The recent revolution in computational protein structure prediction provides folding models for entire proteomes, which can now be integrated with large-scale experimental data. Mass spectrometry ...(MS)-based proteomics has identified and quantified tens of thousands of posttranslational modifications (PTMs), most of them of uncertain functional relevance. In this study, we determine the structural context of these PTMs and investigate how this information can be leveraged to pinpoint potential regulatory sites. Our analysis uncovers global patterns of PTM occurrence across folded and intrinsically disordered regions. We found that this information can help to distinguish regulatory PTMs from those marking improperly folded proteins. Interestingly, the human proteome contains thousands of proteins that have large folded domains linked by short, disordered regions that are strongly enriched in regulatory phosphosites. These include well-known kinase activation loops that induce protein conformational changes upon phosphorylation. This regulatory mechanism appears to be widespread in kinases but also occurs in other protein families such as solute carriers. It is not limited to phosphorylation but includes ubiquitination and acetylation sites as well. Furthermore, we performed three-dimensional proximity analysis, which revealed examples of spatial coregulation of different PTM types and potential PTM crosstalk. To enable the community to build upon these first analyses, we provide tools for 3D visualization of proteomics data and PTMs as well as python libraries for data accession and processing.
Some bioactive properties of p-coumaric acid and fucose-rich polysaccharide in skin health have been studied, including melanogenesis inhibition of the phenolic acid and growth inhibitory effects of ...the polysaccharide on melanoma. The dermatological benefits of bird's nest fern extracts (BNFE), containing both substantial fucose-rich polysaccharide and p-coumaric acid, like promoting collagen production and growth of fibroblast cell and further improving the elasticity and dryness of human skins have been demonstrated in our previous study. Besides, the anti-melanization effects of various BNFE on B16-F10 melanoma and human skin were first studied here. The promising extracts revealed that the main phenolic acid, p-coumaric acid, in BNFE resulted in suppression against tyrosinase activity from melanogenesis. The inhibitory kinetics on the diphenolase activity indicated that AE40 was a noncompetitive inhibitor of mushroom tyrosinase. On the other hand, the fucose-rich mucilage of BNFE showed pronouncedly suppressing effect on B16-F10 melanoma viability. Clinical trial was performed by recruiting 46 female volunteers and the results indicated that the lotions with 1% of BNFE was non-irritant and reduced effectively the pigmentation on human skin after 7–14 days of continuous application. It was suggested that the fucose-rich mucilage and p-coumaric acid in BNFE may have potential for nutricosmetics and phytotherapy applications as a natural hypopigmenting agent.
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•The anti-melanization effects of Asplenium australasicum extracts were identified firstly via cellular and human model.•The relation between melanogenesis-inhibiting activities and potential bioactive compounds was understood.•These extracts were relatively more innocent nutricosmetics for reducing hyperpigmentation in cutaneous applications.
Great advances have been made in mass spectrometric data interpretation for intact glycopeptide analysis. However, accurate identification of intact glycopeptides and modified saccharide units at the ...site-specific level and with fast speed remains challenging. Here, we present a glycan-first glycopeptide search engine, pGlyco3, to comprehensively analyze intact N- and O-glycopeptides, including glycopeptides with modified saccharide units. A glycan ion-indexing algorithm developed for glycan-first search makes pGlyco3 5-40 times faster than other glycoproteomic search engines without decreasing accuracy or sensitivity. By combining electron-based dissociation spectra, pGlyco3 integrates a dynamic programming-based algorithm termed pGlycoSite for site-specific glycan localization. Our evaluation shows that the site-specific glycan localization probabilities estimated by pGlycoSite are suitable to localize site-specific glycans. With pGlyco3, we confidently identified N-glycopeptides and O-mannose glycopeptides that were extensively modified by ammonia adducts in yeast samples. The freely available pGlyco3 is an accurate and flexible tool that can be used to identify glycopeptides and modified saccharide units.
Plants have various self-defense mechanisms against biotic attacks, involving both physical and chemical barriers. Physical barriers include spines, trichomes, and cuticle layers, whereas chemical ...barriers include secondary metabolites (SMs) and volatile organic compounds (VOCs). Complex interactions between plants and herbivores occur. Plant responses to insect herbivory begin with the perception of physical stimuli, chemical compounds (orally secreted by insects and herbivore-induced VOCs) during feeding. Plant cell membranes then generate ion fluxes that create differences in plasma membrane potential (Vm), which provokes the initiation of signal transduction, the activation of various hormones (e.g., jasmonic acid, salicylic acid, and ethylene), and the release of VOCs and SMs. This review of recent studies of plant–herbivore–infection interactions focuses on early and late plant responses, including physical barriers, signal transduction, SM production as well as epigenetic regulation, and phytohormone responses.
Despite the great progress of deep learning and target detection in recent years, the accurate detection of the occluded targets in remote sensing images still remains a challenge. In this letter, we ...propose a new detection method called local attention networks to improve the detection of occluded airplanes. Following the idea of "divide and conquer," the proposed method is designed by first dividing an airplane target into four visual parts: head, left/right wings, body, and tail, and then considering the detection as the prediction of the individual key points in each of the visual parts. We further introduce an additional attention branch in the standard detection pipeline to enhance the features and make the model focus on individual parts of a target even if it is only partially visible in the image. Detection results and ablation studies on three remote sensing target detection data sets (including two publicly available ones) demonstrate the effectiveness of our method, especially for occluded airplane targets. In addition, our method outperforms the other state-of-the-art detection methods on these data sets.
