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Pathological and Functional Amyloid Fibrils
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Pathological and Functional 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 (31 March 2021) | Viewed by 17584

Special Issue Editors

Prof. Dr. Konstantin K. Turoverov

E-Mail Website
Guest Editor
Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, 4 Tikhoretsky Ave., 194064 St. Petersburg, Russia
Interests: protein structure, conformation and dynamics; globule and intrinsically disordered proteins; macromolecular crowding; membraneless organelles; protein aggregates; amyloid fibrils formation and structure; biosensors; biomarkers on the basis of fluorescent proteins and phytochromes; photophysics of fluorescent dyes; molecular rotors; intrinsic fluorescence of proteins; spectrofluorimetry device development
Special Issues, Collections and Topics in MDPI journals
Dr. Irina M. Kuznetsova

E-Mail Website
Guest Editor
Laboratory of Structural Dynamics, Stability and Folding of Proteins, Institute of Cytology, Russian Academy of Sciences, 4 Tikhoretsky Ave., 194064 St. Petersburg, Russia
Interests: amyloid fibrils; thioflafin T fluorescence; equilibrium microdialysis; globule and intrinsically disordered proteins; proteins aggregattion; macromolecular crowding; membraneless organelles
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Amyloid fibrils were first discovered in the tissue of patients suffering from neurodegenerative diseases. This led to keen interest in the study of their structure, causes, and mechanisms of occurrence, toxicity, etc. It was soon established that amyloid fibrils are regular, β-sheet-enriched, long, nanoscale aggregates of proteins with β-strands running perpendicular to the long axis of the fibril. However, a more in-depth study of amyloid fibrils showed that amyloid fibrils formed by various amyloidogenic proteins differ significantly in structure, rate of formation, prone to aggregation, toxicity, etc. It turned out that not all amyloid fibrils are harmful. Many amyloid fibrils are non-toxic and have important functions. The formation of amyloid fibrils can disrupt various technological processes, and at the same time, the unique strength properties of amyloid fibrils are increasingly used in the development of new technologies.

The aim of this Special Issue on “Pathological and Functional amyloid fibrils” is to collect, under one cover, the most important modern ideas about the mechanism of formation, structure, stability, prone-to-plaque formation, and other important features of a wide range of amyloid fibrils. Perhaps this will shed light on the fundamental differences and similarities of pathological and non-pathological amyloid fibrils. Experimental papers, up-to-date review articles, and commentaries are all welcomed. In addition, the Special Issue will provide a forum to exchange views and discuss the prospects of studying amyloid fibrils in the next few years.

Prof. Dr. Konstantin K. Turoverov
Dr. Irina M. Kuznetsova
Guest Editors

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

  • amyloid fibril formation and structure
  • intrinsically disordered proteins, protein aggregates
  • amyloid fibrils and membrane-less organelles
  • amyloid fibril disease, harmful amyloid fibrils
  • functional amyloid fibrils
  • methods of amyloid fibril investigation

Published Papers (6 papers)

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Editorial

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3 pages, 168 KiB  
Editorial
Pathological and Functional Amyloid Fibrils—Part I
by Irina M. Kuznetsova and Konstantin K. Turoverov
Int. J. Mol. Sci. 2022, 23(12), 6447; https://doi.org/10.3390/ijms23126447 - 09 Jun 2022
Viewed by 1008
Abstract
Amyloid fibrils have been known to researchers for a long time [...] Full article
(This article belongs to the Special Issue Pathological and Functional Amyloid Fibrils)

