Protein Allostery Study in Cells Using NMR Spectroscopy.

Protein allostery is commonly observed in vitro. But how protein allostery behaves in cells is unknown. In this work, a protein monomer-dimer equilibrium system was built with the allosteric effect on the binding characterized using NMR spectroscopy through mutations away from the dimer interface. A chemical shift linear fitting method was developed that enabled us to accurately determine the dissociation constant. A total of 28 allosteric mutations were prepared and grouped to negative allosteric, nonallosteric, and positive allosteric modulators. ∼ 50% of mutations displayed the allosteric-state changes when moving from a buffered solution into cells. For example, there were no positive allosteric modulators in the buffered solution but eight in cells. The change in protein allostery is correlated with the interactions between the protein and the cellular environment. These interactions presumably drive the surrounding macromolecules in cells to transiently bind to the monomer and dimer mutational sites and change the free energies of the two species differently which generate new allosteric effects. These surrounding macromolecules create a new protein allostery pathway that is only present in cells.

Ferrous sulphate triggers ferroptosis in Candida albicans and cures vulvovaginal candidiasis in a mouse model.

Candida albicans is the most leading cause of life-threatening fungal invasive infections, especially for vulvovaginal candidiasis (VVC). Resistance and tolerance to common fungicide has risen great demands on alternative strategies for treating C. albicans infections. In the present study, ferroptosis has been proven to occur in C. albicans by directly exposed to FeSO4 via induing hallmarks of ferroptosis, including Fe2+ overload burden, ROS eruption and lipid peroxidation. Transcriptomic profile gave the great hints of the possible mechanism for fungal ferroptosis that FeSO4 disturb pathways associated to ribosome, tyrosine metabolism, triglyceride metabolism and thiamine metabolism, thus mobilizing death-related gene synthesis. Inspired by the results, a FeSO4-loaded hydrogel was prepared as an antifungal agent to treat C. albicans infection. This hydrogel exhibited excellent dressing properties and maintained superior antifungal activity by characterization tests. Besides, mice treated by this composite hydrogel displayed excellent therapeutic efficacy. These results highlighted the potential therapeutic use of FeSO4 as an innovative strategy in treating C. albicans infections by targeting ferroptosis.

Fabrication and 3D printing of Pickering emulsion gel based on Hypsizygus marmoreus by-products protein.

Pickering emulsion gel (PEG) stabilized by the protein extracted from the by-product of Hypsizygus marmoreus, combining with xanthan gum (XG), was formulated as 3D printing ink. Hydrogen bonds are formed in XG/protein hybrid particles. Afterwards, PEG was developed. Results indicated that it has shear-thinning properties. The apparent viscosity, yield stress, Elastic modulus (G') and gel strength increased with the increased XG addition, while the size of emulsion decreased. XG incorporation improved the 3D printing performance with desired self-supporting capability and printing precision if its concentration reached 2.0% (w/v). This study provides ideas for the application of Hypsizygus marmoreus by-products protein in stabilizing PEG used for 3D printing, which has a potential to replace traditional hydrogenated cream for cake decoration.

Structural insight into why S-linked glycosylation cannot adequately mimic the role of natural O-glycosylation.

There is an increasing interest in using S-glycosylation as a replacement for the more commonly occurring O-glycosylation, aiming to enhance the resistance of glycans against chemical hydrolysis and enzymatic degradation. However, previous studies have demonstrated that these two types of glycosylation exert distinct effects on protein properties and functions. In order to elucidate the structural basis behind the observed differences, we conducted a systematic and comparative analysis of 6 differently glycosylated forms of a model glycoprotein, CBM, using NMR spectroscopy and molecular dynamic simulations. Our findings revealed that the different stabilizing effects of S- and O-glycosylation could be attributed to altered hydrogen-bonding capability between the glycan and the polypeptide chain, and their diverse impacts on binding affinity could be elucidated by examining the interactions and motion dynamics of glycans in substrate-bound states. Overall, this study underscores the pivotal role of the glycosidic linkage in shaping the function of glycosylation and advises caution when switching glycosylation types in protein glycoengineering.

