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Abstract G-protein coupled receptors (GPCRs), the largest family of membrane proteins in human body, involve a great variety of biological processes and thus have become highly valuable drug targets. By binding with ligands (e.g., drugs), GPCRs switch between active and inactive conformational states, thereby performing functions such as signal transmission. The changes in binding pockets under different states are important for a better understanding of drug-target interactions. Therefore it is critical, as well as a practical need, to obtain binding sites in human GPCR structures. We report a database (called GPCR-BSD) that collects 127,990 predicted binding sites of 803 GPCRs under active and inactive states (thus 1,606 structures in total). The binding sites were identified from the predicted GPCR structures by executing three geometric-based pocket prediction methods, fpocket, CavityPlus and GHECOM. The server provides query, visualization, and comparison of the predicted binding sites for both GPCR predicted and experimentally determined structures recorded in PDB. We evaluated the identified pockets of 132 experimentally determined human GPCR structures in terms of pocket residue coverage, pocket center distance and redocking accuracy. The evaluation showed that fpocket and CavityPlus methods performed better and successfully predicted orthosteric binding sites in over 60% of the 132 experimentally determined structures. The GPCR Binding Site database is freely accessible at https://gpcrbs.bigdata.jcmsc.cn . This study not only provides a systematic evaluation of the commonly-used fpocket and CavityPlus methods for the first time but also meets the need for binding site information in GPCR studies.

Abstract Background Fibroblast growth factor 21 (FGF21) is a promising candidate for treating metabolic disorder diseases and has been used in phase II clinical trials. Currently, metabolic diseases are prevalent worldwide, underscoring the significant market potential of FGF21. Therefore, the production of FGF21 must be effectively improved to meet market demand. Results Herein, to investigate the impact of vectors and host cells on FGF21 expression, we successfully engineered strains that exhibit a high yield of FGF21. Surprisingly, the data revealed that vectors with various copy numbers significantly impact the expression of FGF21, and the results showed a 4.35-fold increase in expression levels. Furthermore, the performance of the double promoter and tandem gene expression construction design surpassed that of the conventional construction method, with a maximum difference of 2.67 times. Conclusion By exploring engineered vectors and host cells, we successfully achieved high-yield production of the FGF21 strain. This breakthrough lays a solid foundation for the future industrialization of FGF21. Additionally, FGF21 can be easily, quickly and efficiently expressed, providing a better tool and platform for the research and application of more recombinant proteins.

Abstract Indan and tetralin are widely used as fuel additives and the intermediates in the manufacture of thermal-stable jet fuel, many chemicals, medicines, and shockproof agents for rubber industry. Herein, we disclose a two-step route to selectively produce 5-methyl-2,3-dihydro-1H-indene (abbreviated as methylindan) and tetralin with xylose or the hemicelluloses from agricultural or forestry waste. Firstly, cyclopentanone (CPO) was selectively formed with ~60% carbon yield by the direct hydrogenolysis of xylose or hemicelluloses on a non-noble bimetallic Cu-La/SBA-15 catalyst. Subsequently, methylindan and tetralin were selectively produced with CPO via a cascade self-aldol condensation/rearrangement/aromatization reaction catalyzed by a commercial H-ZSM-5 zeolite. When we used cyclohexanone (another lignocellulosic cycloketone) in the second step, the main product switched to dimethyltetralin. This work gives insights into the selective production of bicyclic aromatics with lignocellulose.

Summary: Indanone and its analogs are widely used intermediates for many useful chemicals. Decalin and its alkylated analogs are major components of thermal-stable aviation fuels and the additives used to improve the thermal stability of aviation fuel. In this work, we develop an integrated route to selectively produce trimethyl-indanone or alkylated decalin with cellulose. First, cellulose was hydrogenolyzed to 2,5-hexanedione in a biphasic reaction system of toluene/NH4Br aqueous solution over Pd/C catalyst. Under the catalysis of alkali hydroxide, 2,5-hexanedione was converted to a mixture of C12 oxygenates (with trimethyl-indanone as the main component) at room temperature. Trimethyl-indanone can be used as an intermediate for many useful chemicals. Moreover, the C12 oxygenates can be hydrodeoxygenated to a mixture of dimethyl decalin and C12 monocycloalkanes with a low freezing point (200 K) and high density (0.85 g mL−1). This work provides insights on the preparation of indanone or advanced aviation fuel with cellulose. Science for society: The production of valuable chemicals and sustainable aviation fuel (SAF) with renewable, cheap, and abundant lignocellulose has drawn a lot of attention. Indanone and its analogs are widely used as intermediates in the manufacture of many useful chemicals. Currently, these compounds are obtained from fossil resources at low yields. Decalin and alkylated decalins are additives to improve the thermal stability of aviation fuel. Herein, we report an integrated route for the selective preparation of trimethyl-indanone or alkylated decalins with cellulose, the most abundant biomass. Compared with the reported processes to produce indanone analogs or SAF, this new process has several advantages, such as renewable feedstock, mild reaction conditions, fewer steps, and excellent fuel properties (e.g., lower freezing point, higher volumetric heat value, thermal stability of final products, etc.). This work paves a new way for the high-value utilization of cellulose.

