A photoinduced growth system of peptide nanofibres addressed by DNA hybridization

There is an increasing interest in designing fibrillogenesis modulators for treating amyloid β (Aβ)-peptide-associated diseases. The use of Aβ fragment peptides and their derivatives, as well as nonpeptidyl natural products, is one promising approach to prevent Aβ fibrillation. In this study, we demonstrate that tandem-homodimers (TDs) of a β-sheet-forming short peptide in which the amino acid sequence is duplicated in series and joined via an amino alkanoic acid linker of different chain lengths, preventing the random-to-β structural transition of the original monomer. Ape5-TD, containing 5-amino pentanoate, most potently prevented this transition for at least five days by generating disordered aggregates with reduced tryptic stability. The linkers in the TDs generated this inhibitory activity, probably due to their bent conformations and hydrophobicity, appropriate for accommodating and twisting the monomers, resulting in irregular arrangements of the peptides. The present study could allow the design of a new class of protein/peptide fibrillogenesis modulators.

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Compositional Determinants of Prion Formation in Yeast

Molecular and Cellular Biology ◽

10.1128/mcb.01140-09 ◽

2009 ◽

Vol 30 (1) ◽

pp. 319-332 ◽

Cited By ~ 113

Author(s):

James A. Toombs ◽

Blake R. McCarty ◽

Eric D. Ross

Keyword(s):

Amino Acid ◽

Amino Acid Composition ◽

Amyloid Formation ◽

Yeast Prion ◽

Hydrophobic Residues ◽

Predictive Methods ◽

Infectious Proteins ◽

Β Sheet ◽

Eukaryotic Genomes

ABSTRACT Numerous prions (infectious proteins) have been identified in yeast that result from the conversion of soluble proteins into β-sheet-rich amyloid-like protein aggregates. Yeast prion formation is driven primarily by amino acid composition. However, yeast prion domains are generally lacking in the bulky hydrophobic residues most strongly associated with amyloid formation and are instead enriched in glutamines and asparagines. Glutamine/asparagine-rich domains are thought to be involved in both disease-related and beneficial amyloid formation. These domains are overrepresented in eukaryotic genomes, but predictive methods have not yet been developed to efficiently distinguish between prion and nonprion glutamine/asparagine-rich domains. We have developed a novel in vivo assay to quantitatively assess how composition affects prion formation. Using our results, we have defined the compositional features that promote prion formation, allowing us to accurately distinguish between glutamine/asparagine-rich domains that can form prion-like aggregates and those that cannot. Additionally, our results explain why traditional amyloid prediction algorithms fail to accurately predict amyloid formation by the glutamine/asparagine-rich yeast prion domains.

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Spectroscopic Studies of Structural Changes in Two β-Sheet-Forming Peptides Show an Ensemble of Structures that Unfold Noncooperatively†

Biochemistry ◽

10.1021/bi026893k ◽

2003 ◽

Vol 42 (15) ◽

pp. 4321-4332 ◽

Cited By ~ 27

Author(s):

Serguei V. Kuznetsov ◽

Jovencio Hilario ◽

Timothy A. Keiderling ◽

Anjum Ansari

Keyword(s):

Structural Changes ◽

Spectroscopic Studies ◽

Sheet Forming ◽

Β Sheet

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Amino Acid Sequence Control of the Folding of the Parallel β-Helix, the Simplest β-Sheet Fold

Lecture Notes in Computer Science - Research in Computational Molecular Biology ◽

10.1007/11415770_35 ◽

2005 ◽

pp. 472-473

Author(s):

Jonathan King ◽

Cammie Haase-Pettingell ◽

Ryan Simkovsky ◽

Peter Weigele

Keyword(s):

Amino Acid ◽

Amino Acid Sequence ◽

Β Sheet

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Analysis of Heterodimeric “Mutual Synergistic Folding”-Complexes

International Journal of Molecular Sciences ◽

10.3390/ijms20205136 ◽

2019 ◽

Vol 20 (20) ◽

pp. 5136 ◽

Cited By ~ 3

Author(s):

Mentes ◽

Magyar ◽

Fichó ◽

Simon

Keyword(s):

Amino Acid ◽

Amino Acid Composition ◽

Acid Composition ◽

Intrinsically Disordered Proteins ◽

Driving Forces ◽

Disordered Proteins ◽

Subunit Interactions ◽

Amino Acid Compositions ◽

Intrinsically Disordered ◽

Β Sheet

Several intrinsically disordered proteins (IDPs) are capable to adopt stable structures without interacting with a folded partner. When the folding of all interacting partners happens at the same time, coupled with the interaction in a synergistic manner, the process is called Mutual Synergistic Folding (MSF). These complexes represent a discrete subset of IDPs. Recently, we collected information on their complexes and created the MFIB (Mutual Folding Induced by Binding) database. In a previous study, we compared homodimeric MSF complexes with homodimeric and monomeric globular proteins with similar amino acid sequence lengths. We concluded that MSF homodimers, compared to globular homodimeric proteins, have a greater solvent accessible main-chain surface area on the contact surface of the subunits, which becomes buried during dimerization. The main driving force of the folding is the mutual shielding of the water-accessible backbones, but the formation of further intermolecular interactions can also be relevant. In this paper, we will report analyses of heterodimeric MSF complexes. Our results indicate that the amino acid composition of the heterodimeric MSF monomer subunits slightly diverges from globular monomer proteins, while after dimerization, the amino acid composition of the overall MSF complexes becomes more similar to overall amino acid compositions of globular complexes. We found that inter-subunit interactions are strengthened, and additionally to the shielding of the solvent accessible backbone, other factors might play an important role in the stabilization of the heterodimeric structures, likewise energy gain resulting from the interaction of the two subunits with different amino acid compositions. We suggest that the shielding of the β-sheet backbones and the formation of a buried structural core along with the general strengthening of inter-subunit interactions together could be the driving forces of MSF protein structural ordering upon dimerization.

