Topic Editors

1. Department of Materials Science and Technology, University of Crete, Crete, Greece
2. Institute of Electronic Structure and Laser (I.E.S.L.), Foundation for Research and Technology—Hellas (FO.R.T.H.), Vassilika Vouton, Crete, Greece
Department of Materials Science and Technology, University of Crete and Institute of Electronic Structure and Laser (I.E.S.L.), Foundation for Research and Technology-Hellas (FO.R.T.H.), Vassilika Vouton, Heraklion, 70013 Crete, Greece
Prof. Dr. Vagelis Harmandaris
1. The Cyprus Institute, CaSToRC, 20 Konstantinou Kavafi St. 2121, Aglantzia, P.O. BOX 27456 Nicosia, Cyprus
2. Department of Mathematics and Applied Mathematics, University of Crete, Crete, Greece
3. Institute of Applied and Computational Mathematics (I.A.C.M.), Foundation for Research and Technology - Hellas (FO.R.T.H.), Vassilika Vouton, 70013 Heraklion, Crete, Greece
Dr. Anastassia Rissanou
1. Foundation for Research and Technology Hellas, Institute of Applied and Computational Mathematics, Vassilika Vouton, 70013 Heraklion, Crete, Greece
2. The Cyprus Institute, CaSToRC, 20 Konstantinou Kavafi St., 2121 Aglantzia, P.O. BOX 27456 Nicosia, Cyprus

Fibrous Proteins and Self-Assembling Peptides: From Structure and Assembly to Applications

Abstract submission deadline
closed (30 September 2023)
Manuscript submission deadline
closed (30 November 2023)
Viewed by
11136

Topic Information

Dear Colleagues,

With this Special Issue, we intend to collect a broad range of contributions related to folding, assembly, and applications of fibrous proteins and self-assembling peptides. Natural fibrous proteins such as collagen, elastin, silk fibroins, and spider silks have long fascinated scientists and engineers due to their mechanical and elastic properties. Most of these proteins are built from repetitive self-assembling building blocks that serve as a source of inspiration for designer biomaterials. Amyloid-type fibrils are another class of self-assembled fibrous objects, most often associated with protein aggregation diseases; however, nature often uses amyloid type-folds to build natural biomaterials. Crystal structure information was until recently scarce, especially for beta-structured fibrous folds; however, in recent years, considerable progress has been made due to the emergence of Cryo-EM methodologies that provided atomic-scale information for previously intractable fibrous objects such as amyloid fibrils. The most recent development of artificial intelligence methods such as Alphafold and Alphafold multimer for protein structure prediction is also a remarkable game changer in the field. Last but not least, viral fibers, since they are the viral cell-attachment organelles, are recently the focus of intense investigation, mainly due to the SARS-CoV-2 pandemic. Despite the effervescence of structural insight in the aforementioned areas, much remains to be clarified and understood. Therefore, the present Special Issue aims to substantially contribute to the advancement of this research field by collecting and merging insights ranging from theoretical, biochemical and structural knowledge to nanosciences/technologies towards a long-term vision and applications. Theoretical contributions or contributions combining theoretical and experimental insight are especially encouraged.

Prof. Dr. Anna Mitraki
Dr. Chrysoula Kokotidou
Prof. Dr. Vagelis Harmandaris
Dr. Anastassia Rissanou
Topic Editors

Keywords

  • fibrous folds
  • amyloid
  • viral spikes
  • peptides
  • beta-folds
  • self-assembly
  • biomaterials
  • drug delivery
  • protein and gene carriers
  • computational modelling

Participating Journals

Journal Name Impact Factor CiteScore Launched Year First Decision (median) APC
Biomolecules
biomolecules
5.5 9.4 2011 16.9 Days CHF 2700
International Journal of Molecular Sciences
ijms
5.6 8.1 2000 16.3 Days CHF 2900
Nanomaterials
nanomaterials
5.3 8.5 2010 13.6 Days CHF 2900
Viruses
viruses
4.7 7.3 2009 13.8 Days CHF 2600

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Published Papers (5 papers)