The unsaturated “dangling” bonds on the surface of nanomaterials are extremely sensitive to the external environment, which gives nanomaterials a dual nature, i.e., high reactivity and poor ...stability. However, studies on the long-term effects of stability and reactivity of nanomaterials under practical conditions are rarely found in the literature and lag far behind other research. Furthermore, the long-term effects on the stability and reactivity of a nanomaterial without coating under practical conditions are seriously long-neglected. Herein, by choosing copper nanowire as an example, we systematically study the stability of copper nanowires (CuNWs) in the liquid and gas phase by monitoring the change of morphology, phase, and valence state of CuNWs during storage. CuNWs exhibit good dispersibility and durable chemical stability in polar organic solvents, while CuNWs stored in water or nonpolar organic solvents evolve into a mace-like structure. Additionally, fresh CuNWs are oxidized into CuO nanotubes with thin shells by heating in air. The activation energies of oxidation of CuNWs in the gas phase are determined by the Kissinger method. More importantly, the different oxidation pathways have significant effects on the final morphology, surface area, phase, optical absorption, band gap, and vibrational property of the oxidation products. Understanding the stability and reactivity of Cu nanostructures will add value to their storage and applications. This work emphasizes the significant issue on the stability of nanostructures, which should be taken into account from the viewpoint of their practical application.
Since the launch of Chinese Human Proteome Project (CNHPP) and Clinical Proteomic Tumor Analysis Consortium (CPTAC), large‐scale mass spectrometry (MS) based proteomic profiling of different kinds of ...human tumor samples have provided huge amount of valuable data for both basic and clinical researchers. Accurate prediction for tumor and non‐tumor samples, as well as the tumor types has become a key step for biological and medical research, such as biomarker discovery, diagnosis, and monitoring of diseases. The traditional MS‐based classification strategy mainly depends on the identification and quantification results of MS data, which has some inherent limitations, such as the low identification rate of MS data. Here, a deep learning‐based tumor classifier directly using MS raw data is proposed, which is independent of the identification and quantification results of MS data. The potential precursors with intensities and retention times from MS data as input is first detected and extracted. Then, a deep learning‐based classifier is trained, which can accurately distinguish between the tumor and non‐tumor samples. Finally, it is demonstrated the deep learning‐based classifier has a good performance compared with other machine learning methods and may help researchers find the potential biomarkers which are likely to be missed by the traditional strategy.
Herein we present a new viologen‐based radical‐containing metal–organic framework (RMOF) Gd‐IHEP‐7, which upon heating in air undergoes a single‐crystal‐to‐single‐crystal transformation to generate ...Gd‐IHEP‐8. Both RMOFs exhibit excellent air and water stability as a result of favorable radical‐radical interactions, and their long‐lifetime radicals result in wide spectral absorption in the range 200–2500 nm. Gd‐IHEP‐7 and Gd‐IHEP‐8 show excellent activity toward solar‐driven nitrogen fixation, with ammonia production rates of 128 and 220 μmol h−1 g−1, respectively. Experiments and theoretical calculations indicate that both RMOFs have similar nitrogen fixation pathways. The enhanced catalytic efficiency of Gd‐IHEP‐8 versus Gd‐IHEP‐7 is attributed to intermediates stabilized by enhanced hydrogen bonding.
A single‐crystal‐to‐single‐crystal (SCSC) transformation of stable radical‐containing MOF Gd‐IHEP‐7 generates Gd‐IHEP‐8. It is accompanied by a marked increase in efficiency of sacrificial agent‐free photocatalytic nitrogen fixation to yield NH3 from H2O and N2 under simulated solar light irradiation at ambient temperature. The NH3 production rate of 220 μmol h−1 g−1 for Gd‐IHEP‐8 is a new record for MOF photocatalysts.
The precise and large-scale identification of intact glycopeptides is a critical step in glycoproteomics. Owing to the complexity of glycosylation, the current overall throughput, data quality and ...accessibility of intact glycopeptide identification lack behind those in routine proteomic analyses. Here, we propose a workflow for the precise high-throughput identification of intact N-glycopeptides at the proteome scale using stepped-energy fragmentation and a dedicated search engine. pGlyco 2.0 conducts comprehensive quality control including false discovery rate evaluation at all three levels of matches to glycans, peptides and glycopeptides, improving the current level of accuracy of intact glycopeptide identification. The N-glycoproteome of samples metabolically labeled with
N/
C were analyzed quantitatively and utilized to validate the glycopeptide identification, which could be used as a novel benchmark pipeline to compare different search engines. Finally, we report a large-scale glycoproteome dataset consisting of 10,009 distinct site-specific N-glycans on 1988 glycosylation sites from 955 glycoproteins in five mouse tissues.Protein glycosylation is a heterogeneous post-translational modification that generates greater proteomic diversity that is difficult to analyze. Here the authors describe pGlyco 2.0, a workflow for the precise one step identification of intact N-glycopeptides at the proteome scale.
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