Potent Henipavirus Neutralization by Antibodies Recognizing Diverse Sites on Hendra and Nipah Virus Receptor Binding Protein.

Hendra (HeV) and Nipah (NiV) viruses are emerging zoonotic pathogens in the Henipavirus genus causing outbreaks of disease with very high case fatality rates. Here, we report the first naturally occurring human monoclonal antibodies (mAbs) against HeV receptor binding protein (RBP). All isolated mAbs neutralized HeV, and some also neutralized NiV. Epitope binning experiments identified five major antigenic sites on HeV-RBP. Animal studies demonstrated that the most potent cross-reactive neutralizing mAbs, HENV-26 and HENV-32, protected ferrets in lethal models of infection with NiV Bangladesh 3 days after exposure. We solved the crystal structures of mAb HENV-26 in complex with both HeV-RBP and NiV-RBP and of mAb HENV-32 in complex with HeV-RBP. The studies reveal diverse sites of vulnerability on RBP recognized by potent human mAbs that inhibit virus by multiple mechanisms. These studies identify promising prophylactic antibodies and define protective epitopes that can be used in rational vaccine design.

Structural Titration of Slo2.2, a Na+-Dependent K+ Channel.

The stable structural conformations that occur along the complete reaction coordinate for ion channel opening have never been observed. In this study, we describe the equilibrium ensemble of structures of Slo2.2, a neuronal Na+-activated K+ channel, as a function of the Na+ concentration. We find that Slo2.2 exists in multiple closed conformations whose relative occupancies are independent of Na+ concentration. An open conformation emerges from an ensemble of closed conformations in a highly Na+-dependent manner, without evidence of Na+-dependent intermediates. In other words, channel opening is a highly concerted, switch-like process. The midpoint of the structural titration matches that of the functional titration. A maximum open conformation probability approaching 1.0 and maximum functional open probability approaching 0.7 imply that, within the class of open channels, there is a subclass that is not permeable to ions.

Elucidating the role of water in collagen self-assembly by isotopically modulating collagen hydration.

Water is known to play an important role in collagen self-assembly, but it is still largely unclear how water-collagen interactions influence the assembly process and determine the fibril network properties. Here, we use the H[Formula: see text]O/D[Formula: see text]O isotope effect on the hydrogen-bond strength in water to investigate the role of hydration in collagen self-assembly. We dissolve collagen in H[Formula: see text]O and D[Formula: see text]O and compare the growth kinetics and the structure of the collagen assemblies formed in these water isotopomers. Surprisingly, collagen assembly occurs ten times faster in D[Formula: see text]O than in H[Formula: see text]O, and collagen in D[Formula: see text]O self-assembles into much thinner fibrils, that form a more inhomogeneous and softer network, with a fourfold reduction in elastic modulus when compared to H[Formula: see text]O. Combining spectroscopic measurements with atomistic simulations, we show that collagen in D[Formula: see text]O is less hydrated than in H[Formula: see text]O. This partial dehydration lowers the enthalpic penalty for water removal and reorganization at the collagen-water interface, increasing the self-assembly rate and the number of nucleation centers, leading to thinner fibrils and a softer network. Coarse-grained simulations show that the acceleration in the initial nucleation rate can be reproduced by the enhancement of electrostatic interactions. These results show that water acts as a mediator between collagen monomers, by modulating their interactions so as to optimize the assembly process and, thus, the final network properties. We believe that isotopically modulating the hydration of proteins can be a valuable method to investigate the role of water in protein structural dynamics and protein self-assembly.

MS-BACL: enhancing metabolic stability prediction through bond graph augmentation and contrastive learning.

