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Allylation and Thermosetting of Acetosolv Wheat Straw Lignin
Abstract The acetosolv extraction, allylation and subsequent cross‐linking of wheat straw lignin to thermoset biomaterials is herein described. The extraction temperature proved to be of great importance for the quality of the resulting lignin, with moderate temperature being key for preservation of β‐O‐4’ linkages. The allylation of the acetosolv lignin was carried out using three different synthetic strategies, resulting in selective installation of either benzylic or phenolic allyl ethers, or unselective allylation of various hydroxyl groups via etherification and carboxyallylation. The different allylation protocols employed either allyl alcohol, allyl chloride, or diallylcarbonate as allyl precursors, with the latter resulting in the highest degree of functionalization. Selected allylated acetosolv lignins were cross‐linked using a thiol‐ene approach and the lignin with the highest density of allyl groups was found to form a cross‐linked thermoset material with properties comparable to kraft lignin‐based analogues.
Development of a Novel Equilibrium Passive Sampling Device for Methylmercury in Sediment and Soil Porewaters
In this work, we explored the concept of equilibrium passive sampling for methylmercury (MeHg) using the strategy developed for hydrophobic organic chemicals. Passive sampling should allow prediction of the concentration of the chemically labile fraction of MeHg in sediment porewaters based on equilibrium partitioning into the sampler, without modeling diffusion rates through the sampler material. Our goals were to identify sampler materials with the potential to mimic MeHg partitioning into animals and sediments and provide reversible sorption in a time frame appropriate for in situ samplers. Candidate materials tested included a range of polymers embedded with suitable sorbents for MeHg. The most promising were activated carbon (AC) embedded in agarose, thiol–self-assembled monolayers on mesoporous supports embedded in agarose, and cysteine-functionalized polyethylene terephthalate, which yielded log sampler–water partition coefficients of 2.8 to 5 for MeHgOH and MeHg complexed with dissolved organic matter (Suwannee River humic acid). Sampler equilibration time in sediments was approximately 1 to 2 wk. Investigation of the MeHg accumulation mechanism by AC embedded in agarose suggested that sampling was kinetically influenced by MeHg interactions with AC particles and not limited by diffusion through the gel for this material. Also, AC exhibited relatively rapid desorption of Hg and MeHg, indicating that this sorbent is capable of reversible, equilibrium measurements. In sediment:water microcosms, porewater concentrations made with isotherm-calibrated passive samplers agreed within a factor of 2 (unamended sediment) or 4 (AC-amended sediment) with directly measured concentrations. The present study demonstrates a potential new approach to passive sampling of MeHg.
Scaling Laws for Polymer Chains Grafted onto Nanoparticles
An experimental approach is presented for identifying the scaling laws for polymer chains grafted onto gold nanoparticles. Poly(ethylene oxide) of various molecular weights are grafted onto gold nanoparticles via thiol end-functional groups. The polymer-grafted nanoparticles are self-assembled into monolayers from solvents of different quality. Over a significant range of graft densities, nanoparticle monolayers deposited from good (athermal) solvent exhibit particle spacing that scales according to theoretical predictions for chains in dilute solution. This unexpected result for ordered nanoparticle monolayers is discussed in the context of the deposition process. In monolayers deposited from theta solvent, molecular weight scaling of particle spacing breaks down, possibly due to chain length dependence of solvent quality. In poor solvent, the structure of nanoparticle assemblies is not sufficiently ordered to obtain reliable measurements, possibly due to loss of nanoparticle dispersion. This approach opens up the possibility for accurate measurement of the effect of solvent on grafted chain scaling in nanoparticle assemblies.