Intracellular environment can change protein conformational dynamics in cells through weak interactions.

Conformational dynamics is important for protein functions, many of which are performed in cells. How the intracellular environment may affect protein conformational dynamics is largely unknown. Here, loop conformational dynamics is studied for a model protein in Escherichia coli cells by using nuclear magnetic resonance (NMR) spectroscopy. The weak interactions between the protein and surrounding macromolecules in cells hinder the protein rotational diffusion, which extends the dynamic detection timescale up to microseconds by the NMR spin relaxation method. The loop picosecond to microsecond dynamics is confirmed by nanoparticle-assisted spin relaxation and residual dipolar coupling methods. The loop interactions with the intracellular environment are perturbed through point mutation of the loop sequence. For the sequence of the protein that interacts stronger with surrounding macromolecules, the loop becomes more rigid in cells. In contrast, the mutational effect on the loop dynamics in vitro is small. This study provides direct evidence that the intracellular environment can modify protein loop conformational dynamics through weak interactions.

Improving the Enzymatic Activity and Stability of a Lytic Polysaccharide Monooxygenase.

Lytic Polysaccharide Monooxygenases (LPMOs) are copper-dependent enzymes that play a pivotal role in the enzymatic conversion of the most recalcitrant polysaccharides, such as cellulose and chitin. Hence, protein engineering is highly required to enhance their catalytic efficiencies. To this effect, we optimized the protein sequence encoding for an LPMO from Bacillus amyloliquefaciens (BaLPMO10A) using the sequence consensus method. Enzyme activity was determined using the chromogenic substrate 2,6-Dimethoxyphenol (2,6-DMP). Compared with the wild type (WT), the variants exhibit up to a 93.7% increase in activity against 2,6-DMP. We also showed that BaLPMO10A can hydrolyze p-nitrophenyl-ß-D-cellobioside (PNPC), carboxymethylcellulose (CMC), and phosphoric acid-swollen cellulose (PASC). In addition to this, we investigated the degradation potential of BaLPMO10A against various substrates such as PASC, filter paper (FP), and Avicel, in synergy with the commercial cellulase, and it showed up to 2.7-, 2.0- and 1.9-fold increases in production with the substrates PASC, FP, and Avicel, respectively, compared to cellulase alone. Moreover, we examined the thermostability of BaLPMO10A. The mutants exhibited enhanced thermostability with an apparent melting temperature increase of up to 7.5 °C compared to the WT. The engineered BaLPMO10A with higher activity and thermal stability provides a better tool for cellulose depolymerization.

Engineering the Active Site Lid Dynamics to Improve the Catalytic Efficiency of Yeast Cytosine Deaminase.

Conformational dynamics is important for enzyme catalysis. However, engineering dynamics to achieve a higher catalytic efficiency is still challenging. In this work, we develop a new strategy to improve the activity of yeast cytosine deaminase (yCD) by engineering its conformational dynamics. Specifically, we increase the dynamics of the yCD C-terminal helix, an active site lid that controls the product release. The C-terminal is extended by a dynamical single α-helix (SAH), which improves the product release rate by up to ~8-fold, and the overall catalytic rate kcat by up to ~2-fold. It is also shown that the kcat increase is due to the favorable activation entropy change. The NMR H/D exchange data indicate that the conformational dynamics of the transition state analog complex increases as the helix is extended, elucidating the origin of the enhanced catalytic entropy. This study highlights a novel dynamics engineering strategy that can accelerate the overall catalysis through the entropy-driven mechanism.

Preparation and application of tremella polysaccharide based chrome free tanning agent for sheepskin processing.

