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Advanced Research of Amyloids
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Advanced Research of Amyloids

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Pathology, Diagnostics, and Therapeutics".

Deadline for manuscript submissions: closed (31 January 2022) | Viewed by 10203

Special Issue Information

Dear Colleagues,

The field of research of amyloid diseases is rapidly expanding and is conducted in many different disciplines. This Special Issue will promote interdisciplinary research activity in this important field. The amyloid diseases have become the heaviest load on the economy of the medical services in the developed world, rendering major social and economic importance to any progress in understanding the molecular, cellular, and organismic factors involved in the onset and treatment of these diseases.

It is my pleasure to invite you to submit a research article, short communication, or review article to this Special Issue. This Special Issue will focus on recent advances in research on amyloid proteins, including microbial amyloids, using a variety of studies: in vivo, in vitro, molecular biology, and in silico. This Issue will cover a wide spectrum of topics related to advanced methods for the structural biology of amyloids, the molecular mechanisms and kinetics of amyloid aggregation, the role of metals in amyloid aggregation, the molecular affinity of amyloids with lipid membranes, and novel therapeutic strategies in amyloid diseases.

I look forward to receiving your contributions to this exciting Special Issue.

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.

Please visit the Instructions for Authors page before submitting a manuscript. There is an Article Processing Charge (APC) for publication in this open access journal. For details about the APC please see here. Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • neurodegeneration
  • amyloids oligomers
  • amyloid fibrils
  • NMR
  • crystal structure
  • molecular mechanisms
  • amyloid–membrane interactions
  • drug design
  • inhibitors

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Published Papers (3 papers)

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Research

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13 pages, 2942 KiB  
Article
Combined Modeling Study of the Binding Characteristics of Natural Compounds, Derived from Psoralea Fruits, to β-Amyloid Peptide Monomer
by Awwad Radwan and Fars Alanazi
Int. J. Mol. Sci. 2022, 23(7), 3546; https://doi.org/10.3390/ijms23073546 - 24 Mar 2022
Cited by 3 | Viewed by 2396
Abstract
A dysfunctional protein aggregation in the nervous system can lead to several neurodegenerative disorders that result in intracellular inclusions or extracellular aggregates. An early critical event within the pathogenesis of Alzheimer’s disease is the accumulation of amyloid beta peptide within the brain. Natural [...] Read more.
A dysfunctional protein aggregation in the nervous system can lead to several neurodegenerative disorders that result in intracellular inclusions or extracellular aggregates. An early critical event within the pathogenesis of Alzheimer’s disease is the accumulation of amyloid beta peptide within the brain. Natural compounds isolated from Psoralea Fructus (PF) have significant anti-Alzheimer effects as strong inhibitors of Aβ42 aggregation. Computer simulations provide a powerful means of linking experimental findings to nanoscale molecular events. As part of this research four prenylated compounds, the active ingredients of Psoralea Fructus (PF), were studied as Aβ42 accumulation inhibitors using molecular simulations modeling. In order to resolve the binding modes of the ligands and identify the main interactions of Aβ42 residues, we performed a 100 ns molecular dynamics simulation and binding free energy calculations starting from the model of the compounds obtained from the docking study. This study was able to pinpoint the key amino acid residues in the Aβ42 active site and provide useful information that could benefit the development of new Aβ42 accumulation inhibitors. Full article
(This article belongs to the Special Issue Advanced Research of Amyloids)
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17 pages, 3732 KiB  
Article
Multiscale Modeling of Amyloid Fibrils Formed by Aggregating Peptides Derived from the Amyloidogenic Fragment of the A-Chain of Insulin
by Michał Koliński, Robert Dec and Wojciech Dzwolak
Int. J. Mol. Sci. 2021, 22(22), 12325; https://doi.org/10.3390/ijms222212325 - 15 Nov 2021
Cited by 6 | Viewed by 3482
Abstract
Computational prediction of molecular structures of amyloid fibrils remains an exceedingly challenging task. In this work, we propose a multi-scale modeling procedure for the structure prediction of amyloid fibrils formed by the association of ACC1-13 aggregation-prone peptides derived from the N-terminal region [...] Read more.
Computational prediction of molecular structures of amyloid fibrils remains an exceedingly challenging task. In this work, we propose a multi-scale modeling procedure for the structure prediction of amyloid fibrils formed by the association of ACC1-13 aggregation-prone peptides derived from the N-terminal region of insulin’s A-chain. First, a large number of protofilament models composed of five copies of interacting ACC1-13 peptides were predicted by application of CABS-dock coarse-grained (CG) docking simulations. Next, the models were reconstructed to all-atom (AA) representations and refined during molecular dynamics (MD) simulations in explicit solvent. The top-scored protofilament models, selected using symmetry criteria, were used for the assembly of long fibril structures. Finally, the amyloid fibril models resulting from the AA MD simulations were compared with atomic force microscopy (AFM) imaging experimental data. The obtained results indicate that the proposed multi-scale modeling procedure is capable of predicting protofilaments with high accuracy and may be applied for structure prediction and analysis of other amyloid fibrils. Full article
(This article belongs to the Special Issue Advanced Research of Amyloids)
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Review

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21 pages, 2188 KiB  
Review
Roles and Mechanisms of the Protein Quality Control System in Alzheimer’s Disease
by Yaping Liu, Runrong Ding, Ze Xu, Yuan Xue, Dongdong Zhang, Yujing Zhang, Wenjie Li and Xing Li
Int. J. Mol. Sci. 2022, 23(1), 345; https://doi.org/10.3390/ijms23010345 - 29 Dec 2021
Cited by 17 | Viewed by 3523
Abstract
Alzheimer’s disease (AD) is characterized by the deposition of senile plaques (SPs) and the formation of neurofibrillary tangles (NTFs), as well as neuronal dysfunctions in the brain, but in fact, patients have shown a sustained disease progression for at least 10 to 15 [...] Read more.
Alzheimer’s disease (AD) is characterized by the deposition of senile plaques (SPs) and the formation of neurofibrillary tangles (NTFs), as well as neuronal dysfunctions in the brain, but in fact, patients have shown a sustained disease progression for at least 10 to 15 years before these pathologic biomarkers can be detected. Consequently, as the most common chronic neurological disease in the elderly, the challenge of AD treatment is that it is short of effective biomarkers for early diagnosis. The protein quality control system is a collection of cellular pathways that can recognize damaged proteins and thereby modulate their turnover. Abundant evidence indicates that the accumulation of abnormal proteins in AD is closely related to the dysfunction of the protein quality control system. In particular, it is the synthesis, degradation, and removal of essential biological components that have already changed in the early stage of AD, which further encourages us to pay more attention to the protein quality control system. The review mainly focuses on the endoplasmic reticulum system (ERS), autophagy–lysosome system (ALS) and the ubiquitin–proteasome system (UPS), and deeply discusses the relationship between the protein quality control system and the abnormal proteins of AD, which can not only help us to understand how and why the complex regulatory system becomes malfunctional during AD progression, but also provide more novel therapeutic strategies to prevent the development of AD. Full article
(This article belongs to the Special Issue Advanced Research of Amyloids)
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