Optimization of anionic conductivity through the coexistence of ionomer cluster and backbone-backbone morphologies in anion exchange membranes
Random copolymers of poly(4-vinylpyridine) and polyisoprene were synthesized, and subsequently quaternized with 1-alkylbromides. The number of carbons on the pendant side-chain of the resultant comb-shaped polymer, n, ranged from 2-8. The comb-shaped polymers were crosslinked employing thiol-ene chemistry to give mechanically robust ion conducting membranes. Analysis by wide and medium-angle X-ray scattering show three morphology regimes that are dependent on the number of carbons on the pendant side-chains. When n = 2, ionomer cluster morphology was dominant, when n = 8 backbone-backbone morphology was dominant, and when n = 3-6, the membrane showed a coexistence of both ionomer cluster and backbone-backbone morphologies. Evaluation of the water uptake of the membranes showed a maximum water uptake per cation of 9.5 when n = 5 at 95% relative humidity (RH) and 60 degrees C. Finally, conductivity of the samples characterized by electrochemical impedance spectroscopy showed bromide conductivity as high as 110 mS/cm when n = 3 at 95% RH and 90 degrees C.
Engineered selective biotoxin‐binding hydrogels for toxin sequestration
The development of synthetic selective membranes that separate materials of similar sizes, charges, and/or polarities remains a difficult challenge, and looking towards biology provides inspiration for new designs. In this work, a series of cholera toxin binding peptides (CTBPs) are identified, spanning a range of binding inhibitions, and integrated into chemically cross-linked cholera toxin binding gels (CTBGs) via thiol-Michael polycondensation reactions. All gels demonstrate rheological profiles consistent with elastic solids. The CTBGs are probed via small-angle neutron scattering and exhibit a correlation length, ξ, smaller than most proteins (1.3–2.5 nm). Thus, an effective entropic mesh is formed to block non-targeted proteins. However, the CTBGs have a dynamic mesh size, Ξ, that is larger than cholera toxin (CT) to allow the transport of target proteins. The CTBGs with the highest binding inhibitions both show high selectivity and permeation of CT, rejecting all other tested proteins. In total, two new highly selective CTBGs are synthesized and validated for use in cholera toxin remediation. Together, this platform demonstrates the wide applicability of selectively-diffusive materials for difficult separations.
PTM‐Psi : A python package to facilitate the computational investigation of p ost‐ t ranslational m odification on p rotein s tructures and their i mpacts on dynamics and functions
Abstract Post‐translational modification (PTM) of a protein occurs after it has been synthesized from its genetic template, and involves chemical modifications of the protein's specific amino acid residues. Despite of the central role played by PTM in regulating molecular interactions, particularly those driven by reversible redox reactions, it remains challenging to interpret PTMs in terms of protein dynamics and function because there are numerous combinatorially enormous means for modifying amino acids in response to changes in the protein environment. In this study, we provide a workflow that allows users to interpret how perturbations caused by PTMs affect a protein's properties, dynamics, and interactions with its binding partners based on inferred or experimentally determined protein structure. This Python‐based workflow, called PTM‐Psi , integrates several established open‐source software packages, thereby enabling the user to infer protein structure from sequence, develop force fields for non‐standard amino acids using quantum mechanics, calculate free energy perturbations through molecular dynamics simulations, and score the bound complexes via docking algorithms. Using the S ‐nitrosylation of several cysteines on the GAP2 protein as an example, we demonstrated the utility of PTM‐Psi for interpreting sequence–structure–function relationships derived from thiol redox proteomics data. We demonstrate that the S ‐nitrosylated cysteine that is exposed to the solvent indirectly affects the catalytic reaction of another buried cysteine over a distance in GAP2 protein through the movement of the two ligands. Our workflow tracks the PTMs on residues that are responsive to changes in the redox environment and lays the foundation for the automation of molecular and systems biology modeling.
Integrated data-driven and experimental approaches to accelerate lead optimization targeting SARS-CoV- 2 main protease
Identification of potential therapeutic candidates can be expedited by integrating computational modeling with domain aware machine learning (ML) approaches followed by experimental validation. Generative deep learning models have been recently developed that can generate thousands of new candidates, but their physiochemical properties are typically not optimized. Using our deep learning models and a scaffold as a starting point, we generated tens of thousands of compounds for SARS-CoV-2 M pro that preserve the core scaffold. Here we utilized and implemented several computational tools such as structural alert and toxicity analysis, high throughput virtual screening, ML-based 3D quantitative structure–activity relationships, multi-parameter optimization, and graph neural networks on libraries of generated candidates to predict biological activity and binding affinity a priori. From these collective computational results, eight promising candidates were identified and tested experimentally using Native Mass Spectrometry (MS) and FRET-based functional assays. Two compounds, with quinazoline-2-thiol and acetylpiperidine core moiety showed IC 50 values in the low micromolar range: 2.95±0.0017 µM and 3.41±0.0015 µM, respectively. The molecular dynamics simulations further highlight that binding of these compounds results in allosteric modulations in the chain B and the interface domains of the M pro . The key fragments from these top hits can be used as input for closed loop lead optimization in the integrated pipeline.