Abstract The lack of efficient biomarkers for the early detection of gastric cancer (GC) contributes to its high mortality rate, so it is crucial to discover novel diagnostic targets for GC. Recent studies have implicated the potential of site‐specific glycans in cancer diagnosis, yet it is challenging to perform highly reproducible and sensitive glycoproteomics analysis on large cohorts of samples. Here, a highly robust N‐glycoproteomics (HRN) platform comprising an automated enrichment method, a stable microflow LC‐MS/MS system, and a sensitive glycopeptide‐spectra‐deciphering tool is developed for large‐scale quantitative N‐glycoproteome analysis. The HRN platform is applied to analyze serum N‐glycoproteomes of 278 subjects from three cohorts to investigate glycosylation changes of GC. It identifies over 20 000 unique site‐specific glycans from discovery and validation cohorts, and determines four site‐specific glycans as biomarker candidates. One candidate has branched tetra‐antennary structure capping with sialyl‐Lewis antigen, and it significantly outperforms serum CEA with AUC values > 0.89 compared against < 0.67 for diagnosing early‐stage GC. The four‐marker panel can provide improved diagnostic performances. Besides, discrimination powers of four candidates are also testified with a verification cohort using PRM strategy. This findings highlight the value of this strong tool in analyzing aberrant site‐specific glycans for cancer detection.

Abstract Dispersion of colloidal particles in water or oil is extensively desired for industrial and environmental applications. However, it often strongly depends on indispensable assistance of chemical surfactants or introduction of nanoprotrusions onto the particle surface. Here we demonstrate the omnidispersity of hydrophilic-hydrophobic heterostructure particles (HL-HBPs), synthesized by a surface heterogeneous nanostructuring strategy. Photo-induced force microscopy (PiFM) and adhesion force images both indicate the heterogeneous distribution of hydrophilic domains and hydrophobic domains on the particle surface. These alternating domains allow HL-HBPs to be dispersed in various solvents with different polarity and boiling point. The HL-HBPs can efficiently adsorb organic dyes from water and release them into organic solvents within several seconds. The surface heterogeneous nanostructuring strategy provides an unconventional approach to achieve omnidispersion of colloidal particles beyond surface modification, and the omnidispersible HL-HBPs demonstrate superior capability for dye recycle merely by solvent exchange. These omnidispersible HL-HBPs show great potentials in industrial process and environmental protection.

The Polycomb Repressor Complex (PRC) plays a pivotal role in gene regulation during development and disease, with dysregulation contributing significantly to various human cancers. The intricate interplay between PRC and cellular signaling pathways sheds light on cancer complexity. PRC presents promising therapeutic opportunities, with inhibitors undergoing rigorous evaluation in preclinical and clinical studies. In this review, we emphasize the critical role of PRC complex in gene regulation, particularly PcG proteins mediated chromatin compaction through phase separation. We also highlight the pathological implications of PRC complex dysregulation in various tumors, elucidating underlying mechanisms driving cancer progression. The burgeoning field of therapeutic strategies targeting PRC complexes, notably EZH2 inhibitors, has advanced significantly. However, we explore the need for combination therapies to enhance PRC targeted treatments efficacy, providing a glimpse into the future of cancer therapeutics.

The structural complexity of glycans seriously challenges the currently available analytical methods. Here, the authors report the identification of glycan isomers, glycans with varying chain lengths, and distinct branched glycans, via a glycan derivatization strategy and nanopore sensing.

