.3934/biophy.2019.1.1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
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46
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Sub-Toxic Human Amylin Fragment Concentrations Promote the Survival and Proliferation of SH-SY5Y Cells via the Release of VEGF and HspB5 from Endothelial RBE4 Cells. Int J Mol Sci 2018; 19:ijms19113659. [PMID: 30463298 PMCID: PMC6274958 DOI: 10.3390/ijms19113659] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2018] [Revised: 11/15/2018] [Accepted: 11/16/2018] [Indexed: 12/19/2022] Open
Abstract
Human amylin is a 37-residue peptide hormone (hA1-37) secreted by β-cells of the pancreas and, along with insulin, is directly associated with type 2 diabetes mellitus (T2DM). Amyloid deposits within the islets of the pancreas represent a hallmark of T2DM. Additionally, amylin aggregates have been found in blood vessels and/or brain of patients with Alzheimer’s disease, alone or co-deposited with β-amyloid. The purpose of this study was to investigate the neuroprotective potential of human amylin in the context of endothelial-neuronal “cross-talk”. We initially performed dose-response experiments to examine cellular toxicity (quantified by the [3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide] MTT assay) of different hA17–29 concentrations in endothelial cells (RBE4). In the culture medium of these cells, we also measured heat shock protein B5 (HspB5) levels by ELISA, finding that even a sub-toxic concentration of hA17–29 (3 µM) produced an increase of HspB5. Using a cell medium of untreated and RBE4 challenged for 48 h with a sub-toxic concentration of hA17–29, we determined the potential beneficial effect of their addition to the medium of neuroblastoma SH-SY5Y cells. These cells were subsequently incubated for 48 h with a toxic concentration of hA17–29 (20 µM). We found a complete inhibition of hA17–29 toxicity, potentially related to the presence in the conditioned medium not only of HspB5, but also of vascular endothelial growth factor (VEGF). Pre-treating SH-SY5Y cells with the anti-Flk1 antibody, blocking the VEGF receptor 2 (VEGFR2), significantly decreased the protective effects of the conditioned RBE4 medium. These data, obtained by indirectly measuring VEGF activity, were strongly corroborated by the direct measurement of VEGF levels in conditioned RBE4 media as detected by ELISA. Altogether, these findings highlighted a novel role of sub-toxic concentrations of human amylin in promoting the secretion of proteic factors by endothelial cells (HspB5 and VEGF) that support the survival and proliferation of neuron-like cells.
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47
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Dasari AKR, Hung I, Gan Z, Lim KH. Two distinct aggregation pathways in transthyretin misfolding and amyloid formation. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2018; 1867:344-349. [PMID: 30366153 DOI: 10.1016/j.bbapap.2018.10.013] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Revised: 10/17/2018] [Accepted: 10/22/2018] [Indexed: 01/17/2023]
Abstract
Misfolding and amyloid formation of transthyretin (TTR) is implicated in numerous degenerative diseases. TTR misfolding is greatly accelerated under acidic conditions, and thus most of the mechanistic studies of TTR amyloid formation have been conducted at various acidic pH values (2-5). In this study, we report the effect of pH on TTR misfolding pathways and amyloid structures. Our combined solution and solid-state NMR studies revealed that TTR amyloid formation can proceed via at least two distinct misfolding pathways depending on the acidic conditions. Under mildly acidic conditions (pH 4.4), tetrameric native TTR appears to dissociate to monomers that maintain most of the native-like β-sheet structures. The amyloidogenic protein undergoes a conformational transition to largely unfolded states at more acidic conditions (pH 2.4), leading to amyloid with distinct molecular structures. Aggregation kinetics is also highly dependent upon the acidic conditions. TTR quickly forms moderately ordered amyloids at pH 4.4, while the aggregation kinetics is dramatically reduced at a lower pH of 2.4. The effect of the pathogenic mutations on aggregation kinetics is also markedly different under the two different acidic conditions. Pathogenic TTR variants (V30M and L55P) aggregate more aggressively than WT TTR at pH 4.4. In contrast, the single-point mutations do not affect the aggregation kinetics at the more acidic condition of pH 2.4. Given that the pathogenic mutations lead to more aggressive forms of TTR amyloidoses, the mildly acidic condition might be more suitable for mechanistic studies of TTR misfolding and aggregation.