Ligand Exchange/Scrambling Study of Gold(I)-Phosphine Complexes in the Solid Phase by DESI-MS Analysis
Only a few analytical techniques are available for the characterization of mechanochemical synthetic reaction products. We demonstrate here that DESI-MS is a powerful technique for this purpose, combining the selectivity of MS-based assays with the simplicity and in situ analysis capability of ambient ionization methods. In this work, we report that auranofin, a gold-based drug, and its precursor triethylphosphine gold(I) chloride undergo a complex array of ligand exchange/scrambling reactions with thiol-containing amino acids in the solid state. The products were readily characterized by DESI-MS analysis from the solid-phase reaction, clearly exhibiting ligand exchange and scrambling, with independent confirmation by solid state {sup 13}C-NMR. The thioglucose and triethylphosphine moieties exchanged with cysteine and its derivatives, whereas the glutathione replaced 2,3,4,6-tetra-O-acetyl-β-1-D-glucopyranose only. It was concluded that ligand exchange and scrambling reactions can be carried out in the solid state, and some of the unique products reported in this study can be conveniently prepared through mechanochemical synthesis in good yields (> 98%), as demonstrated by synthesis of (L-cysteinato-S)-triethylphosphine gold(I) from triethylphosphine gold(I) chloride and L-cysteine. .
Engineering of a novel Ca{sup 2+}-regulated kinesin molecular motor using a calmodulin dimer linker
Highlights: Black-Right-Pointing-Pointer Engineered kinesin-M13 and calmodulin involving single cysteine were prepared. Black-Right-Pointing-Pointer CaM mutant was cross-linked to dimer by bifunctional thiol reactive reagent. Black-Right-Pointing-Pointer Kinesin-M13 was dimerized via CaM dimer in the presence of calcium. Black-Right-Pointing-Pointer Function of the engineered kinesin was regulated by a Ca{sup 2+}-calmodulin dimer linker. -- Abstract: The kinesin-microtubule system holds great promise as a molecular shuttle device within biochips. However, one current barrier is that such shuttles do not have 'on-off' control of their movement. Here we report the development of a novel molecular motor powered by an accelerator and brake system, using a kinesin monomer and a calmodulin (CaM) dimer. The kinesin monomer, K355, was fused with a CaM target peptide (M13 peptide) at the C-terminal part of the neck region (K355-M13). We also prepared CaM dimers using CaM mutants (Q3C), (R86C), or (A147C) and crosslinkers that react with cysteine residues. Following induction of K355-M13 dimerization with CaM dimers, we measured K355-M13 motility and found that it can be reversibly regulated in a Ca{sup 2+}-dependent manner. We also found that velocities of K355-M13 varied depending on the type and crosslink position of the CaM dimer used; crosslink length also had a moderate effect on motility. These results suggest Ca{sup 2+}-dependent dimerization of K355-M13 could be used as a novel molecular shuttle, equipped with an accelerator and brake system, for biochip applications.