MOTIVATION: Accurately predicting molecular metabolic stability is of great significance to drug research and development, ensuring drug safety and effectiveness. Existing deep learning methods, especially graph neural networks, can reveal the molecular structure of drugs and thus efficiently predict the metabolic stability of molecules. However, most of these methods focus on the message passing between adjacent atoms in the molecular graph, ignoring the relationship between bonds. This makes it difficult for these methods to estimate accurate molecular representations, thereby being limited in molecular metabolic stability prediction tasks. RESULTS: We propose the MS-BACL model based on bond graph augmentation technology and contrastive learning strategy, which can efficiently and reliably predict the metabolic stability of molecules. To our knowledge, this is the first time that bond-to-bond relationships in molecular graph structures have been considered in the task of metabolic stability prediction. We build a bond graph based on 'atom-bond-atom', and the model can simultaneously capture the information of atoms and bonds during the message propagation process. This enhances the model's ability to reveal the internal structure of the molecule, thereby improving the structural representation of the molecule. Furthermore, we perform contrastive learning training based on the molecular graph and its bond graph to learn the final molecular representation. Multiple sets of experimental results on public datasets show that the proposed MS-BACL model outperforms the state-of-the-art model. AVAILABILITY AND IMPLEMENTATION: The code and data are publicly available at https://github.com/taowang11/MS.

Art and Science of the Cellular Mesoscale.

Experimental information from microscopy, structural biology, and bioinformatics may be integrated to build structural models of entire cells with molecular detail. This integrative modeling is challenging in several ways: the intrinsic complexity of biology results in models with many closely packed and heterogeneous components; the wealth of available experimental data is scattered among multiple resources and must be gathered, reconciled, and curated; and computational infrastructure is only now gaining the capability of modeling and visualizing systems of this complexity. We present recent efforts to address these challenges, both with artistic approaches to depicting the cellular mesoscale, and development and application of methods to build quantitative models.

Molecular Structure Engineering of Isomeric Additives for Long Lifetime Zn Anodes.

Modulating the solvation structure of hydrated zinc ions using organic additives stands as a pragmatic approach to suppress dendrite formation and corrosion on zinc metal anodes (ZMAs), thereby enhancing the rechargeability of aqueous Zn-ion batteries. However, fundamental screening principles for organic additives with diverse molecular structures remain elusive, especially for isomers with the same molecular formula. This study delves into the impact of three isomeric hexagonal alcohols (mannitol, sorbitol, and galactitol) as additives in adjusting Zn2+ solvation structural behaviors within ZnSO4 baseline electrolytes. Electrical measurements and molecular simulations reveal the specific molecular structure of mannitol, which features interweaving electron clouds between adjacent hydroxyl groups, achieving a high local electron cloud density. This phenomenon significantly enhances desolvation abilities, thus establishing a more stable anode/electrolyte interface chemistry. Even at 5 mA cm-2 for 2.5 mAh cm-2 capacity, Zn||Zn symmetric cells with mannitol-regulated electrolyte display an impressive 1170 h lifespan, far exceeding those with other isomer additives and is nearly tenfold longer than that with a pure ZnSO4 electrolyte (120 h). Rather than strictly adhering to focusing on chemical composition, this study with emphasis on optimizing molecular structure offers a promising untapped dimension to screen more efficient additives to enhance the reversibility of ZMAs.

Grouping approaches based on structure alone are insufficient to conclude about toxicological properties-the example of monoamine-based chelates.

Aminocarboxylic acid (monoamine-based) chelating agents such as GLDA, MGDA, NTA, and EDG are widely used in a variety of products and processes. In the European Union, based on the Green Deal and the Chemicals Strategy for Sustainability (CSS), there is an increasing tendency to speed up chemical hazard evaluation and to regulate chemicals by grouping substances based on molecular structure similarity. Recently, it was proposed to group polycarboxylic acid monoamines, hydroxy derivatives and their salts with monovalent cations, and to consider all group members as potential carcinogens based on the official CLP classification of one group member, viz. NTA, which is classified as suspected carcinogen Cat. 2. In this review, we show that a grouping approach for harmonized classification and labeling based on molecular structure alone, disregarding existing animal test data as well as current scientific and regulatory knowledge, would result in incorrect classification. Using such a simplistic, although considered pragmatic approach, classification of all group members upfront would not improve protection of human health. Instead, it could not only lead to unnecessary additional vertebrate animal testing but also to onerous and disproportionate restrictions being placed on the use of these valuable substances; some of these even being considered as green chemicals.

