Hydrogen-Deuterium Exchange Epitope Mapping Reveals Distinct Neutralizing Mechanisms for Two Monoclonal Antibodies against Diphtheria Toxin.

The diphtheria toxoid (DT) antigen is one of the major components in pediatric and booster combination vaccines and is known to raise a protective humoral immune response upon vaccination. However, a structurally resolved analysis of diphtheria toxin (DTx) epitopes with underlying molecular mechanisms of antibody neutralization has not yet been reported. Using hydrogen-deuterium exchange mass spectrometry (HDX-MS) and Biolayer Interferometry (BLI) assays, we have characterized two neutralizing anti-DTx monoclonal antibodies (mAbs), 2-25 and 2-18, by identifying the specific epitopes on the diphtheria toxin responsible for antibody binding. Our results show that both epitopes are conformational, and mechanistically distinct. Monoclonal antibody 2-25 binds selectively to the B-subunit (translocation and receptor domain) of DTx, blocking the heparin-binding EGF-like growth factor (HBEGF) binding site. In contrast, mAb 2-18 binds to the A-subunit (catalytic domain), partially covering the catalytic loop region that shuttles NAD during catalysis. The results are discussed in the context of antigen neutralization mechanisms and can ultimately help to reveal the underlying factors that contribute to Diptheria vaccine efficacy.

Identification of Soybean Seed Varieties Based on Hyperspectral Imaging Technology.

Hyperspectral imaging is a nondestructive testing technology that integrates spectroscopy and iconology technologies, which enables us to quickly obtain both internal and external information of objects and identify crop seed varieties. First, the hyperspectral images of ten soybean seed varieties were collected and the reflectance was obtained. Savitzky-Golay smoothing (SG), first derivative (FD), standard normal variate (SNV), fast Fourier transform (FFT), Hilbert transform (HT), and multiplicative scatter correction (MSC) spectral reflectance pretreatment methods were used. Then, the feature wavelengths and feature information of the pretreated spectral reflectance data were extracted using competitive adaptive reweighted sampling (CARS), the successive projections algorithm (SPA), and principal component analysis (PCA). Finally, 5 classifiers, Bayes, support vector machine (SVM), k-nearest neighbor (KNN), ensemble learning (EL), and artificial neural network (ANN), were used to identify seed varieties. The results showed that MSC-CARS-EL had the highest accuracy among the 90 combinations, with training set, test set, and 5-fold cross-validation accuracies of 100%, 100%, and 99.8%, respectively. Moreover, the contribution of spectral pretreatment to discrimination accuracy was higher than those of feature extraction and classifier selection. Pretreatment methods determined the range of the identification accuracy, feature-selective methods and classifiers only changed within this range. The experimental results provide a good reference for the identification of other crop seed varieties.

A Rapid and Highly Efficient Method for the Identification of Soybean Seed Varieties: Hyperspectral Images Combined with Transfer Learning.

Convolutional neural network (CNN) can be used to quickly identify crop seed varieties. 1200 seeds of ten soybean varieties were selected, hyperspectral images of both the front and the back of the seeds were collected, and the reflectance of soybean was derived from the hyperspectral images. A total of 9600 images were obtained after data augmentation, and the images were divided into a training set, validation set, and test set with a 3:1:1 ratio. Pretrained models (AlexNet, ResNet18, Xception, InceptionV3, DenseNet201, and NASNetLarge) after fine-tuning were used for transfer training. The optimal CNN model for soybean seed variety identification was selected. Furthermore, the traditional machine learning models for soybean seed variety identification were established by using reflectance as input. The results show that the six models all achieved 91% accuracy in the validation set and achieved accuracy values of 90.6%, 94.5%, 95.4%, 95.6%, 96.8%, and 97.2%, respectively, in the test set. This method is better than the identification of soybean seed varieties based on hyperspectral reflectance. The experimental results support a novel method for identifying soybean seeds rapidly and accurately, and this method also provides a good reference for the identification of other crop seeds.

Constructing Universal Ionic Sieves via Alignment of Two-Dimensional Covalent Organic Frameworks (COFs).