New insight into multifunctional role of peroxiredoxin family protein: Determination of DNA protection properties of bacterioferritin comigratory protein under hyperthermal and oxidative stresses
Bacterioferritin comigratory protein (BCP) is a monomeric conformer acting as a putative thiol-dependent bacterial peroxidase, however molecular basis of DNA-protection via DNA-binding has not been clearly understood. In this study, we characterized the DNA binding properties of BCP using various lengths and differently shaped architectures of DNA. An electrophoretic mobility shift assay and electron microscopy analysis showed that recombinant TkBCP bound to DNA of a circular shape (double-stranded DNA and single-stranded DNA) and a linear shape (16–1000 bp) as well as various architectures of DNA. In addition, DNA protection experiments indicated that TkBCP can protect DNA against hyperthermal and oxidative stress by removing highly reactive oxygen species (ROS) or by protecting DNA from thermal degradation. Based on these results, we suggest that TkBCP is a multi-functional DNA-binding protein which has DNA chaperon and antioxidant functions. - Highlights: • Bacterioferritin comigratory protein (BCP) protects DNA from oxidative stress by reducing ROS. • TkBCP does not only scavenge ROS, but also protect DNA from hyperthermal stress. • BCP potentially adopts the multi-functional role in DNA binding activities and anti-oxidant functions.
Human serum albumin hydropersulfide is a potent reactive oxygen species scavenger in oxidative stress conditions such as chronic kidney disease
Recently, hydropersulfide (RSSH) was found to exist in mammalian tissues and fluids. Cysteine hydropersulfide can be found in free cysteine residues as well as in proteins, and it has potent antioxidative activity. Human serum albumin (HSA) is the most abundant protein in mammalian serum. HSA possesses a free thiol group in Cys-34 that could be a site for hydropersulfide formation. HSA hydropersulfide of high purity as a positive control was prepared by treatment of HSA with Na{sub 2}S. The presence of HSA hydropersulfide was confirmed by spectroscopy and ESI-TOFMS analysis where molecular weights of HSA hydropersulfide by increments of approximately 32 Da (Sulfur atom) were detected. The fluorescent probe results showed that Alexa Fluor 680 conjugated maleimide (Red-Mal) was a suitable assay and bromotrimethylammoniumbimane bromide appeared to be a selective reagent for hydropersulfide. The effect of oxidative stress related disease on the existence of albumin hydropersulfides was examined in rat 5/6 nephrectomy model of chronic kidney disease (CKD). Interestingly, the level of hydropersulfides in rat 5/6 nephrectomy model serum was decreased by a uremic toxin that increases oxidative stress in rat 5/6 nephrectomy model. Furthermore, we demonstrated that the levels of HSA hydropersulfide in human subjects were reduced in CKD but restored by hemodialysis using Red-Mal assay. We conclude that HSA hydropersulfide could potentially play an important role in biological anti-oxidative defense, and it is a promising diagnostic and therapeutic marker of oxidative diseases. - Highlights: • Hydropersulfide can behave as potent antioxidants. • We firstly detected human serum albumin hydropersulfide in healthy subjects. • Human serum albumin hydropersulfide in human subjects were reduced in chronic kidney disease but restored by hemodialysis.
Non-invasive imaging of the levels and effects of glutathione on the redox status of mouse brain using electron paramagnetic resonance imaging
Glutathione (GSH) is the most abundant non-protein thiol that buffers reactive oxygen species in the brain. GSH does not reduce nitroxides directly, but in the presence of ascorbates, addition of GSH increases ascorbate-induced reduction of nitroxides. In this study, we used electron paramagnetic resonance (EPR) imaging and the nitroxide imaging probe, 3-methoxycarbonyl-2,2,5,5-tetramethyl-piperidine-1-oxyl (MCP), to non-invasively obtain spatially resolved redox data from mouse brains depleted of GSH with diethyl maleate compared to control. Based on the pharmacokinetics of the reduction reaction of MCP in the mouse heads, the pixel-based rate constant of its reduction reaction was calculated as an index of the redox status in vivo and mapped as a “redox map”. The obtained redox maps from control and GSH-depleted mouse brains showed a clear change in the brain redox status, which was due to the decreased levels of GSH in brains as measured by a biochemical assay. We observed a linear relationship between the reduction rate constant of MCP and the level of GSH for both control and GSH-depleted mouse brains. Using this relationship, the GSH level in the brain can be estimated from the redox map obtained with EPR imaging. - Highlights: • Redox status of glutathione-depleted mouse brain was examined with EPR imaging. • Redox status of mouse brain changed depending on glutathione (GSH) levels in brains. • Linear relationship between GSH levels and redox status in brains was found. • Using this relation, estimation of GSH levels in brains is possible from EPR images.