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Affiliation(s)
- Anvesh K R Dasari
- Department of Chemistry, East Carolina University, Greenville, NC 27858, USA
| | - Ivan Hung
- Center of Interdisciplinary Magnetic Resonance (CIMAR), National High Magnetic Field Laboratory (NHMFL), 1800 East, Paul Dirac Dr., Tallahassee, FL 32310, USA
| | - Zhehong Gan
- Center of Interdisciplinary Magnetic Resonance (CIMAR), National High Magnetic Field Laboratory (NHMFL), 1800 East, Paul Dirac Dr., Tallahassee, FL 32310, USA
| | - Kwang Hun Lim
- Department of Chemistry, East Carolina University, Greenville, NC 27858, USA.
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48
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Al-Halifa S, Babych M, Zottig X, Archambault D, Bourgault S. Amyloid self-assembling peptides: Potential applications in nanovaccine engineering and biosensing. Pept Sci (Hoboken) 2018. [DOI: 10.1002/pep2.24095] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Soultan Al-Halifa
- Department of Chemistry; Université du Québec à Montréal; Montreal, QC Canada
- Quebec Network for Research on Protein Function, Engineering and Applications, PROTEO; Québec QC Canada
| | - Margaryta Babych
- Department of Chemistry; Université du Québec à Montréal; Montreal, QC Canada
- Quebec Network for Research on Protein Function, Engineering and Applications, PROTEO; Québec QC Canada
| | - Ximena Zottig
- Department of Chemistry; Université du Québec à Montréal; Montreal, QC Canada
- Quebec Network for Research on Protein Function, Engineering and Applications, PROTEO; Québec QC Canada
| | - Denis Archambault
- Department of Biological Sciences; Université du Québec à Montréal; Montreal, QC Canada
- Swine and Poultry Infectious Diseases Research Centre, CRIPA; QC Canada
| | - Steve Bourgault
- Department of Chemistry; Université du Québec à Montréal; Montreal, QC Canada
- Quebec Network for Research on Protein Function, Engineering and Applications, PROTEO; Québec QC Canada
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49
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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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Michaels TCT, Šarić A, Habchi J, Chia S, Meisl G, Vendruscolo M, Dobson CM, Knowles TPJ. Chemical Kinetics for Bridging Molecular Mechanisms and Macroscopic Measurements of Amyloid Fibril Formation. Annu Rev Phys Chem 2018; 69:273-298. [PMID: 29490200 DOI: 10.1146/annurev-physchem-050317-021322] [Citation(s) in RCA: 129] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Understanding how normally soluble peptides and proteins aggregate to form amyloid fibrils is central to many areas of modern biomolecular science, ranging from the development of functional biomaterials to the design of rational therapeutic strategies against increasingly prevalent medical conditions such as Alzheimer's and Parkinson's diseases. As such, there is a great need to develop models to mechanistically describe how amyloid fibrils are formed from precursor peptides and proteins. Here we review and discuss how ideas and concepts from chemical reaction kinetics can help to achieve this objective. In particular, we show how a combination of theory, experiments, and computer simulations, based on chemical kinetics, provides a general formalism for uncovering, at the molecular level, the mechanistic steps that underlie the phenomenon of amyloid fibril formation.
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Affiliation(s)
- Thomas C T Michaels
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom; .,Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, Massachusetts 02138, USA
| | - Anđela Šarić
- Department of Physics and Astronomy, and Institute for the Physics of Living Systems, University College London, London WC1E 6BT, United Kingdom
| | - Johnny Habchi
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom;
| | - Sean Chia
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom;
| | - Georg Meisl
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom;
| | - Michele Vendruscolo
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom;
| | - Christopher M Dobson
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom;
| | - Tuomas P J Knowles
- Centre for Misfolding Diseases, Department of Chemistry, University of Cambridge, Cambridge CB2 1EW, United Kingdom; .,Cavendish Laboratory, Department of Physics, University of Cambridge, Cambridge CB3 1HE, United Kingdom; ,
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