Hydrochar and Its Dissolved Organic Matter Aged in a 30-Month Rice-Wheat Rotation System: Do Primary Aging Factors Alter at Different Stages?

Hydrochar, recognized as a green and sustainable soil amendment, has garnered significant attention. However, information on the aging process in soil and the temporal variability of hydrochar remains limited. This study delves deeper into the interaction between hydrochar and soil, focusing on primary factors influencing hydrochar aging during a 30-month rice-wheat rotation system. The results showed that the initial aging of hydrochar (0-16 months) is accompanied by the development of specific surface area and leaching of hydrochar-derived dissolved organic matter (HDOM), resulting in a smaller particle size and reduced carbon content. The initial aging also features a mineral shield, while the later aging (16 to 30 months) involves surface oxidation. These processes collectively alter the surface charge, hydrophilicity, and composition of aged hydrochar. Furthermore, this study reveals a dynamic interaction between the HDOM and DOM derived from soil, plants, and microbes at different aging stages. Initially, there is a preference for decomposing labile carbon, whereas later stages involve the formation of components with higher aromaticity and molecular weight. These insights are crucial for understanding the soil aging effects on hydrochar and HDOM as well as evaluating the interfacial behavior of hydrochar as a sustainable soil amendment.

Advanced tools for molecular characterization of bio-based and biodegradable polymers.

Bio-based and biodegradable materials play a vital role in a sustainable and green economy. These materials must exhibit properties that are similar to or better than the properties of oil- or coal-based materials and require sophisticated synthesis technologies and detailed knowledge of structure-property correlations. For comprehensive molecular structure elucidation, advanced analytical methods, including coupled and hyphenated techniques that combine advanced fractionation and information-rich spectroscopic detectors, are an indispensable tool. One important tool for fractionating complex polymers regarding molecular size is size exclusion chromatography. For fractionating polymers with regard to chemical composition, solvent (or temperature) gradient HPLC has been developed. The combination of different liquid chromatography methods in comprehensive two-dimensional HPLC setups is another important tool. Today, a toolbox of HPLC methods is in place that enables the fractionation of complex bio-based and biodegradable polymers according to the most important molecular parameters including molecular size, composition, functionality, and branching. Here, an overview of the different techniques and some major applications is presented. Some representative developments in the field are discussed, and different techniques, experimental protocols, and applications are highlighted.

Discovery of internal rotation and conformers of 1,2-dichloroethane: the dawn of the concept of conformation.

In 1932, Mizushima and Higasi reported the dependence of the dipole moments of 1,2-dichloroethane on both temperature and solvent in the Proceedings of the Imperial Academy, Japan. This report was followed by their first proposal of the existence of conformers that exchanged by internal rotation about a C-C single bond based on experimental data. Their monumental work marked the beginning of the essential concept of conformation in modern stereochemistry. Their proposal was later confirmed by the direct observation of the anti and gauche conformers of 1,2-dichloroethane by Raman spectroscopy, and further supported by other experimental and theoretical methods. The relative stabilities of the anti and gauche conformers of 1,2-dichloroethane and other 1,2-disubstituted ethanes were discussed in terms of steric, electrostatic, and stereoelectronic effects based on analysis of calculated data. Those studies influenced the development of subsequent research in organic chemistry, such as the conformational analysis of cyclohexane derivatives and the isolation of chiral gauche conformers.

Molecular Structure of Salicylic Acid and Its Hydrates: A Rotational Spectroscopy Study.

We present a study of salicylic acid and its hydrates, with up to four water molecules, done by employing chirped-pulse Fourier transform microwave spectroscopy. We employed the spectral data set of the parent, 13C, and 2H isotopologues to determine the molecular structure and characterize the intra- and intermolecular interactions of salicylic acid and its monohydrate. Complementary theoretical calculations were done to support the analysis of the experimental results. For the monomer, we analyzed structural properties, such as the angular-group-induced bond alternation (AGIBA) effect. In the microsolvates, we analyzed their main structural features dominated by the interaction of water with the carboxylic acid group. This work contributes to seeding information on how water molecules accumulate around this group. Moreover, we discussed the role of cooperative effects further stabilizing the observed inter- and intramolecular hydrogen bond interactions.

