The influence of the hydrophilic–lipophilic environment on the structure of silk fibroin protein

AbstractThe hepatitis B virus (HBV) capsid is an attractive drug target, relevant to combating viral hepatitis as a major public health concern. Among small molecules known to interfere with capsid assembly, the phenylpropenamides, including AT130, represent an important anti-viral paradigm based on disrupting the timing of genome encapsulation. Crystallographic studies of AT130-bound complexes have been essential in explaining the effects of the small molecule on HBV capsid structure; however, computational examination reveals that key changes attributed to AT130 were erroneous, likely a consequence of interpreting poor resolution arising from a highly flexible protein. Here, all-atom molecular dynamics simulations of an intact AT130-bound HBV capsid reveal that, rather than damaging spike helicity, AT130 enhances the capsid’s ability to recover it. A new conformational state is identified, which can lead to dramatic opening of the intradimer interface and disruption of communication within the spike tip. A novel salt bridge is also discovered, which can mediate contact between the spike tip and fulcrum even in closed conformations, revealing a mechanism of direct communication across these domains. Combined with dynamical network analysis, results describe a connection between the intra- and interdimer interfaces and enable mapping of allostery traversing the entire capsid protein dimer.

Download Full-text

Biocompatible, optically transparent, patterned, and flexible electrodes and radio-frequency antennas prepared from silk protein and silver nanowire networks

RSC Advances ◽

10.1039/c6ra25580a ◽

2017 ◽

Vol 7 (1) ◽

pp. 574-580 ◽

Cited By ~ 16

Author(s):

Kyungtaek Min ◽

Muhammad Umar ◽

Haekyo Seo ◽

Jong Hyuk Yim ◽

Dong Gun Kam ◽

...

Keyword(s):

Radio Frequency ◽

Silk Fibroin ◽

Silver Nanowire ◽

Silk Protein ◽

Flexible Electrodes ◽

Silk Fibroin Film ◽

Optically Transparent ◽

Nanowire Networks

We demonstrated biocompatible, optically transparent and flexible electrodes by embedding AgNWs just below the surface of the silk fibroin film.

Download Full-text

Methanol–Water-Dependent Structural Changes of Regenerated Silk Fibroin Probed Using Terahertz Spectroscopy

Applied Spectroscopy ◽

10.1177/0003702817706368 ◽

2017 ◽

Vol 71 (8) ◽

pp. 1785-1794 ◽

Cited By ~ 2

Author(s):

Xu Wu ◽

Xiaodong Wu ◽

Bin Yang ◽

Min Shao ◽

Guojin Feng

Keyword(s):

Silk Fibroin ◽

Structural Changes ◽

Terahertz Spectroscopy ◽

Regenerated Silk Fibroin

Download Full-text

Structural changes and dyeability of silk fibroin fiber following shrinkage in neutral salt solution

Journal of Applied Polymer Science ◽

10.1002/app.1994.070510405 ◽

1994 ◽

Vol 51 (4) ◽

pp. 619-624 ◽

Cited By ~ 7

Author(s):

Masuhiro Tsukada ◽

Hiroshi Kato ◽

Giuliano Freddi ◽

Nobutami Kasai ◽

Hiroshi Ishikawa

Keyword(s):

Silk Fibroin ◽

Salt Solution ◽

Structural Changes ◽

Neutral Salt ◽

Silk Fibroin Fiber

Download Full-text

Potent inhibitors of toxic alpha-synuclein oligomers identified via cellular time-resolved FRET biosensor

10.1101/2020.01.09.900845 ◽

2020 ◽

Cited By ~ 2

Author(s):

Anthony R. Braun ◽

Elly E. Liao ◽

Mian Horvath ◽

Malaney C. Young ◽

Chih Hung Lo ◽

...

Keyword(s):

Small Molecules ◽

High Throughput ◽

Structural Changes ◽

Lewy Bodies ◽

Alpha Synuclein ◽

Time Resolved ◽

Lead Compounds ◽

Fret Biosensors ◽

Self Association ◽

High Throughput Screens

ABSTRACTPreventing or reversing the pathological misfolding and self-association of alpha-synuclein (aSyn) can rescue a broad spectrum of pathological cellular insults that manifest in Parkinson’s Disease (PD), Dementia with Lewy bodies (DLB), and other alpha-synucleinopathies. We have developed a high-throughput, FRET-based drug discovery platform that combines high-resolution protein structural detection in living cells with an array of functional and biophysical assays to identify novel lead compounds that protect SH-SY5Y cells from aSyn induced cytotoxicity as well as inhibiting seeded aSyn aggregation, even at nanomolar concentrations.Our combination of cellular and cell-free assays allow us to distinguish between direct aSyn binding or indirect mechanisms of action (MOA). We focus on targeting oligomers with the requisite sensitivity to detect subtle protein structural changes that may lead to effective therapeutic discoveries for PD, DLB, and other alpha-synucleinopathies. Pilot high-throughput screens (HTS) using our aSyn cellular FRET biosensors has led to the discovery of the first nanomolar-affinity small molecules that disrupt toxic aSyn oligomers in cells and inhibit cell death. Primary neuron assays of aSyn pathology (e.g. phosphorylation of mouse aSyn PFF) show rescue of pathology for two of our tested compounds. Subsequent seeded thioflavin-t (ThioT) aSyn aggregation assays demonstrate these compounds deter or block aSyn fibril assembly. Other hit compounds identified in our HTS are known to modulate oxidative stress, autophagy, and ER stress, providing validation that our biosensor is sensitive to indirect MOA as well.