GPR35 is a G protein-coupled receptor with notable involvement in modulating inflammatory responses. Although the precise role of GPR35 in inflammation is not yet fully understood, studies have suggested that it may have both pro- and anti-inflammatory effects depending on the specific cellular environment. Some studies have shown that GPR35 activation can stimulate the production of pro-inflammatory cytokines and facilitate the movement of immune cells towards inflammatory tissues or infected areas. Conversely, other investigations have suggested that GPR35 may possess anti-inflammatory properties in the gastrointestinal tract, liver and certain other tissues by curbing the generation of inflammatory mediators and endorsing the differentiation of regulatory T cells. The intricate role of GPR35 in inflammation underscores the requirement for more in-depth research to thoroughly comprehend its functional mechanisms and its potential significance as a therapeutic target for inflammatory diseases. The purpose of this review is to concurrently investigate the pro-inflammatory and anti-inflammatory roles of GPR35, thus illuminating both facets of this complex issue.

In the healing of wounds, human-like collagen (hCol) is essential. However, collagen-based composite dressings have poor stability in vivo, which severely limits their current therapeutic potential. Based on the above, we have developed a recombinant fusion protein named hCol-ELP, which consists of hCol and an elastin-like peptide (ELP). Then, we examined the physicochemical and biological properties of hCol-ELP. The results indicated that the stability of the hCol-ELP fusion protein exhibited a more compact and homogeneous lamellar microstructure along with collagen properties, it was found to be significantly superior to the stability of free hCol. The compound hCol-ELP demonstrated a remarkable capacity to induce the proliferation and migration of mouse embryo fibroblast cells (NIH/3T3), as well as enhance collagen synthesis in human skin fibroblasts (HSF) when tested in vitro. In vivo, hCol-ELP demonstrated significant enhancements in healing rate and a reduction in the time required for scab removal, thereby exhibiting a scar-free healing effect. The findings provide a crucial theoretical foundation for the implementation of an hCol-ELP protein dressing in fields associated with the healing of traumatic injuries.

Protein phosphorylation and glycosylation coordinately regulate numerous complex biological processes. However, the main methods to simultaneously enrich them are based on the coordination interactions or Lewis acid-base interactions, which suffer from low coverage of target molecules due to strong intermolecular interactions. Here, we constructed a poly-histidine modified silica (SiO2@Poly-His) microspheres-based method for the simultaneous enrichment, sequential elution and analysis of phosphopeptides and glycopeptides. The SiO2@Poly-His microspheres driven by hydrophilic interactions and multiple hydrogen bonding interactions exhibited high selectivity and coverage for simultaneous enrichment of phosphopeptides and glycopeptides from 1,000 molar folds of bovine serum albumin interference. Furthermore, “on-line deglycosylation” strategy allows sequential elution of phosphopeptides and glycopeptides, protecting phosphopeptides from hydrolysis during deglycosylation and improving the coverage of phosphopeptides. The application of our established method to HT29 cell lysates resulted in a total of 1,601 identified glycopeptides and 694 identified phosphopeptides, which were 1.2-fold and 1.5-fold higher than those obtained from the co-elution strategy, respectively. The SiO2@Poly-His based simultaneous enrichment and sequential separation strategy might have great potential in co-analysis of PTMs-proteomics of biological and clinic samples.

Summary: Developing low cost, yet high-voltage electrolyte is significant to improve the energy density and practicability of lithium metal batteries (LMBs). Low concentration electrolyte has significant merits in terms of cost and viscosity; however, their poor compatibility with high-voltage LMBs hinders its applications. Here, we develop a diluted low concentration electrolyte by replacing solvating cosolvent with a non-solvating cosolvent to facilitate the interaction between BF4− and Li+, resulting in optimized interfacial chemistry and suppressed side reaction. Thus, the high-loading Li-LiCoO2 full cells (20.4 mg cm−2) deliver outstanding cycling stability and rate performance at a cutoff voltage of 4.6 V. More impressively, a Li-LiCoO2 pouch cell achieves an energy density of more than 400 Wh kg−1 under practical conditions with thin Li (50 μm) and lean electrolyte (2.7 g Ah−1). This work provides a rational approach to design a low concentration electrolyte, which can be extended to other high voltage battery systems.

