Search for Articles:
Title / Keyword
Author / Affiliation / Email
Journal
Article Type
 
 
Advanced Search
 
Section
Special Issue
Volume
Issue
Number
Page
 
7.8
5.6
Journals
IJMS
Special Issues
Spectroscopy and Microscopy of Fibrillar Protein Aggregates
ijms-logo
Submit to IJMS Review for IJMS Propose a Special Issue

Journal Menu

► Journal Menu

Journal Browser

► Journal Browser
share announcement

Spectroscopy and Microscopy of Fibrillar Protein Aggregates

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

Deadline for manuscript submissions: closed (15 April 2023) | Viewed by 10277

Special Issue Editor

Prof. Dr. Alessandro Nucara

E-Mail Website
Guest Editor
Department of Physics, Sapienza University of Rome, P.le A. Moro 5, 00185 Rome, Italy
Interests: Infrared spectroscopy; Raman spectroscopy; protein; amyloid fibrils; lipid membranes

Special Issue Information

Dear Colleagues,

Many proteins which are essential to survival show a propensity to form aggregates, which can vary from unordered macro-oligomers to filamentary fibrils. Experiments have provided a large variety of unfolded-to-aggregate kinetics of proteins, depending on environmental as well as molecular variables. However, the aggregation paths and their final states are still largely unpredictable, even for the most studied cases of the Ab class of proteins. Spectroscopy and microscopy have been widely exploited to study the unfolded-aggregate kinetics since the early time of protein discovery and handling. At present, advances in the techniques and synergy between different approaches have provided a deeper understanding of the aggregate kinetics and of the involved molecular interactions. Contributions to this Special Issue will therefore be useful to offer new insights into the mechanisms of oligomer/fibril formation, to disclose the potential of spectroscopic and microscopic techniques in this field, and to deepen our understanding of the inner molecular mechanisms.

Prof. Dr. Alessandro Nucara
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.

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

  • protein aggregate
  • spectroscopy
  • fibrils

Published Papers (5 papers)

Download All Papers
Order results
Result details
Show export options expand_more Show export options expand_less
Select all
Export citation of selected articles as:

Research

11 pages, 2271 KiB  
Communication
β-Carotene, a Potent Amyloid Aggregation Inhibitor, Promotes Disordered Aβ Fibrillar Structure
by Siddhartha Banerjee, Divya Baghel, Ana Pacheco de Oliveira and Ayanjeet Ghosh
Int. J. Mol. Sci. 2023, 24(6), 5175; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms24065175 - 08 Mar 2023
Cited by 1 | Viewed by 1352
Abstract
The aggregation of amyloid beta (Aβ) into fibrillar aggregates is a key feature of Alzheimer’s disease (AD) pathology. β-carotene and related compounds have been shown to associate with amyloid aggregates and have direct impact on the formation of amyloid fibrils. However, the precise [...] Read more.
The aggregation of amyloid beta (Aβ) into fibrillar aggregates is a key feature of Alzheimer’s disease (AD) pathology. β-carotene and related compounds have been shown to associate with amyloid aggregates and have direct impact on the formation of amyloid fibrils. However, the precise effect of β-carotene on the structure of amyloid aggregates is not known, which poses a limitation towards developing it as a potential AD therapeutic. In this report, we use nanoscale AFM-IR spectroscopy to probe the structure of Aβ oligomers and fibrils at the single aggregate level and demonstrate that the main effect of β-carotene towards modulating Aβ aggregation is not to inhibit fibril formation but to alter the secondary structure of the fibrils and promote fibrils that lack the characteristic ordered beta structure. Full article
(This article belongs to the Special Issue Spectroscopy and Microscopy of Fibrillar Protein Aggregates)
►▼ Show Figures