The shuttle effect of electrode materials always leads to capacity loss and poor cycle life of batteries. Two-dimensional (2D) covalent organic frameworks (COFs) with uniform and controllable nanopores provide a promising strategy for fabricating ionic sieves to inhibit the shuttle effect. However, the insoluble nature of COFs made it difficult to fabricate compact and ordered membranes of COFs. Herein, we report a novel method for facilely anisotropic ordering of 2D COFs via depositing COFs onto graphene. The resulted double-layer membranes acting as ionic sieves impressively inhibit the shuttle effect and exhibit versatility to both organic sodium-ion batteries and Li-S batteries, leading to high cyclability.

Enhanced Binding Affinity via Destabilization of the Unbound State: A Millisecond Hydrogen-Deuterium Exchange Study of the Interaction between p53 and a Pleckstrin Homology Domain.

The incorporation of intrinsically disordered domains enables proteins to engage a wide variety of targets, with phosphorylation often modulating target specificity and affinity. Although phosphorylation can clearly act as a chemical driver of complexation in structured proteins, e.g., by abrogating or permitting new charge-charge interactions, the basis for enhancement of the hydrophobically driven interactions that are typical of disordered protein-target complexation is less clear. To determine how phosphorylation can positively impact target recruitment in disordered domains, we have examined the interaction between the disordered N-terminal transactivation domain (TAD) of p53 and the pleckstrin homology (PH) domain of p62. Using time-resolved electrospray ionization with hydrogen-deuterium exchange, we demonstrate that phosphorylation has little effect on the conformation of the p53 TAD when it is bound to the PH domain but instead increases the degree of conformational disorder in the unbound state. We propose that this increase in the degree of disorder creates a wider free energy gap between the free and bound states, providing a target-independent mechanism for enhanced binding when the phosphorylated and unphosphorylated p53-target complexes have similar free energies.

Conformational Dynamics and Allostery in Pyruvate Kinase.

Pyruvate kinase catalyzes the final step in glycolysis and is allosterically regulated to control flux through the pathway. Two models are proposed to explain how Escherichia coli pyruvate kinase type 1 is allosterically regulated: the "domain rotation model" suggests that both the domains within the monomer and the monomers within the tetramer reorient with respect to one another; the "rigid body reorientation model" proposes only a reorientation of the monomers within the tetramer causing rigidification of the active site. To test these hypotheses and elucidate the conformational and dynamic changes that drive allostery, we performed time-resolved electrospray ionization mass spectrometry coupled to hydrogen-deuterium exchange studies followed by mutagenic analysis to test the activation mechanism. Global exchange experiments, supported by thermostability studies, demonstrate that fructose 1,6-bisphosphate binding to the allosteric domain causes a shift toward a globally more dynamic ensemble of conformations. Mapping deuterium exchange to peptides within the enzyme highlight site-specific regions with altered conformational dynamics, many of which increase in conformational flexibility. Based upon these and mutagenic studies, we propose an allosteric mechanism whereby the binding of fructose 1,6-bisphosphate destabilizes an α-helix that bridges the allosteric and active site domains within the monomeric unit. This destabilizes the ß-strands within the (ß/α)8-barrel domain and the linked active site loops that are responsible for substrate binding. Our data are consistent with the domain rotation model but inconsistent with the rigid body reorientation model given the increased flexibility at the interdomain interface, and we can for the first time explain how fructose 1,6-bisphosphate affects the active site.

Berberine inhibits fluphenazine-induced up-regulation of CDR1 in Candida albicans.

Over-expression of the Candida drug resistance gene CDR1 is a common mechanism generating azole-resistant Candida albicans in clinical isolates. CDR1 is transcriptionally activated through the binding of the transcription factor Tac1p to the cis-acting drug-responsive element (DRE) in its promoter. We previously demonstrated that the combination of fluconazole (FLC) and berberine (BBR) produced significant synergy when used against FLC-resistant C. albicans in vitro. In this study, we found that BBR inhibited both the up-regulation of CDR1 mRNA and the transport function of Cdr1p induced by fluphenazine (FNZ). Further, electrophoretic mobility shift assays suggested that the transcription activation complex of protein-DRE was disrupted by BBR, and electrospray ionization mass spectrometry analysis showed that BBR bound to the DRE of CDR1. Thus we propose that BBR inhibits the FNZ-induced transcriptional activation of CDR1 in C. albicans by blocking transcription factor binding to the DRE of CDR1. These results contribute to our understanding of the mechanism of synergistic effect of BBR and FLC.

