Deciphering molecular mechanisms stabilizing the reovirus-binding complex.

Mammalian orthoreoviruses (reoviruses) serve as potential triggers of celiac disease and have oncolytic properties, making these viruses potential cancer therapeutics. Primary attachment of reovirus to host cells is mainly mediated by the trimeric viral protein, σ1, which engages cell-surface glycans, followed by high-affinity binding to junctional adhesion molecule-A (JAM-A). This multistep process is thought to be accompanied by major conformational changes in σ1, but direct evidence is lacking. By combining biophysical, molecular, and simulation approaches, we define how viral capsid protein mechanics influence virus-binding capacity and infectivity. Single-virus force spectroscopy experiments corroborated by in silico simulations show that GM2 increases the affinity of σ1 for JAM-A by providing a more stable contact interface. We demonstrate that conformational changes in σ1 that lead to an extended rigid conformation also significantly increase avidity for JAM-A. Although its associated lower flexibility impairs multivalent cell attachment, our findings suggest that diminished σ1 flexibility enhances infectivity, indicating that fine-tuning of σ1 conformational changes is required to successfully initiate infection. Understanding properties underlying the nanomechanics of viral attachment proteins offers perspectives in the development of antiviral drugs and improved oncolytic vectors.

Effects of acute toxicity of the pesticide Chlorpyrifos and the metal Cadmium, both individually and in mixtures, on two species of native neotropical cladocerans.

The excessive use of pesticides in agriculture and the widespread use of metals in industrial activities and or technological applications has significantly increased the concentrations of these pollutants in both aquatic and terrestrial ecosystems worldwide, making aquatic biota increasingly vulnerable and putting many species at risk of extinction. Most aquatic habitats receive pollutants from various anthropogenic actions, leading to interactions between compounds that make them even more toxic. The aim of this study was to assess the effects of the compounds Chlorpyrifos (insecticide) and Cadmium (metal), both individually and in mixtures, on the cladocerans Ceriodaphnia rigaudi and Ceriodaphnia silvestrii. Acute toxicity tests were conducted for the compounds individually and in mixture, and an ecological risk assessment (ERA) was performed for both compounds. Acute toxicity tests with Cadmium resulted in EC50-48 h of 0.020 mg L-1 for C. rigaudi and 0.026 mg L-1 for C. silvestrii, while tests with Chlorpyrifos resulted in EC50-48 h of 0.047 µg L-1 and 0.062 µg L-1, respectively. The mixture test for C. rigaudi showed the occurrence of additive effects, while for C. silvestrii, antagonistic effects occurred depending on the dose level. The species sensitivity distribution curve for crustaceans, rotifers, amphibians, and fishes resulted in an HC5 of 3.13 and an HC50 of 124.7 mg L-1 for Cadmium; an HC5 of 9.96 and an HC50 of 5.71 µg L-1 for Chlorpyrifos. Regarding the ERA values, Cadmium represented a high risk, while Chlorpyrifos represented an insignificant to a high risk.

Ecological Implications on Aquatic Food Webs Due to Effects of Pesticides on Invertebrate Predators in a Neotropical Region.

Predation presents specific behavioral characteristics for each species, and the interaction between prey and predator influences the structuring of the food web. Concerning insects, predation can be affected in different ways, such as exposure to chemical stressors, e.g., pesticides. Therefore, analyses were carried out of the effects of exposure to insecticide fipronil and the herbicide 2,4-D on predation, parameters of food selectivity, and the swimming behavior of two neotropical predatory aquatic insects of the families Belostomatidae (giant water bugs) and larvae of Libellulidae (dragonfly). These predatory insects were exposed for 24 h to a commercial formulation of the chlorophenoxy herbicide, 2,4-D at nominal concentrations of 200, 300, 700, and 1400 µg L-1, and to a commercial formulation of the phenylpyrazole insecticide, fipronil at nominal concentrations of 10, 70, 140, and 250 µg L-1. In a control treatment, the insects were placed in clean, unspiked water. At the end of the exposure, the maximum swimming speed of the predators was evaluated. Afterward, the predators were placed in clean water in a shared environment for 24 h with several prey species, including the cladoceran Ceriodaphnia silvestrii, larvae of the insect Chironomus sancticaroli, the amphipod Hyalella meinerti, the ostracod Strandesia trispinosa, and the oligochaete Allonais inaequalis for 24 h. After this period, the consumed prey was counted. The results reveal that predators from both families changed prey consumption compared with organisms from the control treatment, marked by a decrease after exposure to fipronil and an increase in consumption caused by 2,4-D. In addition, there were changes in the food preferences of both predators, especially when exposed to the insecticide. Exposure to fipronil decreased the swimming speed of Belostomatidae individuals, possibly due to its neurotoxic effect. Exposure to the insecticide and the herbicide altered prey intake by predators, which could negatively influence the complex prey-predator relationship and the functioning of aquatic ecosystems in contaminated areas.

Molecular Origins of Force-Dependent Protein Complex Stabilization during Bacterial Infections.

The unbinding pathway of a protein complex can vary significantly depending on biochemical and mechanical factors. Under mechanical stress, a complex may dissociate through a mechanism different from that used in simple thermal dissociation, leading to different dissociation rates under shear force and thermal dissociation. This is a well-known phenomenon studied in biomechanics whose molecular and atomic details are still elusive. A particularly interesting case is the complex formed by bacterial adhesins with their human peptide target. These protein interactions have a force resilience equivalent to those of covalent bonds, an order of magnitude stronger than the widely used streptavidin:biotin complex, while having an ordinary affinity, much lower than that of streptavidin:biotin. Here, in an in silico single-molecule force spectroscopy approach, we use molecular dynamics simulations to investigate the dissociation mechanism of adhesin/peptide complexes. We show how the Staphylococcus epidermidis adhesin SdrG uses a catch-bond mechanism to increase complex stability with increasing mechanical stress. While allowing for thermal dissociation in a low-force regime, an entirely different mechanical dissociation path emerges in a high-force regime, revealing an intricate mechanism that does not depend on the peptide's amino acid sequence. Using a dynamic network analysis approach, we identified key amino acid contacts that describe the mechanics of this complex, revealing differences in dynamics that hinder thermal dissociation and establish the mechanical dissociation path. We then validate the information content of the selected amino acid contacts using their dynamics to successfully predict the rupture forces for this complex through a machine learning model.