Calculation of DC Stark Resonances for the Ammonia Molecule.

A model potential previously developed for the ammonia molecule is treated in a single-center partial-wave approximation in analogy with a self-consistent field method developed by Moccia. The latter was used in a number of collision studies. The model potential is used to calculate DC Stark resonance parameters, i.e., resonance positions and shifts using the exterior complex scaling method for the radial coordinate. Three molecular valence orbitals are investigated for fields along the three Cartesian coordinates, i.e., along the molecular axis and in two perpendicular directions. The work extends previous work on the planar-geometry water molecule for which non-monotonic shifts were observed. We find such non-monotonic shifts for fields along the molecular axis. For perpendicular fields, we report the splitting of the 1e orbitals into a fast- and a slow-ionizing orbital.

Internal Factors Affecting the Crystallization of the Lipid System: Triacylglycerol Structure, Composition, and Minor Components.

The process of lipid crystallization influences the characteristics of lipid. By changing the chemical composition of the lipid system, the crystallization behavior could be controlled. This review elucidates the internal factors affecting lipid crystallization, including triacylglycerol (TAG) structure, TAG composition, and minor components. The influence of these factors on the TAG crystal polymorphic form, nanostructure, microstructure, and physical properties is discussed. The interplay of these factors collectively influences crystallization across various scales. Variations in fatty acid chain length, double bonds, and branching, along with their arrangement on the glycerol backbone, dictate molecular interactions within and between TAG molecules. High-melting-point TAG dominates crystallization, while liquid oil hinders the process but facilitates polymorphic transitions. Unique molecular interactions arise from specific TAG combinations, yielding molecular compounds with distinctive properties. Nanoscale crystallization is significantly impacted by liquid oil and minor components. The interaction between the TAG and minor components determines the influence of minor components on the crystallization process. In addition, future perspectives on better design and control of lipid crystallization are also presented.

Targeted Stimulation of Micropores by CS2 Extraction on Molecular of Coal.

The targeted stimulation of micropores based on the transformation of coal's molecular structure is proposed due to the chemical properties and difficult-to-transform properties of micropores. Carbon disulfide (CS2) extraction is used as a targeted stimulation to reveal the internal evolution mechanism of micropore transformation. The variations of microcrystalline structures and micropores of bituminous coal and anthracite extracted by CS2 were analyzed with X-ray diffraction (XRD), low-temperature carbon dioxide (CO2) adsorption, and molecular simulation. The results show that CS2 extraction, with the broken chain effect, swelling effect, and aromatic ring rearrangement effect, can promote micropore generation of bituminous coal by transforming the microcrystalline structure. Furthermore, CS2 extraction on bituminous coal can decrease the average micropore size and increase the micropore volume and area. The aromatic layer fragmentation effect of CS2 extraction on anthracite, compared to the micropore generation effect of the broken chain effect and swelling effect, can enlarge micropores more remarkably, as it induces an enhancement in the average micropore size and a decline in the micropore volume and area. The research is expected to provide a theoretical basis for establishing reservoir stimulation technology based on CS2 extraction.

Investigation on Combustion Characteristics and Molecular Structures of Heiyanquan Mining Area, Xinjiang, China.

In order to comprehend the molecular composition of coal and better understand the process of coal combustion, this study involved the development of a molecular structure model for Heiyanquan coal in Xinjiang, as well as the optimization and annealing dynamics simulation of the model. Thermogravimetric analysis (TG), Fourier transform infrared spectroscopy (FTIR), and high-resolution transmission electron microscopy (HRTEM) were utilized to investigate the spontaneous combustion characteristics of coal at different temperatures (room temperature, 50-500 °C with 50 °C interval). The findings revealed that the coal primarily consists of aromatic carbon, with the aromatic structure mainly comprising naphthalene, anthracene, and phenanthrene, and the aliphatic carbon mainly consisting of CH2 and CH, along with a small quantity of minerals. The empirical molecular formula of Heiyanquan coal was determined to be C175H125O21N3. After the optimization, the total energy of the model was significantly reduced, and the aromatic layers tended to align in a regular parallel manner, with van der Waals energy playing a crucial role in maintaining structural stability. As the temperature increased, the activation energy of the three stages also increased, with the combustion stage exhibiting the highest activation energy. The presence of hydroxyl groups and oxygen-containing functional groups was found to mainly participate in the reaction, while the content of aromatic hydrocarbons remained relatively stable, C=C exhibited a decreasing trend, and C-O displayed an increasing trend. Moreover, it was observed that 1 × 1 and 2 × 2 were the predominant aromatic stripes in the coal samples, accounting for more than 90% of the total stripes.

