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Membranes Apr 2022Thermal and mechanical properties of poly(ionic liquid)s (PILs), an epoxidized ionic liquid-amine network, are studied via molecular dynamics simulations. The poly(ionic...
Thermal and mechanical properties of poly(ionic liquid)s (PILs), an epoxidized ionic liquid-amine network, are studied via molecular dynamics simulations. The poly(ionic liquid)s are designed with two different ionic liquid monomers, 3-[2-(Oxiran-2-yl)ethyl]-1-{4-[(2-oxiran-2-yl)ethoxy]phenyl}imidazolium (EIM2) and 1-{4-[2-(Oxiran-2-yl)ethyl]phenyl}-3-{4-[2-(oxiran-2-yl)ethoxy]benzyl}imidazolium (EIM1), each of which is networked with tris(2-aminoethyl)amine, paired with different anions, bis(trifluoromethanesulfonyl)imide (TFSI) and chloride (Cl). We investigate how ionic liquid monomers with high ionic strength affect structures of the cross-linked polymer networks and their thermomechanical properties such as glass transition temperature (T) and elastic moduli, varying the degree of cross-linking. Strong electrostatic interactions between the cationic polymer backbone and anions build up their strong structures of which the strength depends on their molecular structures and anion size. As the anion size decreases from TFSI to Cl, both T and elastic moduli of the PIL increase due to stronger electrostatic interactions present between their ionic moieties, making it favorable for the PIL to organize with stronger bindings. Compared to the EIM2 monomer, the EIM1 monomers and TFSI ions generate a PIL with higher T and elastic moduli. This attributes to the less flexible structure of the EIM1 monomer for the chain rotation, in which steric hindrance by ring moieties in the EIM1-based PIL enhances their structural rigidity. The π-π stacking structures between the rings are found to increase in EIM1-based PIL compared to the EIM2-based one, which becomes stronger with smaller Cl ion rather than TFSI. The effect of the degree of the cross-linking on thermal and mechanical properties is also examined. As the degree of cross-linking decreases from 100% to 60%, T also decreases by a factor of 10-20%, where the difference among the given PILs becomes decreased with a lower degree of cross-linking. Both the Young's (E) and shear (G) moduli of all the PILs decrease with degree of cross-linking, which the reduction is more significant for the PIL generated with EIM2 monomers. Transport properties of anions in PILs are also studied. Anions are almost immobilized globally with very small structural fluctuations, in which Cl presents lower diffusivity by a factor of ~2 compared to TFSI due to their stronger binding to the cationic polymer backbone.
PubMed: 35629776
DOI: 10.3390/membranes12050450 -
Scientific Reports May 2017Structural investigations have revealed that β hairpin structures are common features in amyloid fibrils, suggesting that these motifs play an important role in amyloid...
Structural investigations have revealed that β hairpin structures are common features in amyloid fibrils, suggesting that these motifs play an important role in amyloid assembly. To test this hypothesis, we characterized the effect of the hairpin fold on the aggregation process using a model β hairpin structure, consisting of two Aβ(14-23) monomers connected by a turn forming YNGK peptide. AFM studies of the assembled aggregates revealed that the hairpin forms spherical structures whereas linear Aβ(14-23) monomers form fibrils. Additionally, an equimolar mixture of the monomer and the hairpin assembles into non-fibrillar aggregates, demonstrating that the hairpin fold dramatically changes the morphology of assembled amyloid aggregates. To understand the molecular mechanism underlying the role of the hairpin fold on amyloid assembly, we performed single-molecule probing experiments to measure interactions between hairpin and monomer and two hairpin complexes. The studies reveal that the stability of hairpin-monomer complexes is much higher than hairpin-hairpin complexes. Molecular dynamics simulations revealed a novel intercalated complex for the hairpin and monomer and Monte Carlo modeling further demonstrated that such nano-assemblies have elevated stability compared with stability of the dimer formed by Aβ(14-23) hairpin. The role of such folding on the amyloid assembly is also discussed.
