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Protein Folding and Misfolding — Structure and Functions 2.0
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Protein Folding and Misfolding — Structure and Functions 2.0

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

Deadline for manuscript submissions: closed (31 March 2023) | Viewed by 8018

Special Issue Editor

Prof. Dr. Stefano Gianni

E-Mail Website1 Website2
Guest Editor
Department of Biochemical Sciences, Sapienza University of Rome, 00185 Rome, Italy
Interests: protein folding; protein dynamics and disorder; protein-protein recognition
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Nearly all biological processes rely on the conformational states of interacting macromolecules. It is, therefore, not surprising that the study of protein folding and misfolding has played a central role in chemistry and biology. In particular, substantial experimental and theoretical efforts have been devoted to understanding the general rules of folding, as well as to deciphering the mechanisms that lead to misfolding and related diseases. Furthermore, the discovery that a large fraction of the proteome is essentially disordered, while being fully functional, has revolutionized our comprehension of the structure–function relationships, posing the description of intrinsically disordered proteins as a key problem in modern science.  

Leading by Prof. Dr. Stefano Gianni and assisting by our Topical Advisory Panel Member Dr. Francesca Malagrinò (University of Naples Federico II), this Special Issue focuses on recent studies that contribute to our understanding of protein folding and misfolding, as well as on the role of intrinsic disorder in protein functions. Original research articles and reviews on these and related topics are welcome in this Special Issue.

Prof. Dr. Stefano Gianni
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 folding
  • chaperones
  • foldases
  • energy landscape
  • molecular dynamics simulation
  • chemical kinetics
  • energy barriers
  • down-hill folding
  • protein misfolding
  • protein unfolding
  • amyloid structure
  • degenerative diseases
  • proteopathy
  • oligomer toxicity
  • intrinsic disorder
  • intrinsically disordered proteins
  • folding upon binding

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Published Papers (3 papers)

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Research

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19 pages, 4532 KiB  
Article
Designed De Novo α-Sheet Peptides Destabilize Bacterial Biofilms and Increase the Susceptibility of E. coli and S. aureus to Antibiotics
by Tatum Prosswimmer, Sarah E. Nick, James D. Bryers and Valerie Daggett
Int. J. Mol. Sci. 2024, 25(13), 7024; https://doi.org/10.3390/ijms25137024 - 27 Jun 2024
Viewed by 983
Abstract
Biofilm-associated microbes are 10–1000 times less susceptible to antibiotics. An emerging treatment strategy is to target the structural components of biofilm to weaken the extracellular matrix without introducing selective pressure. Biofilm-associated bacteria, including Escherichia coli and Staphylococcus aureus, generate amyloid fibrils to [...] Read more.
Biofilm-associated microbes are 10–1000 times less susceptible to antibiotics. An emerging treatment strategy is to target the structural components of biofilm to weaken the extracellular matrix without introducing selective pressure. Biofilm-associated bacteria, including Escherichia coli and Staphylococcus aureus, generate amyloid fibrils to reinforce their extracellular matrix. Previously, de novo synthetic α-sheet peptides designed in silico were shown to inhibit amyloid formation in multiple bacterial species, leading to the destabilization of their biofilms. Here, we investigated the impact of inhibiting amyloid formation on antibiotic susceptibility. We hypothesized that combined administration of antibiotics and α-sheet peptides would destabilize biofilm formation and increase antibiotic susceptibility. Two α-sheet peptides, AP90 and AP401, with the same sequence but inverse chirality at every amino acid were tested: AP90 is L-amino acid dominant while AP401 is D-amino acid dominant. For E. coli, both peptides increased antibiotic susceptibility and decreased the biofilm colony forming units when administered with five different antibiotics, and AP401 caused a greater increase in all cases. For S. aureus, increased biofilm antibiotic susceptibility was also observed for both peptides, but AP90 outperformed AP401. A comparison of the peptide effects demonstrates how chirality influences biofilm targeting of gram-negative E. coli and gram-positive S. aureus. The observed increase in antibiotic susceptibility highlights the role amyloid fibrils play in the reduced susceptibility of bacterial biofilms to specific antibiotics. Thus, the co-administration of α-sheet peptides and existing antibiotics represents a promising strategy for the treatment of biofilm infections. Full article
(This article belongs to the Special Issue Protein Folding and Misfolding — Structure and Functions 2.0)
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14 pages, 7494 KiB  
Article
Secondary Modification of S100B Influences Anti Amyloid-β Aggregation Activity and Alzheimer’s Disease Pathology
by Romina Coelho, Chiara A. De Benedictis, Ann Katrin Sauer, António J. Figueira, Hélio Faustino, Andreas M. Grabrucker and Cláudio M. Gomes
Int. J. Mol. Sci. 2024, 25(3), 1787; https://doi.org/10.3390/ijms25031787 - 1 Feb 2024
Viewed by 1665
Abstract
Proteinaceous aggregates accumulate in neurodegenerative diseases such as Alzheimer’s Disease (AD), inducing cellular defense mechanisms and altering the redox status. S100 pro-inflammatory cytokines, particularly S100B, are activated during AD, but recent findings reveal an unconventional molecular chaperone role for S100B in hindering Aβ [...] Read more.
Proteinaceous aggregates accumulate in neurodegenerative diseases such as Alzheimer’s Disease (AD), inducing cellular defense mechanisms and altering the redox status. S100 pro-inflammatory cytokines, particularly S100B, are activated during AD, but recent findings reveal an unconventional molecular chaperone role for S100B in hindering Aβ aggregation and toxicity. This suggests a potential protective role for S100B at the onset of Aβ proteotoxicity, occurring in a complex biochemical environment prone to oxidative damage. Herein, we report an investigation in which extracellular oxidative conditions are mimicked to test if the susceptibility of S100B to oxidation influences its protective activities. Resorting to mild oxidation of S100B, we observed methionine oxidation as inferred from mass spectrometry, but no cysteine-mediated crosslinking. Structural analysis showed that the folding, structure, and stability of oxidized S100B were not affected, and nor was its quaternary structure. However, studies on Aβ aggregation kinetics indicated that oxidized S100B was more effective in preventing aggregation, potentially linked to the oxidation of Met residues within the S100:Aβ binding cleft that favors interactions. Using a cell culture model to analyze the S100B functions in a highly oxidative milieu, as in AD, we observed that Aβ toxicity is rescued by the co-administration of oxidized S100B to a greater extent than by S100B. Additionally, results suggest a disrupted positive feedback loop involving S100B which is caused by its oxidation, leading to the downstream regulation of IL-17 and IFN-α2 expression as mediated by S100B. Full article
(This article belongs to the Special Issue Protein Folding and Misfolding — Structure and Functions 2.0)
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Review

