Binding with proteins is a critical molecular initiating event through which environmental pollutants exert toxic effects in humans. Previous studies have been limited by the availability of three-dimensional (3D) protein structures and have focused on only a small set of environmental contaminants. Using the highly accurate 3D protein structure predicted by AlphaFold2, this study explored over 60 million interactions obtained through molecular docking between 20,503 human proteins and 1251 potential endocrine-disrupting chemicals. A total of 66,613,773 docking results were obtained, 1.2% of which were considered to be high binding, as their docking scores were lower than -7. Monocyte to macrophage differentiation factor 2 (MMD2) was predicted to interact with the highest number of environmental pollutants (526), with polychlorinated biphenyls and polychlorinated dibenzofurans accounting for a significant proportion. Dimension reduction and clustering analysis revealed distinct protein profiles characterized by high binding affinities for perfluoroalkyl and polyfluoroalkyl substances (PFAS), phthalate-like chemicals, and other pollutants, consistent with their uniquely enriched pathways. Further structural analysis indicated that binding pockets with a high proportion of charged amino acid residues, relatively low α-helix content, and high β-sheet content were more likely to bind to PFAS than others. This study provides insights into the toxicity pathways of various pollutants impacting human health and offers novel perspectives for the establishment and expansion of adverse outcome pathway-based models.

Raffinose family oligosaccharides (RFOs) have diverse structures and exhibit various biological activities. When using RFOs as prebiotics, their structures need to be identified. If we first knew whether an RFO was classical or non-classical, structural identification would become much easier. Here, we cloned and expressed an α-galactosidase (BF0224) from Bacteroides fragilis which showed strict specificity for hydrolyzing α-Gal-(1 → 6)-Gal linkages in RFOs. BF0224 efficiently distinguished classical from non-classical RFOs by identifying the resulting hydrolyzed oligo- and mono-saccharides with HPAEC-PAD-MS. Using this strategy, we identified a non-classical RFO from Pseudostellaria heterophylla (Miquel) Pax with DP6 (termed PHO-6), as well as a classical RFO from Lycopus lucidus Turcz. with DP7 (termed LTO-7). To characterize these RFO structures, we employed four other commercial or reported α-galactosidases in combination with NMR and methylation analysis. Using this approach, we elucidated the accurate chemical structure of PHO-6 and LTO-7. Our study provides an efficient analytical approach to structurally analyze RFOs. This enzyme-based strategy also can be applied to structural analysis of other glycans.

Three different crystal morphologies of α-Fe2O3, including uniform hexagonal, square, and rhombic shapes, were prepared according to the aqueous-thermal reaction. The hexagonal-shaped α-Fe2O3 was enclosed by the 104 plane, while the square and rhombic structures were enclosed by the 110 plane. Two absorption peaks at 455 and 532 cm-1 were found for the perpendicular (⊥) modes, and one absorption peak at 650 cm-1 appeared for the parallel (||) mode for hexagon-shaped α-Fe2O3 during analysis by Fourier-transform infrared spectroscopy. However, the peaks of square- and rhombic-shaped α-Fe2O3 for perpendicular (⊥) mode blueshifted, and the former two peaks merged together forming a broad band at approximately 480 cm-1. For Raman spectra determination, the peaks arose from the Brillouin zone center, and two additional peaks were observed at 660 and 1320 cm-1, belonging to 1 longitudinal optical (1LO) and 2 longitudinal optical (2LO) modes. All three materials exhibited higher intensities when excited at a wavelength of 633 cm-1. Furthermore, in the polarization state, the centers of all peak positions slightly shifted for hexagon-shaped α-Fe2O3, but all peak positions for square-shaped and rhombic-shaped α-Fe2O3 exhibited a significant blueshift. The structure of hexagon-shaped α-Fe2O3 was relatively tolerant regarding the polarization properties of vibration modes; however, the symmetry of crystal square-shaped and rhombic-shaped α-Fe2O3 changed, subsequently revealing different optical properties. RESEARCH HIGHLIGHTS: The hexagon-shaped, square-shaped, and rhombic-shaped α-Fe2O3 enclosed by different planes were synthesized. The Fourier Transform Infrared spectrometer peaks of α-Fe2O3 depended on their hexagon, square and rhombic shapes. Compared with hexagon-shaped α-Fe2O3, the Raman peaks for square and rhombi ones significantly shifted. The hexagon-shaped α-Fe2O3 is relatively tolerant regarding the polarization properties.