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Effect of the Hydrophilic-Hydrophobic Balance of Antigen-Loaded Peptide Nanofibers on Their Cellular Uptake, Cellular Toxicity, and Immune Stimulatory Properties

International Journal of Molecular Sciences ◽

10.3390/ijms20153781 ◽

2019 ◽

Vol 20 (15) ◽

pp. 3781 ◽

Cited By ~ 3

Author(s):

Tomonori Waku ◽

Saki Nishigaki ◽

Yuichi Kitagawa ◽

Sayaka Koeda ◽

Kazufumi Kawabata ◽

...

Keyword(s):

Cellular Uptake ◽

Self Assembly ◽

Sheet Forming ◽

Design Guidelines ◽

Cellular Interactions ◽

Antigenic Peptides ◽

Peptide Nanofibers ◽

Dc Line ◽

Chain Lengths ◽

Β Sheet

Recently, nanofibers (NFs) formed from antigenic peptides conjugated to β-sheet-forming peptides have attracted much attention as a new generation of vaccines. However, studies describing how the hydrophilic-hydrophobic balance of NF components affects cellular interactions of NFs are limited. In this report, three different NFs were prepared by self-assembly of β-sheet-forming peptides conjugated with model antigenic peptides (SIINFEKL) from ovalbumin and hydrophilic oligo-ethylene glycol (EG) of differing chain lengths (6-, 12- and 24-mer) to investigate the effect of EG length of antigen-loaded NFs on their cellular uptake, cytotoxicity, and dendritic cell (DC)-stimulation ability. We used an immortal DC line, termed JAWS II, derived from bone marrow-derived DCs of a C57BL/6 p53-knockout mouse. The uptake of NFs, consisting of the EG 12-mer by DCs, was the most effective and activated DC without exhibiting significant cytotoxicity. Increasing the EG chain length significantly reduced cellular entry and DC activation by NFs. Conversely, shortening the EG chain enhanced DC activation but increased toxicity and impaired water-dispersibility, resulting in low cellular uptake. These results show that the interaction of antigen-loaded NFs with cells can be tuned by the EG length, which provides useful design guidelines for the development of effective NF-based vaccines.

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Deamination gradients within codons after 12 position swap predict amino acid hydrophobicity and parallel β-sheet conformational preference

Biosystems ◽

10.1016/j.biosystems.2020.104116 ◽

2020 ◽

Vol 191-192 ◽

pp. 104116 ◽

Cited By ~ 3

Author(s):

Jacques Demongeot ◽

Hervé Seligmann

Keyword(s):

Amino Acid ◽

Conformational Preference ◽

Β Sheet

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Research on Structure and Property of Silk Fibroin Modified Viscose Fiber

Advanced Materials Research ◽

10.4028/www.scientific.net/amr.175-176.176 ◽

2011 ◽

Vol 175-176 ◽

pp. 176-180

Author(s):

Hui Ying Wu ◽

Bao Qi Zuo

Keyword(s):

Amino Acid ◽

Silk Fibroin ◽

Amino Acid Content ◽

Longitudinal Section ◽

Decomposition Temperature ◽

Viscose Fiber ◽

Random Coil ◽

Wet Strength ◽

Structure And Property ◽

Β Sheet

Silk fibroin modified viscose fiber (SFVF) was a new fiber with silken handling and luster, which was produced via adding silk fibroin (SF) during the viscose process. In this paper, a series of testing had been done to study the structure and properties of SFVF. The amino acid content of SFVF was measured by HITACHI-835-50 amino acid tester. The morphology, structure, thermal and mechanical property of SFVF were characterized by SEM, FTIR, DSC and electronic strength tester. The results indicated that SFVF consisted of many kinds of amino acids compared with pure viscose fiber (VF) yarn. The results of SEM showed more continuous multi fine slots existed in the longitudinal section of SFVF than in that of VF, demonstrating that wet permeability and vapor transmission could be enhanced for the SFVF to certain extent. Results from FTIR indicated that the secondary structure of SFVF was mainly β-sheet and random coil, and its absorption peaks were 1616cm-1 and 1644 cm-1 respectively. The DSC curve shown the thermal decomposition temperature of SFVF was about 328.39°C, which was close to that of VF. It suggested that the SF modification had no obvious influence on thermal stability of VF. At last, the dry-strength and wet-strength of SFVF was close to that of VF. Therefore, the application of VF would be expanded with the SF modification.

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