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Advanced Research in Functional Amyloids

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 (5 March 2024) | Viewed by 5266

Special Issue Editors


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Guest Editor
Department of Chemical Sciences, University of Naples “Federico II”, Via Cintia 4, I-80126 Naples, Italy
Interests: biosurfactants; biosensing; surface bio-functionalization; surface active compounds; biochemistry

E-Mail Website
Guest Editor
Department of Chemical Sciences, University of Naples “Federico II”, Via Cintia 4, I-80126 Naples, Italy
Interests: protein recombinant expression; biosensing; protein immobilization, fungal laccase
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Protein aggregates, and in particular amyloids, are generally considered to be inherently irreversible aberrant clumps, and are often associated with pathologies. However, amyloid has many useful features. Recently, it has become evident that many amyloids, termed “functional amyloids”, are used by nature in multifaceted activities that are beneficial to organisms of different taxa ranging from bacteria to mammals. These amyloids are involved in vital biological functions including the structure of the reservoir, and as information carriers of suppression and signaling. Moreover, with the development of nanotechnology, functional amyloid materials are drawing increasing attention, and numerous remarkable applications are emerging. Overall, functional amyloids at surfaces/interfaces have excellent potential applications in next-generation biotechnology and biomaterials. Amyloid fibrils are promising nanomaterials for technological applications such as biosensors, tissue engineering, drug delivery, and optoelectronics. The scope of the Special Issue is to summarize and enlarge the knowledge of synthesis, characterization, and use of functional amyloids.

Therefore, authors are invited to submit original research and review articles which address the progress and current standing of functional amyloid processes.

Topics may include, but are not limited to:

  • Characterization and identification of new functional amyloids.
  • Analysis of hierarchical process of functional amyloid formation.
  • Applications of functional amyloid as nanomaterials.

Dr. Paola Cicatiello
Dr. Alessandra Piscitelli
Guest Editors

Manuscript Submission Information

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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

  • functional bio-materials
  • self-assembling layer
  • bio-adhesion
  • surface/interface functionalization
  • functional amyloid characterization

Published Papers (5 papers)

