Methods for Structural Analysis of Amyloid Fibrils in Misfolding Diseases

2018 ◽  
pp. 109-122 ◽  
Author(s):  
Devkee M. Vadukul ◽  
Youssra K. Al-Hilaly ◽  
Louise C. Serpell
Keyword(s):  
Structural Analysis ◽  
Amyloid Fibrils ◽  
Misfolding Diseases

scholarly journals Structure and Aggregation Mechanisms in Amyloids

Molecules ◽  
2020 ◽  
Vol 25 (5) ◽  
pp. 1195 ◽  
Author(s):  
Zaida L. Almeida ◽  
Rui M. M. Brito
Keyword(s):  
Molecular Species ◽  
Molecular Mechanisms ◽  
Amyloid Fibrils ◽  
Current Knowledge ◽  
Point Of View ◽  
Resonance Spectroscopy ◽  
Amyloid Formation ◽  
Amyloid Fibril Formation ◽  
Misfolding Diseases ◽  
Amyloid Cascade

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.

scholarly journals Structural identification of individual helical amyloid filaments by integration of cryo-electron microscopy-derived maps in comparative morphometric atomic force microscopy image analysis

2021 ◽  
Author(s):  
Liisa Lutter ◽  
Youssra Al-Hilaly ◽  
Christopher J. Serpell ◽  
Mick F. Tuite ◽  
Claude M. Wischik ◽  
...  
Keyword(s):  
Electron Microscopy ◽  
Atomic Force Microscopy ◽  
Image Analysis ◽  
Structural Analysis ◽  
Amyloid Fibrils ◽  
Structural Identification ◽  
Force Microscopy ◽  
Atomic Force ◽  
Cryo Electron Microscopy

The presence of amyloid fibrils is a hallmark of more than 50 human disorders, including neurodegenerative diseases and systemic amyloidoses. A key unresolved challenge in understanding the involvement of amyloid in disease is to explain the relationship between individual structural polymorphs of amyloid fibrils, in potentially mixed populations, and the specific pathologies with which they are associated. Although cryo-electron microscopy (cryo-EM) and solid-state nuclear magnetic resonance (ssNMR) spectroscopy methods have been successfully employed in recent years to determine the structures of amyloid fibrils with high resolution detail, they rely on ensemble averaging of fibril structures in the entire sample or significant subpopulations. Here, we report a method for structural identification of individual fibril structures imaged by atomic force microscopy (AFM) by integration of high-resolution maps of amyloid fibrils determined by cryo-EM in comparative AFM image analysis. This approach was demonstrated using the hitherto structurally unresolved amyloid fibrils formed in vitro from a fragment of tau (297-391), termed 'dGAE'. Our approach established unequivocally that dGAE amyloid fibrils bear no structural relationship to heparin-induced tau fibrils formed in vitro. Furthermore, our comparative analysis resulted in the prediction that dGAE fibrils are closely related structurally to the paired helical filaments (PHFs) isolated from Alzheimer's disease (AD) brain tissue characterised by cryo-EM. These results show the utility of individual particle structural analysis using AFM, provide a workflow of how cryo-EM data can be incorporated into AFM image analysis and facilitate an integrated structural analysis of amyloid polymorphism.

Fine Structural Analysis of Muscle Degeneration Caused by Amyloid Infiltration

1975 ◽  
Vol 33 ◽  
pp. 424-425
Author(s):  
O. G. Rodgers ◽  
T. Shirahama ◽  
A.S. Cohen
Keyword(s):  
Heart Failure ◽  
Structural Analysis ◽  
Ultrastructural Study ◽  
Amyloid Fibrils ◽  
Muscle Cells ◽  
Primary Amyloidosis ◽  
Muscle Degeneration ◽  
Muscle Ultrastructure ◽  
Primary Type ◽  
Five Phases