Topics: Algorithms; Amino Acid Sequence; Amyloid; Amyloid beta-Peptides; Microscopy, Atomic Force; Molecular Dynamics Simulation; Monte Carlo Method; Nanostructures; Peptide Fragments; Protein Aggregation, Pathological; Protein Folding; Protein Multimerization; Protein Stability; Protein Structure, Secondary; Thermodynamics
PubMed: 28539626
DOI: 10.1038/s41598-017-02454-0 -
Proceedings of the National Academy of... Aug 2021The dynamics and folding of potassium channel pore domain monomers are connected to the kinetics of tetramer assembly. In all-atom molecular dynamics simulations of...
The dynamics and folding of potassium channel pore domain monomers are connected to the kinetics of tetramer assembly. In all-atom molecular dynamics simulations of Kv1.2 and KcsA channels, monomers adopt multiple nonnative conformations while the three helices remain folded. Consistent with this picture, NMR studies also find the monomers to be dynamic and structurally heterogeneous. However, a KcsA construct with a disulfide bridge engineered between the two transmembrane helices has an NMR spectrum with well-dispersed peaks, suggesting that the monomer can be locked into a native-like conformation that is similar to that observed in the folded tetramer. During tetramerization, fluoresence resonance energy transfer (FRET) data indicate that monomers rapidly oligomerize upon insertion into liposomes, likely forming a protein-dense region. Folding within this region occurs along separate fast and slow routes, with τ ∼40 and 1,500 s, respectively. In contrast, constructs bearing the disulfide bond mainly fold via the faster pathway, suggesting that maintaining the transmembrane helices in their native orientation reduces misfolding. Interestingly, folding is concentration independent despite the tetrameric nature of the channel, indicating that the rate-limiting step is unimolecular and occurs after monomer association in the protein-dense region. We propose that the rapid formation of protein-dense regions may help with the assembly of multimeric membrane proteins by bringing together the nascent components prior to assembly. Finally, despite its name, the addition of KcsA's C-terminal "tetramerization" domain does not hasten the kinetics of tetramerization.
Topics: Kinetics; Kv1.2 Potassium Channel; Markov Chains; Molecular Dynamics Simulation; Protein Conformation; Protein Folding; Protein Multimerization
PubMed: 34413192
DOI: 10.1073/pnas.2103674118 -
Nature Communications Jul 2017To rationally design supramolecular polymers capable of self-healing or reconfiguring their structure in a dynamically controlled way, it is imperative to gain access...
To rationally design supramolecular polymers capable of self-healing or reconfiguring their structure in a dynamically controlled way, it is imperative to gain access into the intrinsic dynamics of the supramolecular polymer (dynamic exchange of monomers) while maintaining a high-resolution description of the monomer structure. But this is prohibitively difficult at experimental level. Here we show atomistic, coarse-grained modelling combined with advanced simulation approaches to characterize the molecular mechanisms and relative kinetics of monomer exchange in structural variants of a synthetic supramolecular polymer in different conditions. We can capture differences in supramolecular dynamics consistent with the experimental observations, revealing that monomer exchange in and out the fibres originates from the defects present in their supramolecular structure. At the same time, the submolecular resolution of this approach offers a molecular-level insight into the dynamics of these bioinspired materials, and a flexible tool to obtain structure-dynamics relationships for a variety of polymeric assemblies.Accessing the dynamics of soft self-assembled materials at high resolution is very difficult. Here the authors show atomistic and coarse-grained modelling combined with enhanced sampling to characterize the molecular mechanisms and kinetics of monomer exchange in synthetic supramolecular polymers.
PubMed: 28747661
DOI: 10.1038/s41467-017-00189-0 -
Dental Materials Journal Jul 2021We evaluated the influence of monomer type, plasticizer content, and powder/liquid (P/L) ratio on the setting characteristics of light-cured acrylic permanent soft...
Influence of monomer type, plasticizer content, and powder/liquid ratio on setting characteristics of acrylic permanent soft denture liners based on poly(ethyl methacrylate/butyl methacrylate) and acetyl tributyl citrate.
We evaluated the influence of monomer type, plasticizer content, and powder/liquid (P/L) ratio on the setting characteristics of light-cured acrylic permanent soft denture liners based on poly(ethyl methacrylate/butyl methacrylate). Two monomers, iso-butyl methacrylate (i-BMA) and 2-ethylhexyl methacrylate (2-EHMA), that contained various concentrations of the plasticizer acetyl tributyl citrate (ATBC) and trace amounts of the photo initiator and reducing agent were used. The P/L ratio was 1.0 or 1.2. The gelation time was measured using a controlled stress rheometer. Materials with i-BMA had shorter gelation times than those for materials with 2-EHMA. The gelation time increased exponentially with increasing plasticizer content. A higher P/L ratio led to a shorter gelation time. The effects of monomer type and plasticizer content were larger than that for the P/L ratio. These results show that 2-EHMA is a suitable monomer for soft denture liners and that the setting characteristics can be controlled via ATBC content.