The abuse of chrome tanning agent in leather processing has caused great harm to human health and the natural environment. We use tremella polysaccharides (TP), lentinan (LNT) and konjac gum (KG) as raw materials, and sodium periodate as oxidant to prepare the corresponding polysaccharide tanning agent. Tremella polysaccharide was selected as the best tanning agent according to the shrinkage temperature, and the subsequent experiments were carried out. Tremella polysaccharide (TP) as raw material and sodium periodate as an oxidant, dialdehyde tremella polysaccharide (DTP) was prepared and applied in leather tanning. The effects of different oxidation conditions (sodium periodate dosage, temperature, pH, and reaction time) on the shrinkage temperature of DTP tanned leather were studied. The change of shrinkage temperature showed that the dosage of sodium periodate had the greatest influence on the shrinkage temperature. Therefore, the effects of different dosage of sodium periodate on the aldehyde content and molecular weight of DTP were investigated, including the analysis of physical properties and microstructure of tanned leather. In general, the increase of sodium periodate dosage was found to increase the aldehyde content and reduce the molecular weight, which was more conducive to leather tanning.

Blended cumin/Zanthoxylum essential oil improve the antibacterial, fresh-keeping performance and flavor of chilled fresh mutton.

Microbial pollution and fat oxidation are the main factors that induce the deterioration in the quality of chilled fresh mutton. This study evaluated the effects of cumin (Cuminum cyminum) essential oil (CEO), Zanthoxylum essential oil (ZEO), and blended cumin/zanthoxylum essential oil (BEO) on the antibacterial, preservation of freshness, and flavor improvement of chilled fresh mutton. The results show that BEO exerts a good inhibition effect on microbial growth, lipid oxidation, and the formation of TVB-N, as well as slowing down the rate of juice loss under chilled conditions. GC-IMS assay results showed that BEO can enrich the flavor of roasted mutton with a higher level of volatile organic substances, such as ethyl acetate D. In conclusion, BEO treatments were more efficient than single treatments in ensuring the quality of lamb to improve microbiological safety and improve the flavor of roasted lamb stored under chilled conditions. Overall research indicates that BEO is an effective natural addition that can be used to preserve the quality and safety of chilled fresh mutton during storage.

Ferric chloride induces ferroptosis in Pseudomonas aeruginosa and heals wound infection in a mouse model.

BACKGROUND: Pseudomonas aeruginosa is one of the most common pathogens that lead to fatal human infection. This Gram-negative pathogen has evolved complex drug resistance, which poses significant challenges to the current antibiotic-dependent healthcare system. New therapeutic approaches are urgently required to treat infections caused by P. aeruginosa. METHODS: Inspired by ferroptosis, the antibacterial effects of iron compounds on P. aeruginosa via direct exposure were investigated. In addition, thermal-responsive hydrogels to carry FeCl3 were developed as a wound dressing to treat P. aeruginosa-induced wound infection in a mouse model. RESULTS: The results showed that 200 µM FeCl3 killed more than 99.9% of P. aeruginosa cells. FeCl3-mediated cell death in P. aeruginosa was associated with hallmarks of ferroptosis in mammalian cells, including reactive oxygen species (ROS) burst, lipid peroxidation, and DNA damage. Catalase or Fe2+ chelator alleviated FeCl3-mediated cell death, indicating that H2O2 and labile Fe2+ induced the Fenton reaction leading to cell death. Further proteomics analysis showed that proteins related to glutathione (GSH) synthesis and the glutathione peroxidase (GPX) family were significantly downregulated after FeCl3 treatment, which is equivalent to GPX4 inactivation in mammalian cells. The therapeutic effect of FeCl3 on P. aeruginosa was further evaluated in a mouse wound infection model using polyvinyl alcohol-boric acid (PB) hydrogels as a carrier of FeCl3. FeCl3-PB hydrogels completely cleared pus on wounds and promoted wound healing. CONCLUSION: These results indicated that FeCl3 induces microbial ferroptosis in P. aeruginosa and has high therapeutic potential for the treatment of P. aeruginosa wound infection.

