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Structure and Formation Mechanism of Amyloid Fibrils

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Biophysics".

Deadline for manuscript submissions: closed (30 April 2024) | Viewed by 3005

Special Issue Editors


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Guest Editor
Accelerator Laboratory, High Energy Accelerator Research Organization, 1-1 Oho, Tsukuba, Ibaraki 305-0801, Japan
Interests: amyloid; biopolymers; infrared laser; terahertz radiation
Special Issues, Collections and Topics in MDPI journals

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Guest Editor
CNRS, UPR 9080, Laboratoire de Biochimie Théorique, Institut de Biologie Physico-Chimique, Fondation Edmond de Rothschild, Université Paris Cité, 13 Rue Pierre et Marie Curie, 75005 Paris, France
Interests: amyloid; molecular dynamics of protein; RNA and lipid membrane

Special Issue Information

Dear Colleagues,

Amyloid fibrils are known to cause serious diseases such as neurodegenerative diseases and amyloidosis. Recently, it has been reported that lower-molecular-sized oligomers are found to be more toxic in cells than mature fibrils. The technology for the degradation of those amyloid assemblies has the potential for leading to amyloidosis therapy. However, the formation mechanism of amyloid fibrils is not completely understood, and it is usually difficult to degrade the rigid fibrous conformation under mild conditions unless using denaturants. This special issue welcomes structural studies focusing on the fibrils, proto-fibrils, and oligomers of various types of amyloid peptides and proteins. Especially uses of not only experimental techniques but also computer simulation methods for approaching the formation mechanisms of amyloid assemblies are acceptable. In addition, application studies of physical engineering techniques such as lasers and high-power radiations to develop novel therapeutic ways for amyloidosis should also be welcome.

Dr. Takayasu Kawasaki
Dr. Phuong H. Nguyen
Guest Editors

Manuscript Submission Information

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Keywords

  • amyloid fibril
  • oligomer
  • proto-fibril
  • molecular simulation
  • laser
  • radiation

Published Papers (2 papers)

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Review

22 pages, 2325 KiB  
Review
Understanding Aβ Peptide Binding to Lipid Membranes: A Biophysical Perspective
by Hasna Ahyayauch, Massimo E. Masserini, Alicia Alonso and Félix M. Goñi
Int. J. Mol. Sci. 2024, 25(12), 6401; https://doi.org/10.3390/ijms25126401 - 10 Jun 2024
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Abstract
Aβ peptides are known to bind neural plasma membranes in a process leading to the deposit of Aβ-enriched plaques. These extracellular structures are characteristic of Alzheimer’s disease, the major cause of late-age dementia. The mechanisms of Aβ plaque formation and deposition are far [...] Read more.
Aβ peptides are known to bind neural plasma membranes in a process leading to the deposit of Aβ-enriched plaques. These extracellular structures are characteristic of Alzheimer’s disease, the major cause of late-age dementia. The mechanisms of Aβ plaque formation and deposition are far from being understood. A vast number of studies in the literature describe the efforts to analyze those mechanisms using a variety of tools. The present review focuses on biophysical studies mostly carried out with model membranes or with computational tools. This review starts by describing basic physical aspects of lipid phases and commonly used model membranes (monolayers and bilayers). This is followed by a discussion of the biophysical techniques applied to these systems, mainly but not exclusively Langmuir monolayers, isothermal calorimetry, density-gradient ultracentrifugation, and molecular dynamics. The Methodological Section is followed by the core of the review, which includes a summary of important results obtained with each technique. The last section is devoted to an overall reflection and an effort to understand Aβ-bilayer binding. Concepts such as Aβ peptide membrane binding, adsorption, and insertion are defined and differentiated. The roles of membrane lipid order, nanodomain formation, and electrostatic forces in Aβ–membrane interaction are separately identified and discussed. Full article
(This article belongs to the Special Issue Structure and Formation Mechanism of Amyloid Fibrils)
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18 pages, 5492 KiB  
Review
Disassembly of Amyloid Fibril with Infrared Free Electron Laser
by Takayasu Kawasaki, Koichi Tsukiyama and Phuong H. Nguyen
Int. J. Mol. Sci. 2023, 24(4), 3686; https://doi.org/10.3390/ijms24043686 - 12 Feb 2023
Viewed by 2056
Abstract
Amyloid fibril causes serious amyloidosis such as neurodegenerative diseases. The structure is composed of rigid β-sheet stacking conformation which makes it hard to disassemble the fibril state without denaturants. Infrared free electron laser (IR-FEL) is an intense picosecond pulsed laser that is oscillated [...] Read more.
Amyloid fibril causes serious amyloidosis such as neurodegenerative diseases. The structure is composed of rigid β-sheet stacking conformation which makes it hard to disassemble the fibril state without denaturants. Infrared free electron laser (IR-FEL) is an intense picosecond pulsed laser that is oscillated through a linear accelerator, and the oscillation wavelengths are tunable from 3 μm to 100 μm. Many biological and organic compounds can be structurally altered by the mode-selective vibrational excitations due to the wavelength variability and the high-power oscillation energy (10–50 mJ/cm2). We have found that several different kinds of amyloid fibrils in amino acid sequences were commonly disassembled by the irradiation tuned to amide I (6.1–6.2 μm) where the abundance of β-sheet decreased while that of α-helix increased by the vibrational excitation of amide bonds. In this review, we would like to introduce the IR-FEL oscillation system briefly and describe combination studies of experiments and molecular dynamics simulations on disassembling amyloid fibrils of a short peptide (GNNQQNY) from yeast prion and 11-residue peptide (NFLNCYVSGFH) from β2-microglobulin as representative models. Finally, possible applications of IR-FEL for amyloid research can be proposed as a future outlook. Full article
(This article belongs to the Special Issue Structure and Formation Mechanism of Amyloid Fibrils)
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