Figure 1

19 pages, 4103 KiB  
Article
Structural and Biophysical Characterization of Stable Alpha-Synuclein Oligomers
by Nishant Vaikath, Indulekha Sudhakaran, Ilham Abdi, Vijay Gupta, Nour Majbour, Simona Ghanem, Houari Abdesselem, Kostas Vekrellis and Omar El-Agnaf
Int. J. Mol. Sci. 2022, 23(23), 14630; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms232314630 - 23 Nov 2022
Cited by 6 | Viewed by 1711
Abstract
The aggregation of α-synuclein (α-syn) into neurotoxic oligomers and fibrils is an important pathogenic feature of synucleinopatheis, including Parkinson’s disease (PD). A further characteristic of PD is the oxidative stress that results in the formation of aldehydes by lipid peroxidation. It has been [...] Read more.
The aggregation of α-synuclein (α-syn) into neurotoxic oligomers and fibrils is an important pathogenic feature of synucleinopatheis, including Parkinson’s disease (PD). A further characteristic of PD is the oxidative stress that results in the formation of aldehydes by lipid peroxidation. It has been reported that the brains of deceased patients with PD contain high levels of protein oligomers that are cross-linked to these aldehydes. Increasing evidence also suggests that prefibrillar oligomeric species are more toxic than the mature amyloid fibrils. However, due to the heterogenous and metastable nature, characterization of the α-syn oligomeric species has been challenging. Here, we generated and characterized distinct α-syn oligomers in vitro in the presence of DA and lipid peroxidation products 4-hydroxy-2-nonenal (HNE) and 4-oxo-2-nonenal (ONE). HNE and ONE oligomer were stable towards the treatment with SDS, urea, and temperature. The secondary structure analysis revealed that only HNE and ONE oligomers contain β-sheet content. In the seeding assay, both DA and ONE oligomers significantly accelerated the aggregation. Furthermore, all oligomeric preparations were found to seed the aggregation of α-syn monomers in vitro and found to be cytotoxic when added to SH-SY5Y cells. Finally, both HNE and ONE α-syn oligomers can be used as a calibrator in an α-syn oligomers-specific ELISA. Full article
(This article belongs to the Special Issue Spectroscopy and Microscopy of Fibrillar Protein Aggregates)
►▼ Show Figures

Figure 1

15 pages, 6145 KiB  
Article
Influence of Cortisol on the Fibril Formation Kinetics of Aβ42 Peptide: A Multi-Technical Approach
by Alessandro Nucara, Francesca Ripanti, Simona Sennato, Giacomo Nisini, Emiliano De Santis, Mahta Sefat, Marina Carbonaro, Dalila Mango, Velia Minicozzi and Marilena Carbone
Int. J. Mol. Sci. 2022, 23(11), 6007; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms23116007 - 26 May 2022
Viewed by 2210
Abstract
Amyloid-β peptide (Aβ) aggregates are known to be correlated with pathological neurodegenerative diseases. The fibril formation process of such peptides in solution is influenced by several factors, such as the ionic strength of the buffer, concentration, pH, and presence of other molecules, just [...] Read more.
Amyloid-β peptide (Aβ) aggregates are known to be correlated with pathological neurodegenerative diseases. The fibril formation process of such peptides in solution is influenced by several factors, such as the ionic strength of the buffer, concentration, pH, and presence of other molecules, just to mention a few. In this paper, we report a detailed analysis of in vitro Aβ42 fibril formation in the presence of cortisol at different relative concentrations. The thioflavin T fluorescence assay allowed us to monitor the fibril formation kinetics, while a morphological characterization of the aggregates was obtained by atomic force microscopy. Moreover, infrared absorption spectroscopy was exploited to investigate the secondary structure changes along the fibril formation path. Molecular dynamics calculations allowed us to understand the intermolecular interactions with cortisol. The combined results demonstrated the influence of cortisol on the fibril formation process: indeed, at cortisol-Aβ42 concentration ratio (ρ) close to 0.1 a faster organization of Aβ42 fragments into fibrils is promoted, while for ρ = 1 the formation of fibrils is completely inhibited. Full article
(This article belongs to the Special Issue Spectroscopy and Microscopy of Fibrillar Protein Aggregates)
►▼ Show Figures