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Research

16 pages, 3531 KiB  
Article
Differential Effects of Lipid Bilayers on αPSM Peptide Functional Amyloid Formation
by Kamilla Kristoffersen, Kasper Holst Hansen and Maria Andreasen
Int. J. Mol. Sci. 2024, 25(1), 102; https://doi.org/10.3390/ijms25010102 - 20 Dec 2023
Viewed by 697
Abstract
Phenol-soluble modulins (PSMs) are key virulence factors of S. aureus, and they comprise the structural scaffold of biofilm as they self-assemble into functional amyloids. They have been shown to interact with cell membranes as they display toxicity towards human cells through cell [...] Read more.
Phenol-soluble modulins (PSMs) are key virulence factors of S. aureus, and they comprise the structural scaffold of biofilm as they self-assemble into functional amyloids. They have been shown to interact with cell membranes as they display toxicity towards human cells through cell lysis, with αPSM3 being the most cytotoxic. In addition to causing cell lysis in mammalian cells, PSMs have also been shown to interact with bacterial cell membranes through antimicrobial effects. Here, we present a study on the effects of lipid bilayers on the aggregation mechanism of αPSM using chemical kinetics to study the effects of lipid vesicles on the aggregation kinetics and using circular dichroism (CD) spectroscopy, Fourier-transform infrared (FTIR) spectroscopy and transmission electron microscopy (TEM) to investigate the corresponding secondary structure of the aggregates. We found that the effects of lipid bilayers on αPSM aggregation were not homogeneous between lipid type and αPSM peptides, although none of the lipids caused changes in the dominating aggregation mechanism. In the case of αPSM3, all types of lipids slowed down aggregation to a varying degree, with 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC) having the most pronounced effect. For αPSM1, lipids had opposite effects, where DOPC decelerated aggregation and lipopolysaccharide (LPS) accelerated the aggregation, while 1,2-dioleoyl-sn-glycero-3-phospho-rac-(1-glycerol) (DOPG) had no effect. For αPSM4, both DOPG and LPS accelerated the aggregation, but only at high concentration, while DOPC showed no effect. None of the lipids was capable of inducing aggregation of αPSM2. Our data reveal a complex interaction pattern between PSMs peptides and lipid bilayers that causes changes in the aggregation kinetics by affecting different kinetic parameters along with only subtle changes in morphology. Full article
(This article belongs to the Special Issue Advanced Research in Functional Amyloids)
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22 pages, 9894 KiB  
Article
OmpC and OmpF Outer Membrane Proteins of Escherichia coli and Salmonella enterica Form Bona Fide Amyloids
by Mikhail V. Belousov, Anastasiia O. Kosolapova, Haidar Fayoud, Maksim I. Sulatsky, Anna I. Sulatskaya, Maria N. Romanenko, Alexander G. Bobylev, Kirill S. Antonets and Anton A. Nizhnikov
Int. J. Mol. Sci. 2023, 24(21), 15522; https://doi.org/10.3390/ijms242115522 - 24 Oct 2023
Cited by 1 | Viewed by 1505
Abstract
Outer membrane proteins (Omps) of Gram-negative bacteria represent porins involved in a wide range of virulence- and pathogenesis-related cellular processes, including transport, adhesion, penetration, and the colonization of host tissues. Most outer membrane porins share a specific spatial structure called the β-barrel that [...] Read more.
Outer membrane proteins (Omps) of Gram-negative bacteria represent porins involved in a wide range of virulence- and pathogenesis-related cellular processes, including transport, adhesion, penetration, and the colonization of host tissues. Most outer membrane porins share a specific spatial structure called the β-barrel that provides their structural integrity within the membrane lipid bilayer. Recent data suggest that outer membrane proteins from several bacterial species are able to adopt the amyloid state alternative to their β-barrel structure. Amyloids are protein fibrils with a specific spatial structure called the cross-β that gives them an unusual resistance to different physicochemical influences. Various bacterial amyloids are known to be involved in host-pathogen and host-symbiont interactions and contribute to colonization of host tissues. Such an ability of outer membrane porins to adopt amyloid state might represent an important mechanism of bacterial virulence. In this work, we investigated the amyloid properties of the OmpC and OmpF porins from two species belonging to Enterobacteriaceae family, Escherichia coli, and Salmonella enterica. We demonstrated that OmpC and OmpF of E. coli and S. enterica form toxic fibrillar aggregates in vitro. These aggregates exhibit birefringence upon binding Congo Red dye and show characteristic reflections under X-ray diffraction. Thus, we confirmed amyloid properties for OmpC of E. coli and demonstrated bona fide amyloid properties for three novel proteins: OmpC of S. enterica and OmpF of E. coli and S. enterica in vitro. All four studied porins were shown to form amyloid fibrils at the surface of E. coli cells in the curli-dependent amyloid generator system. Moreover, we found that overexpression of recombinant OmpC and OmpF in the E. coli BL21 strain leads to the formation of detergent- and protease-resistant amyloid-like aggregates and enhances the birefringence of bacterial cultures stained with Congo Red. We also detected detergent- and protease-resistant aggregates comprising OmpC and OmpF in S. enterica culture. These data are important in the context of understanding the structural dualism of Omps and its relation to pathogenesis. Full article
(This article belongs to the Special Issue Advanced Research in Functional Amyloids)
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20 pages, 3174 KiB  
Article
Disrupting the Repeat Domain of Premelanosome Protein (PMEL) Produces Dysamyloidosis and Dystrophic Ocular Pigment Reflective of Pigmentary Glaucoma
by Elizabeth D. Hodges, Paul W. Chrystal, Tim Footz, Lance P. Doucette, Nicole C. L. Noel, Zixuan Li, Michael A. Walter and W. Ted Allison
Int. J. Mol. Sci. 2023, 24(19), 14423; https://doi.org/10.3390/ijms241914423 - 22 Sep 2023
Cited by 2 | Viewed by 855
Abstract