Structural and biochemical rationale for Beta variant protein booster vaccine broad cross-neutralization of SARS-CoV-2.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), responsible for the COVID-19 pandemic, uses a surface expressed trimeric spike glycoprotein for cell entry. This trimer is the primary target for neutralizing antibodies making it a key candidate for vaccine development. During the global pandemic circulating variants of concern (VOC) caused several waves of infection, severe disease, and death. The reduced efficacy of the ancestral trimer-based vaccines against emerging VOC led to the need for booster vaccines. Here we present a detailed characterization of the Sanofi Beta trimer, utilizing cryo-EM for structural elucidation. We investigate the conformational dynamics and stabilizing features using orthogonal SPR, SEC, nanoDSF, and HDX-MS techniques to better understand how this antigen elicits superior broad neutralizing antibodies as a variant booster vaccine. This structural analysis confirms the Beta trimer preference for canonical quaternary structure with two RBD in the up position and the reversible equilibrium between the canonical spike and open trimer conformations. Moreover, this report provides a better understanding of structural differences between spike antigens contributing to differential vaccine efficacy.

Formulation development of a stable influenza recombinant neuraminidase vaccine candidate.

Current influenza vaccines could be augmented by including recombinant neuraminidase (rNA) protein antigen to broaden protective immunity and improve efficacy. Toward this goal, we investigated formulation conditions to optimize rNA physicochemical stability. When rNA in sodium phosphate saline buffer (NaPBS) was frozen and thawed (F/T), the tetrameric structure transitioned from a "closed" to an "open" conformation, negatively impacting functional activity. Hydrogen deuterium exchange experiments identified differences in anchorage binding sites at the base of the open tetramer, offering a structural mechanistic explanation for the change in conformation and decreased functional activity. Change to the open configuration was triggered by the combined stresses of acidic pH and F/T. The desired closed conformation was preserved in a potassium phosphate buffer (KP), minimizing pH drop upon freezing and including 10% sucrose to control F/T stress. Stability was further evaluated in thermal stress studies where changes in conformation were readily detected by ELISA and size exclusion chromatography (SEC). Both tests were suitable indicators of stability and antigenicity and considered potential critical quality attributes (pCQAs). To understand longer-term stability, the pCQA profiles from thermally stressed rNA at 6 months were modeled to predict stability of at least 24-months at 5°C storage. In summary, a desired rNA closed tetramer was maintained by formulation selection and monitoring of pCQAs to produce a stable rNA vaccine candidate. The study highlights the importance of understanding and controlling vaccine protein structural and functional integrity.

Measuring dynamics in weakly structured regions of proteins using microfluidics-enabled subsecond H/D exchange mass spectrometry.

This work introduces an integrated microfluidic device for measuring rapid H/D exchange (HDX) in proteins. By monitoring backbone amide HDX on the millisecond to low second time scale, we are able to characterize conformational dynamics in weakly structured regions, such as loops and molten globule-like domains that are inaccessible in conventional HDX experiments. The device accommodates the entire MS-based HDX workflow on a single chip with residence times sufficiently small (ca. 8 s) that back-exchange is negligible (≤5%), even without cooling. Components include an adjustable position capillary mixer providing a variable-time labeling pulse, a static mixer for HDX quenching, a proteolytic microreactor for rapid protein digestion, and on-chip electrospray ionization (ESI). In the present work, we characterize device performance using three model systems, each illustrating a different application of 'time-resolved' HDX. Ubiquitin is used to illustrate a crude, high throughput structural analysis based on a single subsecond HDX time-point. In experiments using cytochrome c, we distinguish dynamic behavior in loops, establishing a link between flexibility and interactions with the heme prosthetic group. Finally, we localize an unusually high 'burst-phase' of HDX in the large tetrameric enzyme DAHP synthase to a 'molten globule-like' region surrounding the active site.

Epitope screening using Hydrogen/Deuterium Exchange Mass Spectrometry (HDX-MS): An accelerated workflow for evaluation of lead monoclonal antibodies.

BACKGROUND: Epitope mapping is an increasingly important aspect of biotherapeutic and vaccine development. Recent advances in therapeutic antibody design and production have enabled candidate mAbs to be identified at a rapidly increasing rate, resulting in a significant bottleneck in the characterization of "structural" epitopes, that are challenging to determine using existing high throughput epitope mapping tools. Here, a Hydrogen/Deuterium Exchange Mass Spectrometry (HDX-MS) epitope screening workflow was introduced that is well suited for accelerated characterization of epitopes with a common antigen. MAIN METHODS AND MAJOR RESULTS: The method is demonstrated on set of six candidate mAbs targeting Pertactin (PRN). Using this approach, five of the six epitopes were unambiguously determined using two HDX mixing timepoints in 24 h total run time, which is equivalent to the instrument time required to map a single epitope using the conventional workflow. CONCLUSION: An accelerated HDX-MS epitope screening workflow was developed. The "screening" workflow successfully characterized five (out of six attempted) novel epitopes on the PRN antigen; information that can be used to support vaccine antigenicity assays.