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12 pages, 3312 KiB  
Article
Metal-Promoted Higher-Order Assembly of Disulfide-Stapled Helical Barrels
by Ashutosh Agrahari, Mark Lipton and Jean Chmielewski
Nanomaterials 2023, 13(19), 2645; https://doi.org/10.3390/nano13192645 - 26 Sep 2023
Viewed by 1240
Abstract
Peptide-based helical barrels are a noteworthy building block for hierarchical assembly, with a hydrophobic cavity that can serve as a host for cargo. In this study, disulfide-stapled helical barrels were synthesized containing ligands for metal ions on the hydrophilic face of each amphiphilic [...] Read more.
Peptide-based helical barrels are a noteworthy building block for hierarchical assembly, with a hydrophobic cavity that can serve as a host for cargo. In this study, disulfide-stapled helical barrels were synthesized containing ligands for metal ions on the hydrophilic face of each amphiphilic peptide helix. The major product of the disulfide-stapling reaction was found to be composed of five amphiphilic peptides, thereby going from a 16-amino-acid peptide to a stapled 80-residue protein in one step. The structure of this pentamer, 5HB1, was optimized in silico, indicating a significant hydrophobic cavity of ~6 Å within a helical barrel. Metal-ion-promoted assembly of the helical barrel building blocks generated higher order assemblies with a three-dimensional (3D) matrix morphology. The matrix was decorated with hydrophobic dyes and His-tagged proteins both before and after assembly, taking advantage of the hydrophobic pocket within the helical barrels and coordination sites within the metal ion-peptide framework. As such, this peptide-based biomaterial has potential for a number of biotechnology applications, including supplying small molecule and protein growth factors during cell and tissue growth within the matrix. Full article
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15 pages, 3280 KiB  
Article
Degree of Hydrolysis Regulated by Enzyme Mediation of Wheat Gluten Fibrillation: Structural Characterization and Analysis of the Mechanism of Action
by Huijuan Zhang, Shihao Lv, Feiyue Ren, Jie Liu and Jing Wang
Int. J. Mol. Sci. 2023, 24(17), 13529; https://doi.org/10.3390/ijms241713529 - 31 Aug 2023
Cited by 1 | Viewed by 912
Abstract
The impact of different degrees of hydrolysis (DHs) on fibrillation when trypsin mediates wheat gluten (WG) fibrillation has not been thoroughly investigated. This study discussed the differences in amyloid fibrils (AFs) formed from wheat gluten peptides (WGPs) at various DH values. The results [...] Read more.
The impact of different degrees of hydrolysis (DHs) on fibrillation when trypsin mediates wheat gluten (WG) fibrillation has not been thoroughly investigated. This study discussed the differences in amyloid fibrils (AFs) formed from wheat gluten peptides (WGPs) at various DH values. The results from Thioflavin T (ThT) fluorescence analysis indicated that WGPs with DH6 were able to form the most AFs. Changes in Fourier Transform Infrared (FTIR) absorption spectra and secondary structure also suggested a higher degree of fibrillation in DH6 WGPs. Analysis of surface hydrophobicity and ζ-potential showed that DH6 AFs had the highest surface hydrophobicity and the most stable water solutions. Scanning Electron Microscopy (SEM) and Transmission Electron Microscopy (TEM) images revealed the best overall morphology of DH6 AFs. These findings can offer valuable insights into the development of a standardized method for preparing wheat gluten amyloid fibrils. Full article
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18 pages, 2164 KiB  
Review
Peptide Inhibitors of Insulin Fibrillation: Current and Future Challenges
by Beatrice Rosetti and Silvia Marchesan
Int. J. Mol. Sci. 2023, 24(2), 1306; https://doi.org/10.3390/ijms24021306 - 9 Jan 2023
Cited by 6 | Viewed by 3410
Abstract
Amyloidoses include a large variety of local and systemic diseases that share the common feature of protein unfolding or refolding into amyloid fibrils. The most studied amyloids are those directly involved in neurodegenerative diseases, while others, such as those formed by insulin, are [...] Read more.