Coordination Polymer Based on a Triangular Carboxylate Core {Fe(µ3-O)(µ-O2CR)6} and an Aliphatic Diamine.

Interaction of the pre-organized complex of iron(II) trimethylacetate and 1,10-phenanthroline (phen) [Fe2(piv)4(phen)2] (1) (piv = (Me)3CCO2-)) with 1,6-diaminohexane (dahx) in anhydrous acetonitrile yielded a 1D coordination polymer [Fe3O(piv)6(dahx)1.5]n (2) and an organic salt of pivalic acid (H2dahx)(piv)2 (3). The structure of the obtained compounds was determined by single-crystal X-ray diffraction analysis. The phase purity of the complexes was determined by powder X-ray diffraction analysis. According to the single-crystal X-ray analysis, coordination polymer 2 is formed due to the binding of a triangular carboxylate core {Fe3(µ3-O)(µ-piv)6} with an aliphatic diamine ligand. Thermal behavior was investigated for compounds 1 and 2 in an argon atmosphere.

Synthesis, Characterization, X-ray Molecular Structure, Antioxidant, Antifungal, and Allelopathic Activity of a New Isonicotinate-Derived meso-Tetraarylporphyrin.

The present article describes the synthesis of an isonicotinate-derived meso-arylporphyrin, that has been fully characterized by spectroscopic methods (including fluorescence spectroscopy), as well as elemental analysis and HR-MS. The structure of an n-hexane monosolvate has been determined by single-crystal X-ray diffraction analysis. The radical scavenging activity of this new porphyrin against the 2,2-diphenyl-1-picrylhydrazyl (DPPH) radical has been measured. Its antifungal activity against three yeast strains (C. albicans ATCC 90028, C. glabrata ATCC 64677, and C. tropicalis ATCC 64677) has been tested using the disk diffusion and microdilution methods. Whereas the measured antioxidant activity was low, the porphyrin showed moderate but encouraging antifungal activity. Finally, a study of its effect on the germination of lentil seeds revealed interesting allelopathic properties.

Organic Synthesis and Current Understanding of the Mechanisms of CFTR Modulator Drugs Ivacaftor, Tezacaftor, and Elexacaftor.

The monogenic rare disease Cystic Fibrosis (CF) is caused by mutations in the gene encoding the CF transmembrane conductance (CFTR) protein, an anion channel expressed at the apical plasma membrane of epithelial cells. The discovery and subsequent development of CFTR modulators-small molecules acting on the basic molecular defect in CF-have revolutionized the standard of care for people with CF (PwCF), thus drastically improving their clinical features, prognosis, and quality of life. Currently, four of these drugs are approved for clinical use: potentiator ivacaftor (VX-770) alone or in combination with correctors lumacaftor, (VX-809), tezacaftor (VX-661), and elexacaftor (VX-445). Noteworthily, the triple combinatorial therapy composed of ivacaftor, tezacaftor, and elexacaftor constitutes the most effective modulator therapy nowadays for the majority of PwCF. In this review, we exploit the organic synthesis of ivacaftor, tezacaftor, and elexacaftor by providing a retrosynthetic drug analysis for these CFTR modulators. Furthermore, we describe the current understanding of the mechanisms of action (MoA's) of these compounds by discussing several studies that report the key findings on the molecular mechanisms underlying their action on the CFTR protein.

Structural and rheological characterization of water-soluble and alkaline-soluble fibers from hulless barley.