A novel polyamide SL-A92 as a potential fungal resistance blocker: synthesis and bioactivities in Candida albicans.

AIM: To synthesize a novel polyamide SL-A92 and evaluate its bioactivity against drug resistance in Candida albicans. METHODS: SL-A92 was synthesized using N-hydroxybenzotriazole (HOBT)/N,N'-dicyclohexylcarbodiimide (DCC) in solution phase. Its antifungal activities and effects on strain growth were tested using the micro-broth dilution method and growth curves, respectively. Induced drug resistance in the C. albicans collection strain SC5314 was obtained by incubation with fluconazole (12 microg/mL) for 21 passages. Meanwhile, incubations with SL-A92 plus fluconazole were also carried out in SC5314 strains, and the MIC(80)s were used to evaluate the inhibitory effects of SL-A92 on drug resistance during the induction process. Real time RT-PCR was performed to investigate the CDR1 and CDR2 mRNA levels in induced SC5314 strains. RESULTS: SC5314 strain induced by the combination of fluconazole and SL-A92 (200 microg/mL) did not develop drug resistance. On day 24, the CDR1 and CDR2 mRNA levels in SC5314 strain co-treated with fluconazole and SL-A92 relative to fluconazole alone were 26% and 24%, respectively, and on day 30 the CDR1 and CDR2 mRNA levels were 43% and 31%, respectively. CONCLUSION: SL-A92 can block the development of drug resistance during the fluconazole induction process, which partially results from the down-regulation of CDR1 and CDR2.

Exploring the interactions of iron and zinc with the microtubule binding repeats R1 and R4.

The dyshomeostasis of copper, iron and zinc ions in pathological conditions, which are critically involved in many brain activities, may result in an accumulation of them in the brain that has been reported for the patients with Alzheimer's disease. Conformational change is one of the consequences of metal-peptide interaction as we observed for the interaction of the Cu2+ with microtubule binding repeats of tau protein, which ultimately cause peptide aggregation. Herein, we show that interaction of Zn2+, Fe2+, and Fe3+ with full-length tau peptide R1 (tau244-274) and R4 (tau337-368), the first and fourth microtubule binding repeats of tau protein, lead to the conformational changes. And while the Electrospray ionization-mass spectrometry (ESI-MS) confirmed the complexation of Zn2+ and Fe2+ with both R1 and R4, there is no evidence for metalation of R1 or R4 with Fe3+.

Genetically detoxified pertussis toxin displays near identical structure to its wild-type and exhibits robust immunogenicity.

The mutant gdPT R9K/E129G is a genetically detoxified variant of the pertussis toxin (PTx) and represents an attractive candidate for the development of improved pertussis vaccines. The impact of the mutations on the overall protein structure and its immunogenicity has remained elusive. Here we present the crystal structure of gdPT and show that it is nearly identical to that of PTx. Hydrogen-deuterium exchange mass spectrometry revealed dynamic changes in the catalytic domain that directly impacted NAD+ binding which was confirmed by biolayer interferometry. Distal changes in dynamics were also detected in S2-S5 subunit interactions resulting in tighter packing of B-oligomer corresponding to increased thermal stability. Finally, antigen stimulation of human whole blood, analyzed by a previously unreported mass cytometry assay, indicated broader immunogenicity of gdPT compared to pertussis toxoid. These findings establish a direct link between the conserved structure of gdPT and its ability to generate a robust immune response.

A highly conductive conjugated coordination polymer for fast-charge sodium-ion batteries: reconsidering its structures.

Conjugated coordination polymers (CCPs), showing high conductivity, can be expected to be possibly applied in batteries, which, however, have not been well studied. Furthermore, CCPs are so unique that most of their chemical structures have not been well determined. Herein, a highly conductive CCP is reported for sodium-ion batteries, which shows high rate performance and high capacity retention of 84% even at 30C. What's more, the chemical structure is successfully revealed based on the structure variation during the electrochemical redox process.