Amyloidoses include a large variety of local and systemic diseases that share the common feature of protein unfolding or refolding into amyloid fibrils. The most studied amyloids are those directly involved in neurodegenerative diseases, while others, such as those formed by insulin, are surprisingly far less studied. Insulin is a very important polypeptide that plays a variety of biological roles and, first and foremost, is at the basis of the therapy of diabetic patients. It is well-known that it can form fibrils at the site of injection, leading to inflammation and immune response, in addition to other side effects. In this concise review, we analyze the current knowledge on insulin fibrillation, with a focus on the development of peptide-based inhibitors, which are promising candidates for their biocompatibility but still pose challenges to their effective use in therapy. Full article
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13 pages, 1985 KiB  
Article
Zona Pellucida like Domain Protein 1 (ZPLD1) Polymerization Is Regulated by Two Distinguished Hydrophobic Motifs
by Marie Isabell Knepper and Jens Dernedde
Int. J. Mol. Sci. 2022, 23(22), 13894; https://doi.org/10.3390/ijms232213894 - 11 Nov 2022
Viewed by 1509
Abstract
Zona Pellucida Like Domain 1 Protein (ZPLD1) is a main component of the cupula, a gelatinous structure located in the labyrinth organ of the inner ear and involved in vestibular function. The N-glycosylated protein is likely able to organize high-molecular-weight polymers via [...] Read more.
Zona Pellucida Like Domain 1 Protein (ZPLD1) is a main component of the cupula, a gelatinous structure located in the labyrinth organ of the inner ear and involved in vestibular function. The N-glycosylated protein is likely able to organize high-molecular-weight polymers via its zona pellucida (ZP) module, which is common for many extracellular proteins that self-assemble into matrices. In this work, we confirmed that ZPLD1 can form multimers while setting up a cellular model leveraging Madin–Darby canine kidney (MDCK) cells to study protein polymerization. We identified two motifs within ZPLD1 which regulate its polymerization and follow previously published conserved regions, identified across ZP proteins. Mutational depletion of either one of these modules led to diminished or abnormal polymer formation outside of the cells, likely due to altered processing at the plasma membrane. Further, intracellular polymer formation was observed. Proteolytic cleavage during secretion, separating the regulatory motif located distinct of the ZP module from the mature monomer, seems to be necessary to enable polymerization. While the molecular interactions of the identified motifs remain to be proven, our findings suggest that ZPLD1 is a polymer forming ZP protein following an orchestrated mechanism of protein polymerization to finally build up a gelatinous hydrogel. Full article
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12 pages, 4703 KiB  
Review
Exploring Biomolecular Self-Assembly with Far-Infrared Radiation
by Takayasu Kawasaki, Yuusuke Yamaguchi, Hideaki Kitahara, Akinori Irizawa and Masahiko Tani
Biomolecules 2022, 12(9), 1326; https://doi.org/10.3390/biom12091326 - 19 Sep 2022
Cited by 2 | Viewed by 2411
Abstract
Physical engineering technology using far-infrared radiation has been gathering attention in chemical, biological, and material research fields. In particular, the high-power radiation at the terahertz region can give remarkable effects on biological materials distinct from a simple thermal treatment. Self-assembly of biological molecules [...] Read more.
Physical engineering technology using far-infrared radiation has been gathering attention in chemical, biological, and material research fields. In particular, the high-power radiation at the terahertz region can give remarkable effects on biological materials distinct from a simple thermal treatment. Self-assembly of biological molecules such as amyloid proteins and cellulose fiber plays various roles in medical and biomaterials fields. A common characteristic of those biomolecular aggregates is a sheet-like fibrous structure that is rigid and insoluble in water, and it is often hard to manipulate the stacking conformation without heating, organic solvents, or chemical reagents. We discovered that those fibrous formats can be conformationally regulated by means of intense far-infrared radiations from a free-electron laser and gyrotron. In this review, we would like to show the latest and the past studies on the effects of far-infrared radiation on the fibrous biomaterials and to suggest the potential use of the far-infrared radiation for regulation of the biomolecular self-assembly. Full article
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