In this work we developed an eco-friendly valorisation of Citrus wastes (CWs), through a solvent-assisted ultrasonication extraction technique, thus having access to a wide range of bio-active compounds and polysaccharides, extremely useful in different industrial sectors (food, cosmetics, nutraceutical). Water-based low-amplitude ultrasonication was examined as a potential method for pectin extraction as well as polar and non-polar citrus extractives (CEs), among which hesperidin and triglycerides of 18 carbon fatty acids were found to be the most representative ones. In addition, citric acid:glycerol (1:4)-based deep eutectic solvent (DES) in combination with ultrasonic extraction was utilized to extract microcellulose (CMC), from which stable cellulose nanocrystals (CNCs) with glycerol-assisted high amplitude ultrasonication were obtained. The physical and chemical properties of the extracted polysaccharides (pectin, micro and nanocellulose) were analysed through DLS, ζ-potential, XRD, HP-SEC, SEM, AFM, TGA-DSC, FTIR, NMR, and PMP-HPLC analyses. The putative structure of the extracted citrus pectin (CP) was analysed and elucidated through enzyme-assisted hydrolysis in correlation with ESI-MS and monosaccharide composition. The developed extraction methods are expected to influence the industrial process for the valorisation of CWs and implement the circular bio-economy.

Gram-positive bacteria, including lactic acid bacteria (LAB), possess lipoteichoic acid (LTA) on the cell surface. LTA is an amphiphilic molecule typically composed of hydrophilic glycerolphosphate polymer and hydrophobic anchor glycolipid moieties. It is involved in physiological properties of the cell surface and also plays roles in interactions with the host. Appropriate preparation procedures, such as extraction and purification, are required to clarify the structure-activity relationship. Structural diversity of LTA has been reported at the bacterial species and strain levels, and structural differences might affect interactions with the host. This chapter introduces techniques for preparation and structural analysis of LTA derived from LAB. It consists of four sections, covering butanol extraction, hydrophobic interaction chromatography, immunoblotting, and structural analysis. Technical notes containing supplemental information about the individual steps are also provided.

Phellinus igniarius is a commonly used Chinese medicine fungus, and its polysaccharide is a valuable bioactive with antioxidant, antiaging, antitumor activities, etc. However, their bioactivities are influenced by their structural and physicochemical properties. Hence, this research isolated and purified homogeneous water-soluble intracellular polysaccharide (IPSW-1) from P. igniarius mycelia. A coherent study of its structural characteristics, conformation, and antitumor mechanisms was evaluated. The results showed IPSW-1 has no triple helical conformation according to the Congo red test. Based on FT-IR, periodate oxidation, Smith degradation, methylation analysis, 1H and 13C NMR spectroscopy data, and IPSW-1 consisted of α-d-glucopyranose (Glcp). The backbone of IPSW-1 consisted primarily of repeating three (1 → 6)-linked α-d-Glcp and one (1 → 3,4)-linked α-d-Glcp, with one terminal α-d-Glcp as side chains of 3-O-connected to the main chain for every four residues. The IPSW-1 had an inhibitory influence on HepG2 cell proliferation and inhibited the migration and invasion ability by down-regulating the expression levels of MMP-7 and RhoA. Moreover, IPSW-1 could inhibit the lysis of autophagosomes to inhibit autophagy and regulate mitochondrial membrane potential and pro-apoptotic protein Bax, which causes the caspase cascade to promote apoptosis, thereby inhibiting the role of tumor cells. These findings show IPSW-1 holds potential as an innovative functional food.

The precursor nanoparticles of nickel hydroxide (Ni(OH)2) and nickel oxide (NiO) were successfully converted into the latter by the reaction of nickel chloride with hydrazine at ambient temperature. (TGA) and (DSC) were adapted for annealing the precursor products at different annealing temperatures (210, 285, 350, 390, 425, and 450 °C). XRD, TEM, and UV-VIS absorption spectroscopy were used to characterize the products. Both the band edge and energy gap values decrease with increasing annealing temperatures. Hysteresis loops are visible in the M-H curves of annealed (350 °C and 390 °C) precursor NiO NPs, indicating the presence of ferromagnetic Ni domains. However, NiO nanoparticles annealed at higher temperatures (425 °C and 450 °C) had a straight M-H curve, indicating paramagnetic properties. NiO NPs were used to study photocatalysis in the degradation of the MB dye. As annealing temperatures increased, the catalyst caused the degradation of MB. The sample that was annealed at 450 °C, however, exhibits the maximum photocatalytic activity, reaching up to 72.4% after being exposed to visible light. In other words, it was discovered that as the catalyst\'s annealing temperature rose, so did the rate of MB\'s photocatalytic degradation.