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38 pages, 7328 KiB  
Review
Amyloidogenesis: What Do We Know So Far?
by Zeina Alraawi, Nayan Banerjee, Srujana Mohanty and Thallapuranam Krishnaswamy Suresh Kumar
Int. J. Mol. Sci. 2022, 23(22), 13970; https://doi.org/10.3390/ijms232213970 - 12 Nov 2022
Cited by 8 | Viewed by 3620
Abstract
The study of protein aggregation, and amyloidosis in particular, has gained considerable interest in recent times. Several neurodegenerative diseases, such as Alzheimer’s (AD) and Parkinson’s (PD) show a characteristic buildup of proteinaceous aggregates in several organs, especially the brain. Despite the enormous upsurge [...] Read more.
The study of protein aggregation, and amyloidosis in particular, has gained considerable interest in recent times. Several neurodegenerative diseases, such as Alzheimer’s (AD) and Parkinson’s (PD) show a characteristic buildup of proteinaceous aggregates in several organs, especially the brain. Despite the enormous upsurge in research articles in this arena, it would not be incorrect to say that we still lack a crystal-clear idea surrounding these notorious aggregates. In this review, we attempt to present a holistic picture on protein aggregation and amyloids in particular. Using a chronological order of discoveries, we present the case of amyloids right from the onset of their discovery, various biophysical techniques, including analysis of the structure, the mechanisms and kinetics of the formation of amyloids. We have discussed important questions on whether aggregation and amyloidosis are restricted to a subset of specific proteins or more broadly influenced by the biophysiochemical and cellular environment. The therapeutic strategies and the significant failure rate of drugs in clinical trials pertaining to these neurodegenerative diseases have been also discussed at length. At a time when the COVID-19 pandemic has hit the globe hard, the review also discusses the plausibility of the far-reaching consequences posed by the virus, such as triggering early onset of amyloidosis. Finally, the application(s) of amyloids as useful biomaterials has also been discussed briefly in this review. Full article
(This article belongs to the Special Issue Protein Folding and Misfolding — Structure and Functions 2.0)
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