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The Role of Environment in Amyloid Aggregation: 3rd Edition
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The Role of Environment in Amyloid Aggregation: 3rd Edition

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 November 2024) | Viewed by 3089

Special Issue Editor

Dr. Vytautas Smirnovas

E-Mail Website
Guest Editor
Institute of Biothechnology, Life Sciences Center, Vilnius University, LT-10257 Vilnius, Lithuania
Interests: protein misfolding; protein aggregation; amyloid; prion; proteinaceous infectivity
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

This Special Issue is a continuation of our 1st edition Special Issue “The Role of Environment in Amyloid Aggregation”.

The ability to form amyloid structures may be a generic property of polypeptides, and there are two major factors which define the probability of amyloid fibril formation—amino acid sequence of the protein/peptide and the environmental conditions. In the case of folded proteins, at least partial unfolding is necessary to trigger the amyloid formation pathway, so increased temperature, extreme pH conditions, addition of denaturants or any other changes in the environment leading to destabilization of protein structure are used in amyloid aggregation studies. Even in the case of disordered proteins, neutralization of charges or contact with hydrophobic surfaces may be necessary to induce amyloid formation. In addition to the specific conditions required for amyloid formation, changes in the environment may alter the mechanism of aggregation and lead to distinct amyloid fibril conformations. Finally, environment conditions affect the kinetics of aggregation and may alter the effect of anti-amyloid compounds.

The value of protein amyloid studies in vitro for health/pharma industry is limited, as extrapolation of the results toward amyloid formation in cells and organisms is not precise. The precision of extrapolation could increase with comprehensive knowledge of how the broad range of environmental conditions affect protein amyloid aggregation. It is my belief that to increase the value of our research, we must collect more data and periodically overview and condense them. Thus, I would like to invite you to share your knowledge and data on protein aggregation at different conditions and submit research or review articles to this issue.

Dr. Vytautas Smirnovas
Guest Editor

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. International Journal of Molecular Sciences is an international peer-reviewed open access semimonthly journal published by MDPI.

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Keywords

  • protein misfolding
  • protein aggregation
  • amyloid
  • anti-amyloid compounds
  • amyloid polymorphism
  • prion
  • protein folding and stability
  • neurodegenerative diseases
  • aggregation kinetics
  • drug discovery

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Published Papers (2 papers)

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Research

11 pages, 3858 KiB  
Article
Mica Lattice Orientation of Epitaxially Grown Amyloid β25–35 Fibrils
by György G. Ferenczy, Ünige Murvai, Lívia Fülöp and Miklós Kellermayer
Int. J. Mol. Sci. 2024, 25(19), 10460; https://doi.org/10.3390/ijms251910460 - 28 Sep 2024
Viewed by 1082
Abstract
β-amyloid (Aβ) peptides form self-organizing fibrils in Alzheimer’s disease. The biologically active, toxic Aβ25–35 fragment of the full-length Aβ-peptide forms a stable, oriented filament network on the mica surface with an epitaxial mechanism at the timescale of seconds. While many of the structural [...] Read more.
β-amyloid (Aβ) peptides form self-organizing fibrils in Alzheimer’s disease. The biologically active, toxic Aβ25–35 fragment of the full-length Aβ-peptide forms a stable, oriented filament network on the mica surface with an epitaxial mechanism at the timescale of seconds. While many of the structural and dynamic features of the oriented Aβ25–35 fibrils have been investigated before, the β-strand arrangement of the fibrils and their exact orientation with respect to the mica lattice remained unknown. By using high-resolution atomic force microscopy, here, we show that the Aβ25–35 fibrils are oriented along the long diagonal of the oxygen hexagon of mica. To test the structure and stability of the oriented fibrils further, we carried out molecular dynamics simulations on model β-sheets. The models included the mica surface and a single fibril motif built from β-strands. We show that a sheet with parallel β-strands binds to the mica surface with its positively charged groups, but the C-terminals of the strands orient upward. In contrast, the model with antiparallel strands preserves its parallel orientation with the surface in the molecular dynamics simulation, suggesting that this model describes the first β-sheet layer of the mica-bound Aβ25–35 fibrils well. These results pave the way toward nanotechnological construction and applications for the designed amyloid peptides. Full article
(This article belongs to the Special Issue The Role of Environment in Amyloid Aggregation: 3rd Edition)
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17 pages, 3974 KiB  
Article
Study of Insulin Aggregation and Fibril Structure under Different Environmental Conditions
by Mantas Ziaunys, Kamile Mikalauskaite, Andrius Sakalauskas and Vytautas Smirnovas
Int. J. Mol. Sci. 2024, 25(17), 9406; https://doi.org/10.3390/ijms25179406 - 29 Aug 2024
Cited by 1 | Viewed by 1492
Abstract
Protein amyloid aggregation is linked with widespread and fatal neurodegenerative disorders as well as several amyloidoses. Insulin, a small polypeptide hormone, is associated with injection-site amyloidosis and is a popular model protein for in vitro studies of amyloid aggregation processes as well as [...] Read more.
Protein amyloid aggregation is linked with widespread and fatal neurodegenerative disorders as well as several amyloidoses. Insulin, a small polypeptide hormone, is associated with injection-site amyloidosis and is a popular model protein for in vitro studies of amyloid aggregation processes as well as in the search for potential anti-amyloid compounds. Despite hundreds of studies conducted with this specific protein, the procedures used have employed a vast array of different means of achieving fibril formation. These conditions include the use of different solution components, pH values, ionic strengths, and other additives. In turn, this variety of conditions results in the generation of fibrils with different structures, morphologies and stabilities, which severely limits the possibility of cross-study comparisons as well as result interpretations. In this work, we examine the condition–structure relationship of insulin amyloid aggregation under a range of commonly used pH and ionic strength conditions as well as solution components. We demonstrate the correlation between the reaction solution properties and the resulting aggregation kinetic parameters, aggregate secondary structures, morphologies, stabilities and dye-binding modes. Full article
(This article belongs to the Special Issue The Role of Environment in Amyloid Aggregation: 3rd Edition)
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