Amyloidosis, especially the primary type, often causes myopathies including heart failure. These myopathies are believed to be secondary to the infiltration of amyloid around and into the muscle cells. However no detailed ultrastructural study has been available on this subject in either skeletal or cardiac muscle.The intrinsic muscle ultrastructure of tongue obtained at hemiglossectomy from two patients with systemic primary amyloidosis with macroglossia were studied. The results were analysed to assess the process of muscle atrophy caused by infiltration of the amyloid fibrils.The atrophic process can be classified into five phases. 1) In the area free of and remote from the amyloid deposition muscle ultrastructure was normal (Fig. 1). 2) While larger amounts of amyloid fibrils were deposited around the muscle cells, amyloid fibrils were also found in the muscle cells forming relatively large islands or in small amounts among the myofibrils.

scholarly journals Microcin Amyloid Fibrils A Are Reservoir of Toxic Oligomeric Species

2012 ◽  
Vol 287 (15) ◽  
pp. 11665-11676 ◽  
Author(s):  
Mohammad Shahnawaz ◽  
Claudio Soto
Keyword(s):  
Environmental Conditions ◽  
Protein Misfolding ◽  
Amyloid Fibrils ◽  
Target Cells ◽  
Low Molecular Weight ◽  
Toxic Species ◽  
Soluble Species ◽  
Misfolding Diseases

Microcin E492 (Mcc), a low molecular weight bacteriocin produced by Klebsiella pneumoniae RYC492, has been shown to exist in two forms: soluble forms that are believed to be toxic to the bacterial cell by forming pores and non-toxic fibrillar forms that share similar biochemical and biophysical properties with amyloids associated with several human diseases. Here we report that fibrils polymerized in vitro from soluble forms sequester toxic species that can be released upon changing environmental conditions such as pH, ionic strength, and upon dilution. Our results indicate that basic pH (≥8.5), low NaCl concentrations (≤50 mm), and dilution (>10-fold) destabilize Mcc fibrils into more soluble species that are found to be toxic to the target cells. Additionally, we also found a similar conversion of non-toxic fibrils into highly toxic oligomers using Mcc aggregates produced in vivo. Moreover, the soluble protein released from fibrils is able to rapidly polymerize into amyloid fibrils under fibril-forming conditions and to efficiently seed aggregation of monomeric Mcc. Our findings indicate that fibrillar forms of Mcc constitute a reservoir of toxic oligomeric species that is released into the medium upon changing the environmental conditions. These findings may have substantial implications to understand the dynamic process of interconversion between toxic and non-toxic aggregated species implicated in protein misfolding diseases.

scholarly journals 2P-008 Structural Analysis of Amyloid Fibrils of β2-Microglobulin by Solid-State NMR(The 46th Annual Meeting of the Biophysical Society of Japan)

2008 ◽  
Vol 48 (supplement) ◽  
pp. S76
Author(s):  
Miwako Saeka ◽  
Yasuto Todokoro ◽  
Ayako Egawa ◽  
Atsushi Kameda ◽  
Eri Chatani ◽  
...  
Keyword(s):  
Solid State ◽  
Structural Analysis ◽  
Annual Meeting ◽  
Solid State Nmr ◽  
Amyloid Fibrils ◽  
Β2 Microglobulin ◽  
Biophysical Society

scholarly journals 3P046 Structural analysis of amyloid fibrils ofβ2-microglobulin using tryptophan fluorescence probe

2005 ◽  
Vol 45 (supplement) ◽  
pp. S215
Author(s):  
M. Kihara ◽  
K. Yamamoto ◽  
K. Iwata ◽  
E. Chatani ◽  
K. Hasegawa ◽  
...  
Keyword(s):  
Structural Analysis ◽  
Amyloid Fibrils ◽  
Fluorescence Probe ◽  
Tryptophan Fluorescence

scholarly journals Exploring the sequence–structure relationship for amyloid peptides