An "intelligent -responsive" bactericidal system based on OSA-starch Pickering emulsion.

Pickering emulsion based on OSA-starch was developed in this study as an intelligent delivery system for the application of thymol against foodborne pathogens. Morphology and microstructure characterization showed that the Pickering emulsion was an O/W type emulsion and stayed stable at starch concentration of 200 mg/mL and oil fraction at 30 % with particle size of 10 µm and absolute Zeta potential of -12.5 mV. Low field nuclear magnetic resonance and rheology experiments indicated that a denser network structure was formed in this stable Pickering emulsion. Besides, the Pickering emulsion could endure long-time storage, low pH (3,5) and additional NaCl (50, 100, 200, 400 mM) and it showed enhanced bactericidal effects against Escherichia coli, Staphylococcus aureus (thymol =1.48 µmol/L) and Aspergillus flavus (thymol = 0.624 µmol/L) by inducing ROS eruption, membrane lipid peroxidation and cell shrink. Moreover, the bactericidal assay demonstrated that thymol could be intelligently released and a considerable 75 % timely bactericidal effect was detected after 9 days' intermittently exposing to E. coli, S. aureus and A. flavus in vitro, by comparison thymol alone showed only 20 % bactericidal effect due to its volatility. The results are of great importance to offer an intelligent delivery system of bio-actives defending foodborne pathogens.

Detecting the Hydrogen Bond Cooperativity in a Protein ß-Sheet by H/D Exchange.

The hydrogen bond (H-bond) cooperativity in the ß-sheet of GB3 is investigated by a NMR hydrogen/deuterium (H/D) exchange method. It is shown that the weakening of one backbone N-H…O=C H-bond between two ß-strands, ß1 and ß2, due to the exchange of NH to ND of the H-bond donor in ß1, perturbs the chemical shift of 13Cα, 13Cß, 1Hα, 1HN, and 15N of the H-bond acceptor and its following residue in ß2. Quantum mechanical calculations suggest that the -H-bond chemical shift isotope effect is caused by the structural reorganization in response to the H-bond weakening. This structural reorganization perturbs four neighboring H-bonds, with three being weaker and one being stronger, indicating that three H-bonds are cooperative and one is anticooperative with the perturbed H-bond. The sign of the cooperativity depends on the relative position of the H-bonds. This H-bond cooperativity, which contributes to ß-sheet stability overall, can be important for conformational coupling across the ß-sheet.

Fe2+ protects postharvest pitaya (Hylocereus undulatus britt) from Aspergillus. flavus infection by directly binding its genomic DNA.

Aspergillus flavus (A. flavus) is a postharvest fungus, causing pitaya fruit decay and limiting pitaya value and shelf life. However, safer and more efficient methods for preventing A. flavus contamination for pitaya fruit remain to be investigated. In this study, we successfully proved exogenous Fe2+ could inhibit A. flavus colonization in pitaya fruit and extend pitaya's shelf life after harvest. Moreover, gel electrophoresis, CD analysis and Raman spectrum tests revealed Fe2+ could more effectively and thoroughly promote conidial death by directly binding to A. flavus DNA. Increased expression of DNA damage repair-related genes after Fe2+ treatment was observed by transcription analysis, which might eventually lead to SOS response in A. flavus. These results indicated Fe2+ could prevent A. flavus infestation on pitaya in a novel, quickly responsive mechanism. Our results shed light on the potential application of Fe2+ in the food industry and provided a more universal antifungal agent against food pathogens.

Water-Locked Eutectic Electrolyte Enables Long-Cycling Aqueous Sodium-Ion Batteries.