Research

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22 pages, 4341 KiB  
Article
Trypsin Induced Degradation of Amyloid Fibrils
by Olga V. Stepanenko, Maksim I. Sulatsky, Ekaterina V. Mikhailova, Olesya V. Stepanenko, Irina M. Kuznetsova, Konstantin K. Turoverov and Anna I. Sulatskaya
Int. J. Mol. Sci. 2021, 22(9), 4828; https://doi.org/10.3390/ijms22094828 - 02 May 2021
Cited by 14 | Viewed by 3387
Abstract
Proteolytic enzymes are known to be involved in the formation and degradation of various monomeric proteins, but the effect of proteases on the ordered protein aggregates, amyloid fibrils, which are considered to be extremely stable, remains poorly understood. In this work we study [...] Read more.
Proteolytic enzymes are known to be involved in the formation and degradation of various monomeric proteins, but the effect of proteases on the ordered protein aggregates, amyloid fibrils, which are considered to be extremely stable, remains poorly understood. In this work we study resistance to proteolytic degradation of lysozyme amyloid fibrils with two different types of morphology and beta-2-microglobulun amyloids. We showed that the proteolytic enzyme of the pancreas, trypsin, induced degradation of amyloid fibrils, and the mechanism of this process was qualitatively the same for all investigated amyloids. At the same time, we found a dependence of efficiency and rate of fibril degradation on the structure of the amyloid-forming protein as well as on the morphology and clustering of amyloid fibrils. It was assumed that the discovered relationship between fibrils structure and the efficiency of their degradation by trypsin can become the basis of a new express method for the analysis of amyloids polymorphism. Unexpectedly lower resistance of both types of lysozyme amyloids to trypsin exposure compared to the native monomeric protein (which is not susceptible to hydrolysis) was attributed to the higher availability of cleavage sites in studied fibrils. Another intriguing result of the work is that the cytotoxicity of amyloids treated with trypsin was not only failing to decline, but even increasing in the case of beta-2-microglobulin fibrils. Full article
(This article belongs to the Special Issue Pathological and Functional Amyloid Fibrils)
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16 pages, 39255 KiB  
Article
Amyloid Aggregates of Smooth-Muscle Titin Impair Cell Adhesion
by Alexander G. Bobylev, Roman S. Fadeev, Liya G. Bobyleva, Margarita I. Kobyakova, Yuri M. Shlyapnikov, Daniil V. Popov and Ivan M. Vikhlyantsev
Int. J. Mol. Sci. 2021, 22(9), 4579; https://doi.org/10.3390/ijms22094579 - 27 Apr 2021
Cited by 5 | Viewed by 2720
Abstract
Various amyloid aggregates, in particular, aggregates of amyloid β-proteins, demonstrate in vitro and in vivo cytotoxic effects associated with impairment of cell adhesion. We investigated the effect of amyloid aggregates of smooth-muscle titin on smooth-muscle-cell cultures. The aggregates were shown to impair cell [...] Read more.
Various amyloid aggregates, in particular, aggregates of amyloid β-proteins, demonstrate in vitro and in vivo cytotoxic effects associated with impairment of cell adhesion. We investigated the effect of amyloid aggregates of smooth-muscle titin on smooth-muscle-cell cultures. The aggregates were shown to impair cell adhesion, which was accompanied by disorganization of the actin cytoskeleton, formation of filopodia, lamellipodia, and stress fibers. Cells died after a 72-h contact with the amyloid aggregates. To understand the causes of impairment, we studied the effect of the microtopology of a titin-amyloid-aggregate-coated surface on fibroblast adhesion by atomic force microscopy. The calculated surface roughness values varied from 2.7 to 4.9 nm, which can be a cause of highly antiadhesive properties of this surface. As all amyloids have the similar structure and properties, it is quite likely that the antiadhesive effect is also intrinsic to amyloid aggregates of other proteins. These results are important for understanding the mechanisms of the negative effect of amyloids on cell adhesion. Full article
(This article belongs to the Special Issue Pathological and Functional Amyloid Fibrils)
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17 pages, 2193 KiB  
Article
Assessment of Amyloid Forming Tendency of Peptide Sequences from Amyloid Beta and Tau Proteins Using Force-Field, Semi-Empirical, and Density Functional Theory Calculations
by Charuvaka Muvva, Natarajan Arul Murugan and Venkatesan Subramanian
Int. J. Mol. Sci. 2021, 22(6), 3244; https://doi.org/10.3390/ijms22063244 - 23 Mar 2021
Cited by 2 | Viewed by 2334
Abstract
A wide variety of neurodegenerative diseases are characterized by the accumulation of protein aggregates in intraneuronal or extraneuronal brain regions. In Alzheimer’s disease (AD), the extracellular aggregates originate from amyloid-β proteins, while the intracellular aggregates are formed from microtubule-binding tau proteins. The amyloid [...] Read more.
A wide variety of neurodegenerative diseases are characterized by the accumulation of protein aggregates in intraneuronal or extraneuronal brain regions. In Alzheimer’s disease (AD), the extracellular aggregates originate from amyloid-β proteins, while the intracellular aggregates are formed from microtubule-binding tau proteins. The amyloid forming peptide sequences in the amyloid-β peptides and tau proteins are responsible for aggregate formation. Experimental studies have until the date reported many of such amyloid forming peptide sequences in different proteins, however, there is still limited molecular level understanding about their tendency to form aggregates. In this study, we employed umbrella sampling simulations and subsequent electronic structure theory calculations in order to estimate the energy profiles for interconversion of the helix to β-sheet like secondary structures of sequences from amyloid-β protein (KLVFFA) and tau protein (QVEVKSEKLD and VQIVYKPVD). The study also included a poly-alanine sequence as a reference system. The calculated force-field based free energy profiles predicted a flat minimum for monomers of sequences from amyloid and tau proteins corresponding to an α-helix like secondary structure. For the parallel and anti-parallel dimer of KLVFFA, double well potentials were obtained with the minima corresponding to α-helix and β-sheet like secondary structures. A similar double well-like potential has been found for dimeric forms for the sequences from tau fibril. Complementary semi-empirical and density functional theory calculations displayed similar trends, validating the force-field based free energy profiles obtained for these systems. Full article
(This article belongs to the Special Issue Pathological and Functional Amyloid Fibrils)
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12 pages, 3543 KiB  
Article
Aggregation of Mouse Serum Amyloid A Protein Was Promoted by Amyloid-Enhancing Factors with the More Genetically Homologous Serum Amyloid A
by Xuguang Lin, Kenichi Watanabe, Masahiro Kuragano and Kiyotaka Tokuraku
Int. J. Mol. Sci. 2021, 22(3), 1036; https://doi.org/10.3390/ijms22031036 - 21 Jan 2021
Cited by 3 | Viewed by 3339
Abstract
Amyloid A (AA) amyloidosis is a condition in which amyloid fibrils characterized by a linear morphology and a cross-β structure accumulate and are deposited extracellularly in organs, resulting in chronic inflammatory diseases and infections. The incidence of AA amyloidosis is high in humans [...] Read more.
Amyloid A (AA) amyloidosis is a condition in which amyloid fibrils characterized by a linear morphology and a cross-β structure accumulate and are deposited extracellularly in organs, resulting in chronic inflammatory diseases and infections. The incidence of AA amyloidosis is high in humans and several animal species. Serum amyloid A (SAA) is one of the most important precursor amyloid proteins and plays a vital step in AA amyloidosis. Amyloid enhancing factor (AEF) serves as a seed for fibril formation and shortens the onset of AA amyloidosis sharply. In this study, we examined whether AEFs extracted and purified from five animal species (camel, cat, cattle, goat, and mouse) could promote mouse SAA (mSAA) protein aggregation in vitro using quantum-dot (QD) nanoprobes to visualize the aggregation. The results showed that AEFs shortened and promoted mSAA aggregation. In addition, mouse and cat AEFs showed higher mSAA aggregation-promoting activity than the camel, cattle, and goat AEFs. Interestingly, homology analysis of SAA in these five animal species revealed a more similar amino acid sequence homology between mouse and cat than between other animal species. Furthermore, a detailed comparison of amino acid sequences suggested that it was important to mSAA aggregation-promoting activity that the 48th amino acid was a basic residue (Lys) and the 125th amino acid was an acidic residue (Asp or Glu). These data imply that AA amyloidosis exhibits higher transmission activity among animals carrying genetically homologous SAA gene, and may provide a new understanding of the pathogenesis of amyloidosis. Full article
(This article belongs to the Special Issue Pathological and Functional Amyloid Fibrils)
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Review