BACKGROUND: Highland hulless barley has garnered attention as a promising economic product and a potential healthy food ingredient. The present study aimed to comprehensively investigate the molecular structure of extractable fibers obtained from a specific highland hulless barley. Water-soluble fiber (WSF) and alkaline-soluble fiber (ASF) were extracted using enzymatic digestion and an alkaline method, respectively. The purified fibers underwent a thorough investigation for their structural characterization. RESULTS: The monosaccharide composition revealed that WSF primarily consisted of glucose (91.7%), whereas ASF was composed of arabinose (54.5%) and xylose (45.5%), indicating the presence of an arabinoxylan molecule with an A/X ratio of 1.2. The refined structural information was further confirmed through methylation, 1 H NMR and Fourier-transform infrared spectroscopy analyses. WSF fiber exclusively exhibited α-anomeric patterns, suggesting it was an α-glucan. It has a low molecular weight of 5 kDa, as determined by gel permeation chromatography. Conversely, ASF was identified as a heavily branched arabinoxylan with 41.55% of '→2,3,4)-Xylp-(1→' linkages. ASF and WSF exhibited notable differences in their morphology, water absorption capabilities and rheological properties. CONCLUSION: Based on these findings, molecular models of WSF and ASF were proposed. The deep characterization of these fiber structures provides valuable insights into their physicochemical and functional properties, thereby unlocking their potential applications in the food industry. © 2023 Society of Chemical Industry.

Cereal type and conditioning temperature altered protein and carbohydrate molecular structure, nutrient retention and performance in broilers fed pellet diets during starter and grower period.

1. Effects of cereal type and conditioning temperature (CT) on protein and carbohydrate (CHO) molecular structures, nutrient retention, carcass and blood characteristics, caecal microbial population and growth criteria of broilers fed pellet diet were evaluated for a total period of 35 d.2. In total, 336-day-old Cobb 500 broiler chicks were randomly allotted into a 2 × 2 factorial arrangement with two different cereal types (maize or wheat) processed in two different temperatures (CT; 68°C or 90°C) with seven pen replicates containing 12 birds each.3. Chicks fed the maize-based diets significantly gained higher body weight (BW) and lower feed conversion ratio (FCR) in comparison to the chicks fed wheat-based diets during the whole grow-out period (p < 0.01). Overall, the highest BW and feed intake (FI) were seen in birds fed wheat-based diets conditioned at 68°C, but the lowest FCR was observed in maize-based diet conditioned at 90°C at 7, 14 and 21 d of age (p < 0.01). However, BW was higher and FCR lower in chicks fed maize-based diets conditioned at 90°C in the grower period (28 and 35 d; p < 0.01).4. The α-helix height was higher in wheat-based starter diets in comparison to the maize-based diet (p < 0.01). Ratio of amide I to II area and total CHO peak height were increased when diets were processed at 90°C in both maize and wheat-based starter diet (p < 0.05). Increasing the CT from 68°C to 90°C reduced CHO peak 1 and 2 height by 11.6% and 3.95%, respectively, in maize-based starter diets, while increasing the CT from 68°C to 90°C reduced CHO peak 1 and 2 height by 54.3% and 57.2%, respectively, in wheat-based starter diets. In the grower diets, increasing the CT from 68°C to 90°C increased CHO peak 1 by 23% in maize-based diets, but reduced CHO peak 1 by 24.5% in wheat-based diets.5. Calcium and phosphorous retention were highest in chicks fed wheat-based diets conditioned at 90°C and lowest in chicks fed maize-based diets conditioned at 90°C (p < 0.01). Salmonella, E. coli and coliforms in the caeca reduced significantly (p < 0.05) in chicks fed wheat-based diets conditioned at 90°C on d 11 and increased with the same diet at 35 d of age compared to the chicks fed maize-based diets conditioned at both 68°C and 90°C or wheat-based diets conditioned at 68°C.6. Conditioning the wheat-based diets at 68°C improved production responses without causing any adverse effects on protein and CHO molecular structures, however increasing the conditioning temperature to 90°C impaired performance due to alteration of protein and CHO molecular structures. In contrast, conditioning of the maize-based diets at 90°C had the opposite effect, and improved production performance compared to diets conditioned at 68°C.