Aqueous sodium batteries are one of the awaited technologies for large-scale energy storage, but remain poorly rechargeable because of the reactivity issues of water. Here, we present a hydrated eutectic electrolyte featuring a water-locked effect, which is exceptional in that the O-H bond of water is essentially strengthened via weak hydrogen bonding (relative to the original H2O-H2O hydrogen bonds) to low-donor-number anions and ligands. Even without interphase protection, both the anodic and cathodic water electrodecomposition reactions are delayed, extending the aqueous potential window to 3.4 V. Combined with the alleviated electrode dissolution, Na2MnFe(CN)6||NaTi2(PO4)3 batteries deliver a high energy density of ∼80 W h kg-1 at 0.5 C and undergo over 1000 cycles with a 74.5% capacity retention and a 99.4% Coulombic efficiency at 4.2 C. This work may offer a general guide to ultimately exploit the water's innate stability for realizing the promise of aqueous battery technologies.

A Tyrosine Phosphoproteome Analysis Approach Enabled by Selective Dephosphorylation with Protein Tyrosine Phosphatase.

Protein tyrosine phosphorylation (pTyr) plays a prominent role in signal transduction and regulation in all eukaryotic cells. In conventional immunoaffinity purification (IP) methods, phosphotyrosine peptides are isolated from the digest of cellular protein extracts with a phosphotyrosine-specific antibody and are identified by tandem mass spectrometry. However, low sensitivity, poor reproducibility, and high cost are universal concerns for IP approaches. In this study, we presented an antibody-free approach to identify phosphotyrosine peptides by using protein tyrosine phosphatase (PTP). It was found that most of the PTPs including PTP1B, TCPTP, and SHP1 can efficiently and selectively dephosphorylate phosphotyrosine peptides. We then designed a workflow by combining two Ti4+-IMAC-based phosphopeptide enrichment steps with PTP-catalyzed dephosphorylation for tyrosine phosphoproteomics analysis. This workflow was first validated by selective detection of phosphotyrosine peptides from semicomplex samples and then applied to analyze the tyrosine phosphoproteome of Jurkat T cells. Around 1000 putative former phosphotyrosine peptides were identified from less than 500 µg of cell lysate. The tyrosine phosphosites on the majority of these peptides could be unambiguously determined for over 70% of them possessing only one tyrosine residue. It was also found that the tyrosine sites identified by this method were highly complementary to those identified by the SH2 superbinder-based method. Therefore, the combination of Ti4+-IMAC enrichment with PTP dephosphorylation provides an alternative and cost-effective approach for tyrosine phosphoproteomics analysis.

Exogenous Iron Induces NADPH Oxidases-Dependent Ferroptosis in the Conidia of Aspergillus flavus.

Aspergillus flavus is saprophytic soil fungus that contaminates seed crops with the carcinogenic secondary metabolite aflatoxin, posing a significant threat to humans and animals. Ferrous sulfate is a common iron supplement that is used to the treatment of iron-deficiency anemia. Here, we identified an unexpected inhibitory role of ferrous sulfate on A. flavus. With specific fluorescent dyes, we detected several conidial ferroptosis hallmarks in conidia under the treatment of 1 mM Fe2+, including nonapoptosis necrosis, iron-dependent, lipid peroxide accumulation, and ROS burst. However, unlike traditional ferroptosis in mammals, Fe2+ triggered conidial ferroptosis in A. flavus was regulated by NADPH oxidase (NOXs) activation instead of Fenton reaction. Transcriptomic and some other bioinformatics analyses showed that NoxA in A. flavus might be a potential target of Fe2+, and thus led to the occurrence of conidial ferroptosis. Furthermore, noxA deletion mutant was constructed, and both ROS generation and conidial ferroptosis in ΔnoxA was reduced when exposed to Fe2+. Taken together, our study revealed an exogenous Fe2+-triggered conidial ferroptosis pathway mediated by NoxA of A. flavus, which greatly contributes to the development of an alternative strategy to control this pathogen.

Quantifying Protein Electrostatic Interactions in Cells by Nuclear Magnetic Resonance Spectroscopy.