OsPRX2 contributes to stomatal closure and improves potassium deficiency tolerance in rice
Highlights: • The function of 2-Cys Prxs in rice associated with potassium deficiency tolerance is presented. • OsPRX2 contributes to stomatal closure and improves potassium deficiency tolerance is proposed. • OsPRX2 may be a good candidate to improve K{sup +} efficient tolerance in rice. Peroxiredoxins (Prxs) which are thiol-based peroxidases have been implicated in the toxic reduction and intracellular concentration regulation of hydrogen peroxide. In Arabidopsis thaliana At2-CysPrxB (At5g06290) has been demonstrated to be essential in maintaining the water-water cycle for proper H{sub 2}O{sub 2} scavenging. Although the mechanisms of 2-Cys Prxs have been extensively studied in Arabidopsis thaliana, the function of 2-Cys Prxs in rice is unclear. In this study, a rice homologue gene of At2-CysPrxB, OsPRX2 was investigated aiming to characterize the effect of 2-Cys Prxs on the K{sup +}-deficiency tolerance in rice. We found that OsPRX2 was localized in the chloroplast. Overexpressed OsPRX2 causes the stomatal closing and K{sup +}-deficiency tolerance increasing, while knockout of OsPRX2 lead to serious defects in leaves phenotype and the stomatal opening under the K{sup +}-deficiency tolerance. Detection of K{sup +} accumulation, antioxidant activity of transgenic plants under the starvation of potassium, further confirmed that OsPRX2 is a potential target for engineering plants with improved potassium deficiency tolerance.
Resveratrol prolongs lifespan and improves 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine-induced oxidative damage and behavioural deficits in Drosophila melanogaster
Highlights: • D. melanogaster was exposed to resveratrol (RES) and 1-Methyl-4-Phenyl-1,2,3,6-Tetrahydropyridine (MPTP). • RES increased longevity and ameliorated MPTP-mediated oxidative stress and inflammation in flies. • RES protected against MPTP-induced behavioural deficits and brain lesions in flies. • Thus, protective role of RES is via antioxidative and anti-inflammatory mechanisms. 1-Methyl-4-Phenyl-1,2,3,6-Tetrahydropyridine (MPTP) is a neurotoxin that causes Parkinson's disease in animals via mechanisms linked with oxidative stress and inflammation. Resveratrol is a natural polyphenol and a phytoalexin with antioxidative and antiinflammatory properties. Here, we investigated the rescue role of resveratrol on MPTP-triggered toxicity in Drosophila melanogaster for the first time. D. melanogaster (Harwich strain, 1-to 3- days old) were first orally exposed to resveratrol (0, 7.5, 15, 30, 60 and 120 mg/kg diet) and MPTP (0, 250, 500, 1000, 2000, and 3000 μM) for longevity and 7 days survival assays respectively. Consequently, we selected resveratrol (30 and 60 mg/kg diet) to evaluate its rescue role on MPTP (250 and 500 μM)-induced toxicity in D. melanogaster after 3 days of oral treatment. Specifically, we evaluated markers of neurotoxicity (acetylcholinesterase and negative geotaxis), inflammation (nitric oxide), oxidative stress-antioxidant status (hydrogen peroxide, total thiol, catalase and glutathione-S-transferase), cell viability and fecundity. The data showed that resveratrol increased lifespan of D. melanogaster in a dose-dependent manner up to 60 mg/kg diet. Further, resveratrol restored MPTP-induced inhibition of catalase, glutathione-S-transferase and acetylcholinesterase activities in D. melanogaster. Moreover, resveratrol ameliorated MPTP-triggered cell death, histological alterations, behavioural deficits and accumulation of nitric oxide and hydrogen peroxide levels in flies (p < 0.05). Conclusively, the lifespan extension effects of resveratrol and its rescue role on MPTP- mediated toxicity in the flies may be due to its antioxidant and anti-inflammatory properties.