Separation of phosphoproteins is essential for understanding their vital roles in biological processes and pathology. Transition metal-based receptors and antibodies, the routinely used materials for phosphoproteins enrichment, both suffer from low sensitivity, low recovery and coverage. In this work, a novel smart copolymer material was synthesized by modifying porous silica gel with a poly[(N-isopropylacrylamide-co-4-(3-acryloylthioureido) benzoic acid)0.35] (denoted as NIPAAm-co-ATBA0.35@SiO2). Driven by the hydrogen bonds complexation of ATBA monomers with phosphate groups, the copolymer-modified surface exhibited a remarkable adsorption toward native α-casein (a model phosphoprotein), accompanied with significant changes in surface viscoelasticity and roughness. Moreover, this adsorption was tunable and critically dependent on the polarity of carrier solvent. Benefiting from these features, selective enrichment of phosphoprotein was obtained using NIPAAm-co-ATBA0.35@SiO2 under a dispersive solid-phase extraction (dSPE) mode. This result displays a good potential of smart polymeric materials in phosphoprotein enrichment, which may facilitate top-down phosphoproteomics studies.

Curcuma kwangsiensis, one species of Curcumae zedoaria Ros. c, is a commonly used traditional Chinese medicine (TCM) for treating cardiovascular disease, cancer, asthma and inflammation. Polar compounds are abundant in water decoction, which would be responsible for critical pharmacological effects. However, current research on polar compounds in Curcumae zedoaria Ros. c remains scarce. In this study, the polar fraction from Curcuma kwangsiensis was firstly profiled on G protein-coupled receptor 109A (GPR109A), β2-adrenergic receptor (β2-AR), neurotensin receptor (NTSR), muscarinic-3 acetylcholine receptor (M3) and G protein-coupled receptor 35 (GPR35), which were involved in its clinical indications and exhibited excellent β2-AR and GPR109A receptor activities. Then, an offline two-dimensional reversed-phase liquid chromatography (RPLC) coupled with the hydrophilic interaction chromatography (HILIC) method was developed to separate polar compounds. By the combination of a polar-copolymerized XAqua C18 column and an amide-bonded XAmide column, an orthogonality of 47.6% was achieved. As a result of coupling with the mass spectrometry (MS), a four-dimensional data plot was presented in which 373 mass peaks were detected and 22 polar compounds tentatively identified, including the GPR109A agonist niacin. Finally, molecular docking of these 22 identified compounds to β2-AR, M3, GPR35 and GPR109A receptors was performed to predict potential active ingredients, and compound 9 was predicted to have a similar interaction to the β2-AR partial agonist salmeterol. These results were supplementary to the material basis of Curcuma kwangsiensis and facilitated the bioactivity research of polar compounds. The integration of RPLC×HILIC-MS and molecular docking can be a powerful tool for characterizing and predicting polar active components in TCM.

Reversible protein glycosylation and phosphorylation tightly modulate important cellular processes and are closely involved in pathological processes in a crosstalk dependent manner. Because of their significance and low abundances of glyco- and phosphopeptides, several strategies have been developed to simultaneously enrich and co-elute glyco- and phosphopeptides. However, the co-existence of deglycosylated peptides and phosphopeptides aggravates the mass spectrometry analysis. Herein we developed a novel strategy to analyze glyco- and phosphopeptides based on simultaneous enrichment with TiO2, on-line deglycosylation and collection of deglycosylated peptides, and subsequent elution of phosphopeptides. To optimize on-line deglycosylation conditions, the solution pH, buffer types and concentrations, and deglycosylation time were investigated. The application of this novel strategy to 100 μg mouse brain resulted in 355 glycopeptides and 1,975 phosphopeptides, which were 2.5 and 1.4 folds of those enriched with the reported method. This study will expand the application of TiO2 and may shed light on simultaneously monitoring protein multiple post-translational modifications.

HKU1 is a human beta coronavirus and infects host cells via highly glycosylated spike protein (S). The N-glycosylation of HKU1 S has been reported. However, little is known about its O-glycosylation, which hinders the in-depth understanding of its biological functions. Herein, a comprehensive study of O-glycosylation of HKU1 S was carried out based on dual-functional histidine-bonded silica (HBS) materials. The enrichment method for O-glycopeptides with HBS was developed and validated using standard proteins. The application of the developed method to the HKU1 S1 subunit resulted in 46 novel O-glycosylation sites, among which 55.6% were predicted to be exposed on the outer protein surface. Moreover, the O-linked glycans and their abundance on each HKU1 S1 site were analyzed. The obtained O-glycosylation dataset will provide valuable insights into the structure of HKU1 S.