Download Full-text

Effect of Solvent on the Characteristics of Electrospun Regenerated Silk Fibroin Nanofibers

Key Engineering Materials ◽

10.4028/www.scientific.net/kem.342-343.813 ◽

2007 ◽

Vol 342-343 ◽

pp. 813-816 ◽

Cited By ~ 13

Author(s):

Lim Jeong ◽

Kuen Yong Lee ◽

Won Ho Park

Keyword(s):

Secondary Structure ◽

Formic Acid ◽

Silk Fibroin ◽

Structural Changes ◽

Effective Means ◽

Electrospun Nanofibers ◽

Random Coil ◽

Regenerated Silk Fibroin ◽

Silk Fibroin Nanofibers ◽

Β Sheet

Nonwoven nanofiber matrices were prepared by electrospinning a solution of silk fibroin (SF) dissolved either in formic acid or in 1,1,1,3,3,3-hexafluoro-2-isopropyl alcohol (HFIP). The mean diameter of the electrospun nanofibers prepared from SF dissolved in formic acid was 80 nm with a unimodal size distribution, which was smaller than those prepared from HFIP (380 nm). SF nanofibers were then treated with an aqueous methanol solution, and structural changes due to solvent-induced crystallization of SF were investigated using IR and 13C solid-state CP/MAS NMR spectroscopy. SF nanofibers prepared from formic acid were found to have a higher proportion of β-sheet conformations than those prepared from HFIP. Methanol treatment provided a fast and effective means to alter the secondary structure of both types of SF nanofibers from a random coil form to a β-sheet form. As demonstrated in the present study, this approach to controlling the dimensions and secondary structure of proteins using various solvents may be useful for the design and tailoring of materials for biomedical applications, especially for tissue engineering applications.

Download Full-text

Biosynthesis of β-Glucosidase-Silk Fibroin Nanoparticles Conjugates and Enzymatic Characteristics

Advanced Materials Research ◽

10.4028/www.scientific.net/amr.175-176.186 ◽

2011 ◽

Vol 175-176 ◽

pp. 186-191 ◽

Cited By ~ 9

Author(s):

Zhen Zhen Zhou ◽

Yu Qing Zhang

Keyword(s):

Silk Fibroin ◽

Water Soluble ◽

Silk Protein ◽

Free Enzyme ◽

Cross Linking ◽

Experimental Conditions ◽

Protein Nanoparticles ◽

Silk Fibroin Nanoparticles ◽

Long Time ◽

Molecular Masses

Silk fibroin derived from Bombyx mori is a biomacromolecular protein with outstanding biocompatibility. When it was dissolved in highly concentrated CaCl2 solution and then the mixture of the protein and salt was subjected to desalting treatments for long time in flowing water, the resulting liquid silk was water-soluble polypeptides with different molecular masses, ranging from 10 to 200 kDa. When the liquid silk were introduced rapidly into acetone, silk protein nanoparticles (SFNs) with a range of 40~120 nm in diameter could be obtained. The crystalline silk nanoparticles could be conjugated with β-glucosidase with cross-linking of reagent glutaraldehyde. In this work, the activity of β-glucosidase-silk fibroin nanoparticles (βG-SFNs) bioconjugates was determined by p-nitrophenyl-β-D-glucoside (p-NPG) as a substrate and the optimal conditions for the biosynthesis of βG-SFNs bioconjugates were investigated. βG-SFN constructs obtained by 5h of covalent cross-linking time at the experimental conditions of 0.25% cross-linking reagent, 37 °C and the proportion of β-glucosidase and SFNs (75 : 100, U/mg) showed 46% of recoveries. Results showed that kinetic parameters of βG-SFNs were the same as for the free β-glucosidase. The optimal pH was 5.0 and the optimal temperature was 60°C. When β-glucosidase was coupled covalently with silk nanoparticles, the thermal stability of βG-SFNs was slightly enhanced as compared with free β-glucosidase. The apparent Km of βG-SFNs (1.41×10-3 mol•L-1) was near five-fold less than that of the free enzyme (7.26×10−3 mol•L-1), this fully shows that after the free enzyme conjugated with silk fibroin nanoparticles, the enzyme affinity with substrate increased. These results fully demonstrated the silk protein nanoparticles were good carriers as bioconjugation or modification of enzymes. Moreover, they had potential values for research and development in food processing and flavor processing agents.

Download Full-text

Effects of end-capped acceptors subject to subtle structural changes on solution-processable small molecules for organic solar cells

Physical Chemistry Chemical Physics ◽

10.1039/c5cp00042d ◽

2015 ◽

Vol 17 (14) ◽

pp. 8894-8900 ◽

Cited By ~ 17

Author(s):

Dan Deng ◽

Yajie Zhang ◽

Lingyun Zhu ◽

Jianqi Zhang ◽

Kun Lu ◽

...

Keyword(s):

Solar Cells ◽

Small Molecules ◽

Organic Solar Cells ◽

Structural Changes ◽

Photovoltaic Properties ◽

Solution Processable ◽

The Relationship

Three subtle structural changed end-capped acceptors with increased electron withdrawing ability were synthesized and introduced into a planar conjugated backbone. The relationship between molecules bearing the three end-capped acceptors and their photovoltaic properties was studied.

Download Full-text