Figure 1

15 pages, 9082 KiB  
Article
Influence of Urea and Dimethyl Sulfoxide on K-Peptide Fibrillation
by Jarosław Wawer, Jakub Karczewski, Robert Aranowski, Rafał Piątek, Danuta Augustin-Nowacka and Piotr Bruździak
Int. J. Mol. Sci. 2022, 23(6), 3027; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms23063027 - 11 Mar 2022
Viewed by 1832
Abstract
Protein fibrillation leads to formation of amyloids—linear aggregates that are hallmarks of many serious diseases, including Alzheimer’s and Parkinson’s diseases. In this work, we investigate the fibrillation of a short peptide (K-peptide) from the amyloidogenic core of hen egg white lysozyme in the [...] Read more.
Protein fibrillation leads to formation of amyloids—linear aggregates that are hallmarks of many serious diseases, including Alzheimer’s and Parkinson’s diseases. In this work, we investigate the fibrillation of a short peptide (K-peptide) from the amyloidogenic core of hen egg white lysozyme in the presence of dimethyl sulfoxide or urea. During the studies, a variety of spectroscopic methods were used: fluorescence spectroscopy and the Thioflavin T assay, circular dichroism, Fourier-transform infrared spectroscopy, optical density measurements, dynamic light scattering and intrinsic fluorescence. Additionally, the presence of amyloids was confirmed by atomic force microscopy. The obtained results show that the K-peptide is highly prone to form fibrillar aggregates. The measurements also confirm the weak impact of dimethyl sulfoxide on peptide fibrillation and distinct influence of urea. We believe that the K-peptide has higher amyloidogenic propensity than the whole protein, i.e., hen egg white lysozyme, most likely due to the lack of the first step of amyloidogenesis—partial unfolding of the native structure. Urea influences the second step of K-peptide amyloidogenesis, i.e., folding into amyloids. Full article
(This article belongs to the Special Issue Spectroscopy and Microscopy of Fibrillar Protein Aggregates)
►▼ Show Figures

Figure 1

13 pages, 28162 KiB  
Article
A Palette of Fluorescent Aβ42 Peptides Labelled at a Range of Surface-Exposed Sites
by Dev Thacker, Mara Bless, Mohammad Barghouth, Enming Zhang and Sara Linse
Int. J. Mol. Sci. 2022, 23(3), 1655; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms23031655 - 31 Jan 2022
Cited by 6 | Viewed by 2312
Abstract
Fluorescence-based single molecule techniques provide important tools towards understanding the molecular mechanism of complex neurodegenerative diseases. This requires efficient covalent attachment of fluorophores. Here we create a series of cysteine mutants (S8C, Y10C, S26C, V40C, and A42C) of Aβ42, involved in [...] Read more.
Fluorescence-based single molecule techniques provide important tools towards understanding the molecular mechanism of complex neurodegenerative diseases. This requires efficient covalent attachment of fluorophores. Here we create a series of cysteine mutants (S8C, Y10C, S26C, V40C, and A42C) of Aβ42, involved in Alzheimer’s disease, based on exposed positions in the fibril structure and label them with the Alexa-fluorophores using maleimide chemistry. Direct stochastic optical reconstruction microscopy imaging shows that all the labelled mutants form fibrils that can be detected by virtue of Alexa fluorescence. Aggregation assays and cryo-electron micrographs establish that the careful choice of labelling position minimizes the perturbation of the aggregation process and fibril structure. Peptides labelled at the N-terminal region, S8C and Y10C, form fibrils independently and with wild-type. Peptides labelled at the fibril core surface, S26C, V40C and A42C, form fibrils only in mixture with wild-type peptide. This can be understood on the basis of a recent fibril model, in which S26, V40 and A42 are surface exposed in two out of four monomers per fibril plane. We provide a palette of fluorescently labelled Aβ42 peptides that can be used to gain understanding of the complex mechanisms of Aβ42 self-assembly and help to develop a more targeted approach to cure the disease. Full article
(This article belongs to the Special Issue Spectroscopy and Microscopy of Fibrillar Protein Aggregates)
►▼ Show Figures

Figure 1

Show export options expand_more Show export options expand_less
Select all
Export citation of selected articles as:
 
Displaying articles 1-5
Back to TopTop