The breadth and depth of traditional Chinese medicine (TCM) applications have been expanding in recent years, yet the problem of quality control has arisen in the application process. It is essential to design an algorithm to provide blending ratios that ensure a high overall product similarity to the target with controlled deviations in individual ingredient content. We developed a new blending algorithm and scheme by comparing different samples of ginkgo leaves. High-consistency samples were used to establish the blending target, and qualified samples were used for blending. Principal component analysis (PCA) was used as the sample screening method. A nonlinear programming algorithm was applied to calculate the blending ratio under different blending constraints. In one set of calculation experiments, the result was blended by the same samples under different conditions. Its relative deviation coefficients (RDCs) were controlled within ±10%. In another set of calculations, the RDCs of more component blending by different samples were controlled within ±20%. Finally, the near-critical calculation ratio was used for the actual experiments. The experimental results met the initial setting requirements. The results show that our algorithm can flexibly control the content of TCMs. The quality control of the production process of TCMs was achieved by improving the content stability of raw materials using blending. The algorithm provides a groundbreaking idea for quality control of TCMs.

Ginseng, which contains abundant ginsenosides, grows mainly in the Jilin, Liaoning, and Heilongjiang in China. It has been reported that the quality and traits of ginsengs from different origins were greatly different. To date, the accurate prediction of the origins of ginseng samples is still a challenge. Here, we integrated ultra-high-performance liquid chromatography quadrupole time-of-flight mass spectrometry (UHPLC-Q-TOF-MS) with a support vector machine (SVM) for rapid discrimination and prediction of ginseng from the three main regions where it is cultivated in China. Firstly, we develop a stable and reliable UHPLC-Q-TOF-MS method to obtain robust information for 31 batches of ginseng samples after reasonable optimization. Subsequently, a rapid pre-processing method was established for the rapid screening and identification of 69 characteristic ginsenosides in 31 batches ginseng samples from three different origins. The SVM model successfully distinguished ginseng origin, and the accuracy of SVM model was improved from 83% to 100% by optimizing the normalization method. Six crucial quality markers for different origins of ginseng were screened using a permutation importance algorithm in the SVM model. In addition, in order to validate the method, eight batches of test samples were used to predict the regions of cultivation of ginseng using the SVM model based on the six selected quality markers. As a result, the proposed strategy was suitable for the discrimination and prediction of the origin of ginseng samples.

Inflammatory response contributes to brain injury after ischemia and reperfusion (I/R). Our previous literature has shown isoquercetin plays an important role in protecting against cerebral I/R injury. The present study was conducted to further investigate the effect of isoquercetin on inflammation-induced neuronal injury in I/R rats with the involvement of cyclic adenosine monophosphate (cAMP)/protein kinase A (PKA) and inhibitor of NF-κB (I-κB)/nuclear factor-kappa B (NF-κB) signaling pathway mediated by Toll-like receptor 4 (TLR4) and C5a receptor 1 (C5aR1). In vivo middle cerebral artery occlusion and reperfusion (MCAO/R) rat model and in vitro oxygen-glucose deprivation and reperfusion (OGD/R) neuron model were used. MCAO/R induced neurological deficits, cell apoptosis, and release of cytokines such as tumor necrosis factor (TNF)-α, interleukin (IL)-1β, and IL-6 in ischemic brain in rats. Simultaneously, the expression of TLR4 and C5aR1 was significantly up-regulated in both MCAO/R rats and OGD/R neurons, accompanied with the inhibition of cAMP/PKA signaling and activation of I-κB/NF-κB signaling in the cortex of MCAO/R rats. Over-expression of C5aR1 in neurons induced decrease of cell viability, exerting similar effects with OGD/R injury. Isoquercetin acted as a neuroprotective agent against I/R brain injury to suppress inflammatory response and improve cell recovery by inhibiting TLR4 and C5aR1 expression, promoting cAMP/PKA activation, and inhibiting I-κB/NF-κB activation and Caspase 3 expression. TLR4 and C5aR1 contributed to inflammation and apoptosis via activating cAMP/PKA/I-κB/NF-κB signaling during cerebral I/R, suggesting that this signaling pathway may be a potent therapeutic target in ischemic stroke. Isoquercetin was identified as a neuroprotective agent, which maybe a promising therapeutic agent used for the treatment of ischemic stroke and related diseases.

Capture of low-abundance multiply phosphorylated peptides (MPPs) is difficult due to limitation of enrichment materials and their interactions with phosphates. Here the authors show, a smart polymer driven by specific but tunable hydrogen bonding interactions can differentially complex with MPPs, singly phosphorylated and non-modified peptides.