Interaction of metal ions with tau protein. The case for a metal-mediated tau aggregation.

Tau protein aggregation and its hyperphosphorylation play an important role in the pathogenesis of Alzheimer's disease. There is also considerable evidence for the accumulation of Fe2/3+, Cu2+, and Zn2+ in the brain of Alzheimer's patients, although their involvement in the etiology of the disease remains unknown. Here, interactions of the 3d metal ions Fe2/3+, Cu2+, and Zn2+ with the longest isoform of the human tau protein (htau40) are studied in detail. Electrospray mass spectrometry and ion mobility mass spectrometry analyses confirm the interactions of metal species with tau and that these interactions cause structural changes. Phosphorylation of the full-length htau40 with glycogen synthase kinase 3ß (GSK3ß), a protein kinase, causes a reduction in metal interactions. Transmission electron microscopy studies of the tau aggregates formed in the presence of metal ions suggest that the presence of metal ions influences the aggregation process. Fluorescence studies of full-length htau40 in the presence of Cu2+ indicate the formation of reactive oxygen species, which may contribute further to oxidative stress and neuronal death.

Aggregation of Microtubule Binding Repeats of Tau Protein is Promoted by Cu2.

Understanding the factors that give rise to tau aggregation and reactive oxygen species (ROS) is the key aspect in Alzheimer's disease pathogenesis. Microtubule (MT) binding repeats of tau protein were suggested to play a critical role in tau aggregation. Here, we show that the interaction of Cu2+ with full-length MT binding repeats R1-R4 leads to the aggregation, and a Cys-based redox chemistry is critically involved in tau aggregation leading to disulfide-bridge dimerization of R2 and R3 and further aggregation into a fibrillar structure. Notably, ascorbate and glutathione, the most abundant antioxidants in neurons, cannot prevent the effect of Cu2+ on R2 and R3 aggregation. Detailed ESI-MS and NMR experiments demonstrate the interaction of Cu2+ with MT binding repeats. We show that redox activity of copper increases when bound to the MT repeats leading to ROS formation, which significantly contribute to cellular damage and neuron death. Results presented here provide new insights into the molecular mechanism of tau aggregation and ROS formation and suggest a new target domain for tau aggregation inhibitors.

Synthesis and SAR studies of biaryloxy-substituted triazoles as antifungal agents.

A series of 1-(substituted biaryloxy)-2-(2,4-difluorophenyl)-3-(1H-1,2,4-triazol-1-yl) propan-2-ol were synthesized and their antifungal activities were evaluated against eight human pathogenic fungi in vitro. Seventeen compounds showed activity 4- to 64-fold higher than voriconazole against Candida albicans. SAR clearly suggested that introduction of a biaryloxy side chain greatly enhanced the antifungal activity of triazole analogs against Candida species.

[Advances in the chemical and biological studies of polyamides].

Polyamides, containing N-methylpyrrole (Py) and N-methyl-imidazole (Im) amino acids, are synthetic oligomers programmed to read the DNA double helix in the minor groove with high affinities and sequence specificities resulting in modulation of gene expression. They are cell permeable, stable and have no cytotoxicity, which provide a promising tool of gene regulation. We describe here recent advances in the field of DNA binding polyamides, including pairing rules, specifities and affinities to DNA, synthesis methods, cellular and nuclear uptake properties, gene regulation and effectiveness in vivo. The potential problems and difficulties in future research are also discussed.

Large π-Conjugated Porous Frameworks as Cathodes for Sodium-Ion Batteries.

Organic sodium-ion batteries (OSIBs) are promising alternatives of inorganic lithium-ion batteries. The cathodes of OSIBs still suffer from low capacity, poor rate performance, and low cyclability. For the first time, we demonstrate the large π-conjugated porous frameworks (CPFs) as cathodes for OSIBs, motivated by the speculation that the CPFs are capable of enhancing charge transport, facilitating ionic diffusion, inhibiting dissolution, as well as improving stability. The batteries based on the obtained CPFs indeed delivered much better electrochemical performance than the small molecular construction units without any complex post-treatments. The moderate BET surface area of CPFs and the detailed analyses suggested that the micropores and the lamellar structure should be responsible for the fast ionic diffusion. We believe that this work will provoke growing interest of CPFs for OSIBs with functional molecular design toward high performance and pave a venue to achieve OSIBs in large-scale applications.