Chloroplast stromal processing peptidase activity is modulated by transit peptide determinants that include inhibitory roles for its N-terminal domain and initial Met
Highlights: • Inactivation of SPP is not through a “cysteine switch” mechanism. • Thiol-modifying reagents do not stimulate preSPP activity but diminish mature SPP activity. • NEM disrupts both substrate binding and peptide bond cleavage by SPP. • Deletion of N terminus of preSPP transit peptide including initial Met triggers processing activity. • The active preSPP deletion mutants no longer possess predicted Hsp70 binding sites. The stromal processing peptidase (SPP) removes transit peptides as precursor proteins enter the chloroplast and different plastid types. SPP is synthesized as a latent, inactive precursor (preSPP) with an atypically long transit peptide. Determinants in the pea (Pisum sativum) SPP transit peptide that regulate mature SPP activation were investigated. Mutational and chemical analyses with protein modifying agents (NEM and APMA) showed a conserved transit peptide Cys-X-Ser/Thr-Cys motif did not inhibit SPP via a “cysteine switch” mechanism through His-X-X-Glu-His site interactions, although cysteines in mature SPP contribute to an active conformation. Significantly, a transit peptide deletion of only the N-terminal 28 amino acids activates SPP located downstream. Short deletions within this region suggest removal of the initial Met plays a pivotal, mechanistic role. Other deletions of ∼30 amino acids along the length of the transit peptide do not individually trigger activity, but larger deletions including Met have an additive effect indicating its removal may be a critical early step during preSPP import. Interestingly, the active preSPP deletion mutants no longer possess predicted Hsp70 binding sites including initial Met, thus Hsp70 interactions may restrict SPP from attaining an active conformation.
Tuning crosslinking of hybrid preceramic polymers in vat photopolymerization toward controlled ceramic yields
Control of preceramic polymer crosslinking for UV-curable processing is essential for fine 3D printing with high ceramic conversion for sustainable polymer-derived ceramics (PDC) engineering. While various factors influencing ceramic yield have been studied, the systematic exploration of the relationship between crosslinking and ceramic yield, especially when crosslinking increases volatile elements, remains open for further investigation. This study addresses this gap by utilizing vat photopolymerization (VP) additive manufacturing (AM) as a versatile platform for controlling preceramic crosslinking and ceramic yield. By rationally designing and tuning the photochemical crosslinking through digital light processing (DLP), we demonstrate that the ceramic yield can be enhanced from 64% to over 86%, even with added volatile elements. We reveal that the post-pyrolysis ceramic yield can be closely correlated with the pre-pyrolysis crosslinking of the preceramic network represented by its stiffness. This correlation thereby suggests a fast, energy-efficient, non-destructive methodology to predict and improve ceramic yield. Combined with these findings, our one-pot thiol-ene hybridization of polycarbosilane and polycarbosiloxane via DLP offers an exemplary method to generate hybrid preceramic polymers with tailored material properties toward target applications, and potentially even higher ceramic yields. This study thus contributes to achieving better resource- and energy-efficient preceramic polymer and PDC processing routes toward sustainable, advanced organic–inorganic materials manufacturing.
Snapshots of C-S Cleavage in Egt2 Reveals Substrate Specificity and Reaction Mechanism
Sulfur incorporation in the biosynthesis of ergothioneine, a histidine thiol derivative, differs from other well-characterized transsulfurations. A combination of a mononuclear non-heme iron enzyme-catalyzed oxidative C-S bond formation and a subsequent pyridoxal 5'-phosphate (PLP)-mediated C-S lyase reaction leads to the net transfer of a sulfur atom from a cysteine to a histidine. In this study, we structurally and mechanistically characterized a PLP-dependent C-S lyase Egt2, which mediates the sulfoxide C-S bond cleavage in ergothioneine biosynthesis. A cation-π interaction between substrate and enzyme accounts for Egt2's preference of sulfoxide over thioether as a substrate. Using mutagenesis and structural biology, we captured three distinct states of the Egt2 C-S lyase reaction cycle, including a labile sulfenic intermediate captured in Egt2 crystals. Additionally, chemical trapping and high-resolution mass spectrometry were used to confirm the involvement of the sulfenic acid intermediate in Egt2 catalysis.