Pigmentary glaucoma has recently been associated with missense mutations in PMEL that are dominantly inherited and enriched in the protein’s fascinating repeat domain. PMEL pathobiology is intriguing because PMEL forms functional amyloid in healthy eyes, and this PMEL amyloid acts to scaffold melanin [...] Read more.
Pigmentary glaucoma has recently been associated with missense mutations in PMEL that are dominantly inherited and enriched in the protein’s fascinating repeat domain. PMEL pathobiology is intriguing because PMEL forms functional amyloid in healthy eyes, and this PMEL amyloid acts to scaffold melanin deposition. This is an informative contradistinction to prominent neurodegenerative diseases where amyloid formation is neurotoxic and mutations cause a toxic gain of function called “amyloidosis”. Preclinical animal models have failed to model this PMEL “dysamyloidosis” pathomechanism and instead cause recessively inherited ocular pigment defects via PMEL loss of function; they have not addressed the consequences of disrupting PMEL’s repetitive region. Here, we use CRISPR to engineer a small in-frame mutation in the zebrafish homolog of PMEL that is predicted to subtly disrupt the protein’s repetitive region. Homozygous mutant larvae displayed pigmentation phenotypes and altered eye morphogenesis similar to presumptive null larvae. Heterozygous mutants had disrupted eye morphogenesis and disrupted pigment deposition in their retinal melanosomes. The deficits in the pigment deposition of these young adult fish were not accompanied by any detectable glaucomatous changes in intraocular pressure or retinal morphology. Overall, the data provide important in vivo validation that subtle PMEL mutations can cause a dominantly inherited pigment pathology that aligns with the inheritance of pigmentary glaucoma patient pedigrees. These in vivo observations help to resolve controversy regarding the necessity of PMEL’s repeat domain in pigmentation. The data foster an ongoing interest in an antithetical dysamyloidosis mechanism that, akin to the amyloidosis of devastating dementias, manifests as a slow progressive neurodegenerative disease. Full article
(This article belongs to the Special Issue Advanced Research in Functional Amyloids)
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14 pages, 12358 KiB  
Article
Evidence of Small Fungal Cysteine-Rich Proteins Acting as Biosurfactants and Self-Assembling into Large Fibers
by Rossana Pitocchi, Ilaria Stanzione, Anna Illiano, Angela Amoresano, Oreste Tarallo, Paola Cicatiello, Alessandra Piscitelli and Paola Giardina
Int. J. Mol. Sci. 2023, 24(18), 13843; https://doi.org/10.3390/ijms241813843 - 08 Sep 2023
Cited by 1 | Viewed by 679
Abstract
Fungi produce surface-active proteins, among which hydrophobins are the most characterized and attractive also for their ability to form functional amyloids. Our most recent findings show that these abilities are shared with other classes of fungal proteins. Indeed, in this paper, we compared [...] Read more.
Fungi produce surface-active proteins, among which hydrophobins are the most characterized and attractive also for their ability to form functional amyloids. Our most recent findings show that these abilities are shared with other classes of fungal proteins. Indeed, in this paper, we compared the characteristics of a class I hydrophobin (Vmh2 from Pleurotus ostreatus) and an unknown protein (named PAC3), extracted from the marine fungal strain Acremonium sclerotigenum, which does not belong to the same protein family based on its sequence features. They both proved to be good biosurfactants, stabilizing emulsions in several conditions (concentration, pH, and salinity) and decreasing surface tension to a comparable value to that of some synthetic surfactants. After that, we observed for both Vmh2 and PAC3 the formation of giant fibers without the need for harsh conditions or long incubation time, a remarkable ability herein reported for the first time. Full article
(This article belongs to the Special Issue Advanced Research in Functional Amyloids)
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25 pages, 2039 KiB  
Article
Amyloid-β Tetramers and Divalent Cations at the Membrane/Water Interface: Simple Models Support a Functional Role
by Pawel Krupa, Giovanni La Penna and Mai Suan Li
Int. J. Mol. Sci. 2023, 24(16), 12698; https://doi.org/10.3390/ijms241612698 - 11 Aug 2023
Viewed by 874
Abstract
Charge polarization at the membrane interface is a fundamental process in biology. Despite the lower concentration compared to the abundant monovalent ions, the relative abundance of divalent cations (Ca2+, Mg2+, Zn2+, Fe2+, Cu2+) [...] Read more.
Charge polarization at the membrane interface is a fundamental process in biology. Despite the lower concentration compared to the abundant monovalent ions, the relative abundance of divalent cations (Ca2+, Mg2+, Zn2+, Fe2+, Cu2+) in particular spaces, such as the neuron synapse, raised many questions on the possible effects of free multivalent ions and of the required protection of membranes by the eventual defects caused by the free forms of the cations. In this work, we first applied a recent realistic model of divalent cations to a well-investigated model of a polar lipid bilayer, di-myristoyl phosphatidyl choline (DMPC). The full atomistic model allows a fairly good description of changes in the hydration of charged and polar groups upon the association of cations to lipid atoms. The lipid-bound configurations were analyzed in detail. In parallel, amyloid-β 1–42 (Aβ42) peptides assembled into tetramers were modeled at the surface of the same bilayer. Two of the protein tetramers’ models were loaded with four Cu2+ ions, the latter bound as in DMPC-free Aβ42 oligomers. The two Cu-bound models differ in the binding topology: one with each Cu ion binding each of the monomers in the tetramer; one with pairs of Cu ions linking two monomers into dimers, forming tetramers as dimers of dimers. The models here described provide hints on the possible role of Cu ions in synaptic plasticity and of Aβ42 oligomers in storing the same ions away from lipids. The release of structurally disordered peptides in the synapse can be a mechanism to recover ion homeostasis and lipid membranes from changes in the divalent cation concentration. Full article
(This article belongs to the Special Issue Advanced Research in Functional Amyloids)
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