A novel thermo-responsive multiblock architecture composed of a sequential peptide and an amino acid-derived vinyl polymer: toward protein-mimicking single-chain folding

2019 ◽  
Vol 55 (10) ◽  
pp. 1498-1501 ◽  
Author(s):  
Shin-nosuke Nishimura ◽  
Nobuyuki Higashi ◽  
Tomoyuki Koga
Keyword(s):  
Amino Acid ◽  
Single Chain ◽  
Chain Folding ◽  
Hybrid Copolymer ◽  
Vinyl Polymer ◽  
Β Sheet

A novel multiblock hybrid copolymer composed of a β-sheet peptide and a glycine-derived vinyl polymer was developed to achieve single-chain folding into well-defined nanoparticles.

scholarly journals Compositional Determinants of Prion Formation in Yeast

2009 ◽  
Vol 30 (1) ◽  
pp. 319-332 ◽  
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.

Single-Chain Folding Nanoparticles as Carbon Nanotube Catchers

2018 ◽  
Vol 56 (24) ◽  
pp. 2709-2714 ◽  
Author(s):  
Mesut Bilgi ◽  
Demet Karaca Balta ◽  
Binnur Aydogan Temel ◽  
Gokhan Temel
Keyword(s):  
Carbon Nanotube ◽  
Single Chain ◽  
Chain Folding

scholarly journals An antibody that prevents serpin polymerisation acts by inducing a novel allosteric behaviour

2016 ◽  
Vol 473 (19) ◽  
pp. 3269-3290 ◽  
Author(s):  
Neda Motamedi-Shad ◽  
Alistair M. Jagger ◽  
Maximilian Liedtke ◽  
Sarah V. Faull ◽  
Arjun Scott Nanda ◽  
...  
Keyword(s):  
Rational Design ◽  
Conformational Transition ◽  
Structural Basis ◽  
Linear Polymers ◽  
Single Chain ◽  
Opposite Face ◽  
Induced Changes ◽  
Β Sheet ◽  
Chain Form ◽  
Antiprotease Activity

Serpins are important regulators of proteolytic pathways with an antiprotease activity that involves a conformational transition from a metastable to a hyperstable state. Certain mutations permit the transition to occur in the absence of a protease; when associated with an intermolecular interaction, this yields linear polymers of hyperstable serpin molecules, which accumulate at the site of synthesis. This is the basis of many pathologies termed the serpinopathies. We have previously identified a monoclonal antibody (mAb4B12) that, in single-chain form, blocks α1-antitrypsin (α1-AT) polymerisation in cells. Here, we describe the structural basis for this activity. The mAb4B12 epitope was found to encompass residues Glu32, Glu39 and His43 on helix A and Leu306 on helix I. This is not a region typically associated with the serpin mechanism of conformational change, and correspondingly the epitope was present in all tested structural forms of the protein. Antibody binding rendered β-sheet A — on the opposite face of the molecule — more liable to adopt an ‘open’ state, mediated by changes distal to the breach region and proximal to helix F. The allosteric propagation of induced changes through the molecule was evidenced by an increased rate of peptide incorporation and destabilisation of a preformed serpin–enzyme complex following mAb4B12 binding. These data suggest that prematurely shifting the β-sheet A equilibrium towards the ‘open’ state out of sequence with other changes suppresses polymer formation. This work identifies a region potentially exploitable for a rational design of ligands that is able to dynamically influence α1-AT polymerisation.

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

2005 ◽  
pp. 472-473
Author(s):  
Jonathan King ◽  
Cammie Haase-Pettingell ◽  
Ryan Simkovsky ◽  
Peter Weigele
Keyword(s):  
Amino Acid ◽  
Amino Acid Sequence ◽  
Β Sheet

scholarly journals Analysis of Heterodimeric “Mutual Synergistic Folding”-Complexes

2019 ◽  
Vol 20 (20) ◽  
pp. 5136 ◽  
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.

scholarly journals The Primary Structure of Antithrombin-III

1977 ◽  
Author(s):  
T. E. Petersen ◽  
G. Dudek-Wojciechowska ◽  
L. Sottrup-Jensen ◽  
S. Magnusson
Keyword(s):  
Amino Acid ◽  
Antithrombin Iii ◽  
Factor Xa ◽  
Amino Acid Residues ◽  
Disulfide Bridges ◽  
Single Chain ◽  
Terminal Sequence ◽  
Chymotryptic Peptide ◽  
Sequence Region ◽  
Bovine Factor

Human antithrombin-III is a single-chain glycoprotein with three disulfide bridges and four prosthetic glucosamine-based oligosaccharide groups. The disulfide bridges have been established. In four fragments of 208, 168, 3 and 46 amino acid residues, resp. 415 of the appr. 425 residues have been sequenced. The four oligosaccharide groups are attached to four Asn-residues within a sequence region of 95 residues. No extensive sequence homology with the trypsin inhibitors has been observed. One chymotryptic peptide was found to be a substrate for bovine factor Xa, cleaving the arginyl bond in the sequence -Ile-Val-Ala-Glu-Gly-Arg-Asp-. A second peptide is cleaved by thrombin. It is not clear whether these sites are inhibitor sites in the native molecule. Other possible candidates for inhibitor sites are a -Val-Leu-Ile-Leu-Pro-Lys-Pro- sequence (similar to the sequence 40-48 of hirudin, which also includes a -Pro-Lys-Pro- sequence) and also the C-terminal sequence -Gly-Arg-Val-Ala-Asn-Pro-Cys-Val-Lys.

Research on Structure and Property of Silk Fibroin Modified Viscose Fiber

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.

Correlation of the β-sheet crystal size in silk fibers with the protein amino acid sequence

Soft Matter ◽  
2007 ◽  
Vol 3 (7) ◽  
pp. 877-882 ◽  
Author(s):  
Lawrence F. Drummy ◽  
B. L. Farmer ◽  
Rajesh R. Naik
Keyword(s):  
Amino Acid ◽  
Amino Acid Sequence ◽  
Crystal Size ◽  
Protein Amino Acid ◽  
Silk Fibers ◽  
Protein Amino Acid Sequence ◽  
Β Sheet
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