Topics: Citrates; Denture Liners; Materials Testing; Methacrylates; Plasticizers; Powders
PubMed: 33814534
DOI: 10.4012/dmj.2020-319 -
Biochemistry Dec 2014We have developed new procedures to examine the early steps in fibrin polymerization. First, we isolated fibrinogen monomers from plasma fibrinogen by gel filtration....
We have developed new procedures to examine the early steps in fibrin polymerization. First, we isolated fibrinogen monomers from plasma fibrinogen by gel filtration. Polymerization of fibrinogen monomers differed from that of plasma fibrinogen. The formation of protofibrils was slower and the transformation of protofibrils to fibers faster for the fibrinogen monomers. Second, we used formaldehyde to terminate the polymerization reactions. The formaldehyde-fixed products obtained at each time point were examined by dynamic light scattering and transmission electron microscopy (TEM). The data showed the formaldehyde-fixed products were stable and representative of the reaction intermediates. TEM images showed monomers, short oligomers, protofibrils, and thin fibers. The amount and length of these species varied with time. Short oligomers were less than 5% of the molecules at all times. Third, we developed models that recapitulate the TEM images. Fibrin monomer models were assembled into protofibrils, and protofibrils were assembled into two-strand fibers using Chimera software. Monomers were based on fibrinogen crystal structures, and the end-to-end interactions between monomers were based on D-dimer crystal structures. Protofibrils assembled from S-shaped monomers through asymmetric D:D interactions were ordered helical structures. Fibers were modeled by duplicating a protofibril and rotating the duplicate 120° around its long axis. No specific interactions were presumed. The two protofibrils simply twisted around one another to form a fiber. This model suggests that the conformation of the protofibril per se promotes the assembly into fibers. These findings introduce a novel mechanism for fibrin assembly that may be relevant to other biopolymers.
Topics: Animals; Blood Coagulation; Databases, Protein; Dimerization; Fibrin; Fibrinogen; Fixatives; Formaldehyde; Humans; Kinetics; Microscopy, Electron, Transmission; Models, Molecular; Molecular Weight; Nephelometry and Turbidimetry; Polymerization; Protein Conformation; Protein Structure, Secondary; Proteolysis; Surface Properties; Thrombin
PubMed: 25419972
DOI: 10.1021/bi500986z -
Pharmaceutics Jul 2023This study analyse the type of release kinetic of specific monomers from dental resin composites containing various fluoride-doped calcium phosphates. The release...
This study analyse the type of release kinetic of specific monomers from dental resin composites containing various fluoride-doped calcium phosphates. The release behavior of urethane dimethacrylate (UDMA), ethoxylated bisphenol-A dimethacrylate (bis-EMA) and 1.6-hexanediol ethoxylate diacrylate (HEDA) was evaluated over a period of 35 days. Two tailored calcium phosphates doped with different concentrations of fluoride salts (VS10% and VS20%) were prepared and incorporated in the dimethacrylate matrix at various concentrations to generate a range of experimental composites. The release kinetics were characterized using mathematical models such as zero-order, first-order, Peppas and Higuchi models. The results showed that the first-order model best described the release kinetics. UDMA and HEDA exhibited significant differences in release compared to bis-EMA from day 1, while no significant differences were observed between UDMA and HEDA, except on day 35, when UDMA exhibited a higher release rate than HEDA. When comparing the release of each monomer, VS20-R20% had the highest total release percentage, with 3.10 ± 0.25%, whereas the composite VS10-R5% showed the lowest release percentage, with a total of 1.66 ± 0.08%. The release kinetics were influenced by the composition of the resin composites and the presence of calcium fluoride and sodium fluoride in the calcium phosphate played a role in the maximum amounts of monomer released. In conclusion, the release of monomers from the tested resin composites followed a first-order kinetic behaviour, with an initial rapid release that decreased over time. The composition of the resin monomers and the presence of fluoride salts influenced the release kinetics. The VS10-R5% and VS10-R10% resin composites exhibited the lowest total monomer release, suggesting its potential favourable composition with reduced monomer elution. These findings contribute to understanding the release behavior of dental resin composites and provide insights for the development of resin-based bioactive dental materials.