Single-atom catalysts (SACs) have attracted extensive attention due to their unique catalytic properties and wide range of applications. Advanced characterization techniques, such as energy-dispersive X-ray spectroscopy, X-ray photoelectron spectroscopy, transmission electron microscopy, scanning electron microscopy, and X-ray absorption fine-structure spectroscopy, have been used to investigate the elemental compositions, structural morphologies, and chemical bonding states of SACs in detail, aiming at unraveling the catalytic mechanism. Meanwhile, theoretical calculations, such as quantum chemical calculations and kinetic simulations, were used to predict the catalytic reaction pathways, active sites, and reaction kinetic behaviors of SACs, providing theoretical guidance for the design and optimization of SACs. This review overviews advanced characterization techniques and theoretical calculations for SACs in Fenton-like chemistry. Moreover, this work highlights the importance of advanced characterization techniques and theoretical calculations in the study of SACs and provides perspectives on the potential applications of SACs in the field of environmental remediation and the challenges of practical engineering.

Beta turns, in which the protein backbone abruptly changes direction over four amino acid residues, are the most common type of protein secondary structure after alpha helices and beta sheets and play key structural and functional roles. Previous work has produced classification systems for turn geometry at multiple levels of precision, but these operate in backbone dihedral-angle (Ramachandran) space, and the absence of a local Euclidean-space coordinate system and structural alignment for turns, or of any systematic Euclidean-space characterization of turn backbone shape, presents challenges for the visualization, comparison and analysis of the wide range of turn conformations and the design of turns and the structures that incorporate them. This work derives a turn-local coordinate system that implicitly aligns turns, together with a set of geometric descriptors that characterize the bulk BB shapes of turns and describe modes of structural variation not explicitly captured by existing systems. These modes are shown to be meaningful by the demonstration of clear relationships between descriptor values and the electrostatic energy of the beta-turn H-bond, the overrepresentations of key side-chain motifs, and the structural contexts of turns. Geometric turn descriptors complement Ramachandran-space classifications, and they can be used to select turn structures for compatibility with particular side-chain interactions or contexts. Potential applications include protein design and other tasks in which an enhanced Euclidean-space characterization of turns may improve understanding or performance. The web-based tools ExploreTurns, MapTurns, and ProfileTurn, available at www.betaturn.com, incorporate turn-local coordinates and turn descriptors and demonstrate their utility.

Glycosaminoglycans (GAGs) are sulfated linear O-glycan chains abundantly expressed in the extracellular matrix (ECM). Among GAGs, chondroitin sulfate (CS) and dermatan sulfate (DS) play important roles at the brain level, where the distribution and location of the sulfates within the CS/DS chains are responsible for numerous biological events. The diversity of the neural hybrid CS/DS expressed in the brain and the need to elucidate their structure gave rise to considerable efforts toward the development of analytical methods able to discover novel regularly and irregularly sulfated domains. In this context, we report here the introduction of ion mobility separation (IMS) mass spectrometry (MS) in brain glycosaminoglycomics. Based on IMS MS and tandem MS (MS/MS) by collision-induced dissociation (CID), we have developed a powerful approach for the screening and structural analysis of neural CS/DS and optimized and validated the method for the structural analysis of octasaccharides that were released from brain proteoglycans by β-elimination and pooled after chain depolymerization using chondroitin AC lyase. The IMS MS data revealed the separation of CS/DS octamers into mobility families based on the amount of sulfation. Among the discovered oversulfated domains, of major biological importance is the pentasulfated-[4,5-Δ-GlcAGalNAc(IdoAGalNAc)3], for which the (-) nanoESI IMS CID MS/MS analysis disclosed through the presence of distinct drift times, the incidence of two isomers. Moreover, the generated fragment ions revealed an uncommon trisulfated motif and an uncommon pentasulfated motif. Hence, using IMS MS and CID MS/MS, novel brain-related CS/DS domains of atypical sulfation patterns were discovered and structurally characterized in detail.