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14 pages, 316 KiB  
Review
Stress Response Is the Main Trigger of Sporadic Amyloidoses
by Alexey P. Galkin and Evgeniy I. Sysoev
Int. J. Mol. Sci. 2021, 22(8), 4092; https://doi.org/10.3390/ijms22084092 - 15 Apr 2021
Cited by 6 | Viewed by 3860
Abstract
Amyloidoses are a group of diseases associated with the formation of pathological protein fibrils with cross-β structures. Approximately 5–10% of the cases of these diseases are determined by amyloidogenic mutations, as well as by transmission of infectious amyloids (prions) between organisms. The most [...] Read more.
Amyloidoses are a group of diseases associated with the formation of pathological protein fibrils with cross-β structures. Approximately 5–10% of the cases of these diseases are determined by amyloidogenic mutations, as well as by transmission of infectious amyloids (prions) between organisms. The most common group of so-called sporadic amyloidoses is associated with abnormal aggregation of wild-type proteins. Some sporadic amyloidoses are known to be induced only against the background of certain pathologies, but in some cases the cause of amyloidosis is unclear. It is assumed that these diseases often occur by accident. Here we present facts and hypotheses about the association of sporadic amyloidoses with vascular pathologies, trauma, oxidative stress, cancer, metabolic diseases, chronic infections and COVID-19. Generalization of current data shows that all sporadic amyloidoses can be regarded as a secondary event occurring against the background of diseases provoking a cellular stress response. Various factors causing the stress response provoke protein overproduction, a local increase in the concentration or modifications, which contributes to amyloidogenesis. Progress in the treatment of vascular, metabolic and infectious diseases, as well as cancers, should lead to a significant reduction in the risk of sporadic amyloidoses. Full article
(This article belongs to the Special Issue Pathological and Functional Amyloid Fibrils)
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