2013 ◽  
Vol 450 (2) ◽  
pp. 275-283 ◽  
Author(s):  
Kyle L. Morris ◽  
Alison Rodger ◽  
Matthew R. Hicks ◽  
Maya Debulpaep ◽  
Joost Schymkowitz ◽  
...  
Keyword(s):  
Self Assembly ◽  
Amyloid Fibrils ◽  
Linear Dichroism ◽  
Model Systems ◽  
Molecular Architecture ◽  
Amyloid Peptides ◽  
Amyloid Fibril Formation ◽  
Structure Relationship ◽  
Fibre Diffraction ◽  
Misfolding Diseases

Amyloid fibril formation is associated with misfolding diseases, as well as fulfilling a functional role. The cross-β molecular architecture has been reported in increasing numbers of amyloid-like fibrillar systems. The Waltz algorithm is able to predict ordered self-assembly of amyloidogenic peptides by taking into account the residue type and position. This algorithm has expanded the amyloid sequence space, and in the present study we characterize the structures of amyloid-like fibrils formed by three peptides identified by Waltz that form fibrils but not crystals. The structural challenge is met by combining electron microscopy, linear dichroism, CD and X-ray fibre diffraction. We propose structures that reveal a cross-β conformation with ‘steric-zipper’ features, giving insights into the role for side chains in peptide packing and stability within fibrils. The amenity of these peptides to structural characterization makes them compelling model systems to use for understanding the relationship between sequence, self-assembly, stability and structure of amyloid fibrils.

Exploiting amyloid: how and why bacteria use cross-β fibrils

2012 ◽  
Vol 40 (4) ◽  
pp. 728-734 ◽  
Author(s):  
Elizabeth B. Sawyer ◽  
Dennis Claessen ◽  
Sally L. Gras ◽  
Sarah Perrett
Keyword(s):  
Alzheimer’S Disease ◽  
Alzheimer's Disease ◽  
Protein Misfolding ◽  
Amyloid Fibrils ◽  
Streptomyces Coelicolor ◽  
Present Review ◽  
Protein Fibrils ◽  
Recent Developments ◽  
Misfolding Diseases

Many bacteria produce protein fibrils that are structurally analogous to those associated with protein misfolding diseases such as Alzheimer's disease. However, unlike fibrils associated with disease, bacterial amyloids have beneficial functions including conferring stability to biofilms, regulating development or imparting virulence. In the present review, we consider what makes amyloid fibrils so suitable for these roles and discuss recent developments in the study of bacterial amyloids, in particular the chaplins from Streptomyces coelicolor. We also consider the broader impact of the study of bacterial amyloids on our understanding of infection and disease and on developments in nanotechnology.

scholarly journals Dynamics of oligomer populations formed during the aggregation of Alzheimer’s Aβ42 peptide

2020 ◽  
Author(s):  
Thomas C. T. Michaels ◽  
Andela Šarić ◽  
Samo Curk ◽  
Katja Bernfur ◽  
Paolo Arosio ◽  
...  
Keyword(s):  
Protein Misfolding ◽  
Amyloid Fibrils ◽  
Amyloid Fibril ◽  
Fibril Formation ◽  
Therapeutic Interventions ◽  
Molecular Pathways ◽  
Amyloid Fibril Formation ◽  
Aβ42 Peptide ◽  
Heterogeneous Ensemble ◽  
Misfolding Diseases

AbstractOligomeric aggregates populated during the aggregation of the Aβ42 peptide have been identified as potent cytotoxins linked to Alzheimer’s disease, but the fundamental molecular pathways that control their dynamics have yet to be elucidated. By developing a general approach combining theory, experiment, and simulation, we reveal in molecular detail the mechanisms of Aβ42 oligomer dynamics during amyloid fibril formation. Even though all mature amyloid fibrils must originate as oligomers, we find that most Aβ42 oligomers dissociate to their monomeric precursors without forming new fibrils. Only a minority of oligomers converts into fibrillar species. Moreover, the heterogeneous ensemble of oligomeric species interconverts on timescales comparable to aggregation. Our results identify fundamentally new steps that could be targeted by therapeutic interventions designed to combat protein misfolding diseases.

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