PubMed: 37514133
DOI: 10.3390/pharmaceutics15071948 -
Beilstein Journal of Organic Chemistry 2022The synthesis of protected precursors of chitin oligosaccharides by electrochemical polyglycosylation of thioglycosides as monomer is described. Oligosaccharides up to...
The synthesis of protected precursors of chitin oligosaccharides by electrochemical polyglycosylation of thioglycosides as monomer is described. Oligosaccharides up to the hexasaccharide were synthesized under optimized reaction conditions. Further, a modified method enabled the synthesis of oligosaccharides up to the octasaccharide by repeating electrolysis with additional monomers. The mechanism of the electrochemical polyglycosylation is also discussed, based on the oxidation potential of the monomer and oligosaccharides.
PubMed: 36105733
DOI: 10.3762/bjoc.18.117 -
Micromachines Dec 2022Microfluidic devices (MFDs) printed in 3-D geometry using digital light projection to polymerize monomers often have surfaces that are not as hydrophobic as MFDs made...
Microfluidic devices (MFDs) printed in 3-D geometry using digital light projection to polymerize monomers often have surfaces that are not as hydrophobic as MFDs made from polydimethylsiloxane. Droplet microfluidics in these types of devices are subject to droplet adhesion and aqueous spreading on less hydrophobic MFD surfaces. We have developed a post-processing technique using hydrophobic monomers that renders the surfaces of these devices much more hydrophobic. The technique is fast and easy, and involves flowing monomer without initiator into the channels and then exposing the entire device to UV light that generates radicals from the initiator molecules remaining in the original 3-D polymerization. After treatment the channels can be cleared and the surface is more hydrophobic, as evidenced by higher contact angles with aqueous droplets. We hypothesize that radicals generated near the previously printed surfaces initiate polymerization of the hydrophobic monomers on the surfaces without bulk polymerization extending into the channels. The most hydrophobic surfaces were produced by treatment with an alkyl acrylate and a fluorinated acrylate. This technique could be used for surface treatment with other types of monomers to impart unique characteristics to channels in MFDs.
PubMed: 36677067
DOI: 10.3390/mi14010006 -
Frontiers in Plant Science 2022To clarify the influences of shading stress and planting density on the lignin monomer composition of wheat stems and their relationship with lodging resistance, Lodging...
To clarify the influences of shading stress and planting density on the lignin monomer composition of wheat stems and their relationship with lodging resistance, Lodging resistant variety Shannong 23 (SN23) and lodging sensitive variety Shannong 16 (SN16) were grown during 2018-2019 and 2019-2020 growing seasons. The planting densities were 150 × 10 plants ha (D1), 225 × 10 plants ha (D2) and 300 × 10 plants ha (D3). At the jointing stage, an artificial shading shed was used to simulate shading stress. Then the effects of shading on stem morphological characteristics, lignin monomer composition and lodging resistance of wheat under different planting densities were studied. Results indicate that shading at the jointing stage increased the length of basal internodes and the plant height and moved the height of center of gravity (CG) upward. Moreover, the stem diameter and the wall thickness decreased by 0.10-0.53 mm and 0.18-0.40 mm, respectively. The stem filling degree was reduced accordingly. As indicated by the correlation analysis and the stepwise regression analysis, shading-induced lodging mainly resulted from changes in the stem morphological characteristics and lignin accumulation. The influential magnitude of these factors was ordered as follows: stem filling degree, wall thickness, lignin content, contents and proportions of monomers S and H, and length of the second internode. The expression abundance of , , , and declined in response to shading stress and high planting density. As a result, the distribution ratios of photosynthetic carbon sources to lignin monomers S, G and H were changed. The lignin content of stems on the day 42 after the jointing stage decreased by 18.48%. The monomer S content decreased, while the content and proportion of monomer H increased, thus weakening the breaking strength of wheat stems.
PubMed: 36466230
DOI: 10.3389/fpls.2022.1056193