Most proteins perform their functions in cells. How the cellular environment modulates protein interactions is an important question. In this work, electrostatic interactions between protein charges were studied using in-cell nuclear magnetic resonance (NMR) spectroscopy. A total of eight charge pairs were introduced in protein GB3. Compared to the charge pair electrostatic interactions in a buffer, five charge pairs in cells displayed no apparent changes whereas three pairs had the interactions weakened by more than 70%. Further investigation suggests that the transfer free energy is responsible for the electrostatic interaction modulation. Both the transfer free energy of the folded state and that of the unfolded state can contribute to the cellular environmental effect on protein electrostatics, although the latter is generally larger (more negative) than the former. Our work highlights the importance of direct in-cell studies of protein interactions and thus protein function.

EGCG Alleviates Oxidative Stress and Inhibits Aflatoxin B1 Biosynthesis via MAPK Signaling Pathway.

Aflatoxin biosynthesis has established a connection with oxidative stress, suggesting a prevention strategy for aflatoxin contamination via reactive oxygen species (ROS) removal. Epigallocatechin gallate (EGCG) is one of the most active and the richest molecules in green tea with well-known antioxidant effects. Here, we found EGCG could inhibit aflatoxin B1 (AFB1) biosynthesis without affecting mycelial growth in Aspergillus flavus, and the arrest occurred before the synthesis of toxin intermediate metabolites. Further RNA-seq analysis indicated that multiple genes involved in AFB1 biosynthesis were down-regulated. In addition, EGCG exposure facilitated the significantly decreased expression of AtfA which is a bZIP (basic leucine zipper) transcription factor mediating oxidative stress. Notably, KEGG (Kyoto Encyclopedia of Genes and Genomes) analysis indicated that the MAPK signaling pathway target transcription factor was down-regulated by 1 mg/mL EGCG. Further Western blot analysis showed 1 mg/mL EGCG could decrease the levels of phosphorylated SakA in both the cytoplasm and nucleus. Taken together, these data evidently supported that EGCG inhibited AFB1 biosynthesis and alleviated oxidative stress via MAPK signaling pathway. Finally, we evaluated AFB1 contamination in soy sauce fermentation and found that EGCG could completely control AFB1 contamination at 8 mg/mL. Conclusively, our results supported the potential use of EGCG as a natural agent to prevent AFB1 contamination in fermentation industry.

Enabling highly (R)-enantioselective epoxidation of styrene by engineering unique non-natural P450 peroxygenases.

Unlike the excellent (S)-enantioselective epoxidation of styrene performed by natural styrene monooxygenases (ee > 99%), the (R)-enantioselective epoxidation of styrene has not yet achieved a comparable efficiency using natural or engineered oxidative enzymes. This report describes the H2O2-dependent (R)-enantioselective epoxidation of unfunctionalized styrene and its derivatives by site-mutated variants of a unique non-natural P450BM3 peroxygenase, working in tandem with a dual-functional small molecule (DFSM). The observed (R)-enantiomeric excess (ee) of styrene epoxidation is up to 99% with a turnover number (TON) of 918 by the best enantioselective mutant F87A/T268I/L181Q, while the best active mutant F87A/T268I/V78A/A184L (with 98% ee) gave a catalytic TON of 4350, representing the best activity of a P450 peroxygenase towards styrene epoxidation to date. Following this approach, a set of styrene derivatives, such as o-, m-, p-chlorostyrenes and fluorostyrenes, could also be epoxidized with modest to very good TONs (362-3480) and high (R)-enantioselectivities (95-99% ee). The semi-preparative scale synthesis of (R)-styrene oxide performed at 0 °C with high conversion, maintaining enantioselectivity, and moderate isolated yields, further suggests the potential application of the current P450 enzymatic system in styrene epoxidation. This study indicates that the synergistic use of protein engineering and an exogenous DFSM constitutes an efficient strategy to control the enantioselectivity of styrene epoxidation, thus substantially expanding the chemical scope of P450 enzymes as useful bio-oxidative catalysts.