ChemFlow─From 2D Chemical Libraries to Protein-Ligand Binding Free Energies.

The accurate prediction of protein-ligand binding affinities is a fundamental problem for the rational design of new drug entities. Current computational approaches are either too expensive or inaccurate to be effectively used in virtual high-throughput screening campaigns. In addition, the most sophisticated methods, e.g., those based on configurational sampling by molecular dynamics, require significant pre- and postprocessing to provide a final ranking, which hinders straightforward applications by nonexpert users. We present a novel computational platform named ChemFlow to bridge the gap between 2D chemical libraries and estimated protein-ligand binding affinities. The software is designed to prepare a library of compounds provided in SMILES or SDF format, dock them into the protein binding site, and rescore the poses by simplified free energy calculations. Using a data set of 626 protein-ligand complexes and GPU computing, we demonstrate that ChemFlow provides relative binding free energies with an RMSE < 2 kcal/mol at a rate of 1000 ligands per day on a midsize computer cluster. The software is publicly available at https://github.com/IFMlab/ChemFlow.

Comparison between genetic and pharmaceutical disruption of Ldlr expression for the development of atherosclerosis.

Antisense oligonucleotides (ASOs) against Ldl receptor (Ldlr-ASO) represent a promising strategy to promote hypercholesterolemic atherosclerosis in animal models without the need for complex breeding strategies. Here, we sought to characterize and contrast atherosclerosis in mice given Ldlr-ASO with those bearing genetic Ldlr deficiency. To promote atherosclerosis, male and female C57Bl6/J mice were either given weekly injections of Ldlr-ASO (5 mg/kg once per week) or genetically deficient in Ldlr (Ldlr-/-). Mice consumed either standard rodent chow or a diet high in saturated fat and sucrose with 0.15% added cholesterol for 16 weeks. While both models of Ldlr deficiency promoted hypercholesterolemia, Ldlr-/- mice exhibited nearly 2-fold higher cholesterol levels than Ldlr-ASO mice, reflected by increased VLDL and LDL levels. Consistent with this, the en face atherosclerotic lesion area was 3-fold and 3.6-fold greater in male and female mice with genetic Ldlr deficiency, respectively, as compared with the modest atherosclerosis observed following Ldlr-ASO treatment. Aortic sinus lesion sizes, fibrosis, smooth muscle actin, and necrotic core areas were also larger in Ldlr-/- mice, suggesting a more advanced phenotype. Despite a more modest effect on hypercholesterolemia, Ldlr-ASO induced greater hepatic inflammatory gene expression, macrophage accumulation, and histological lobular inflammation than was observed in Ldlr-/- mice. We conclude Ldlr-ASO is a promising tool for the generation of complex rodent models with which to study atherosclerosis but does not promote comparable levels of hypercholesterolemia or atherosclerosis as Ldlr-/- mice and increases hepatic inflammation. Thus, genetic Ldlr deficiency may be a superior model, depending on the proposed use.

Sexually Dimorphic Relationships Among Saa3 (Serum Amyloid A3), Inflammation, and Cholesterol Metabolism Modulate Atherosclerosis in Mice.

[Figure: see text].

Regression models to stratify the copper toxicity responses and tolerance mechanisms of Glycine max (L.) Merr. plants.

MAIN CONCLUSION: Root antioxidant defense, restricted root-to-shoot Cu translocation, altered nutrient partition, and leaf gas exchange adjustments occurred as tolerance mechanisms of soybean plants to increasing soil Cu levels. The intensive application of copper (Cu) fungicides has been related to the accumulation of this metal in agricultural soils. This study aimed to evaluate the effects of increasing soil Cu levels on soybean (Glycine max) plants. Soybean was cultivated under greenhouse conditions in soils containing different Cu concentrations (11.2, 52.3, 79.4, 133.5, 164.0, 205.1, or 243.8 mg kg-1), and biochemical and morphophysiological plant responses were analyzed through linear and nonlinear regression models. Although Cu concentrations around 50 mg kg-1 promoted some positive effects on the initial development of soybean plants (e.g., increased root length and dry weight), these Cu concentrations also induced root oxidative stress and activated defense mechanisms (such as the induction of antioxidant response, N and S accumulation in the roots). At higher concentrations, Cu led to growth inhibition (mainly of the root), nutritional imbalance, and damage to the photosynthetic apparatus of soybean plants, resulting in decreased CO2 assimilation and stomatal conductance. In contrast, low translocation of Cu to the leaves, conservative water use, and increased carboxylation efficiency contributed to the partial mitigation of Cu-induced stress. These responses allowed soybean plants treated with Cu levels in the soil as high as 90 mg kg-1 to maintain growth parameters higher than or similar to those of plants in the non-contaminated soil. These data provide a warning for the potentially deleterious consequences of the increasing use of Cu-based fungicides. However, it is necessary to verify how the responses to Cu contamination are affected by different types of soil and soybean cultivars.

The Glycine Receptor Allosteric Ligands Library (GRALL).

MOTIVATION: Glycine receptors (GlyRs) mediate fast inhibitory neurotransmission in the brain and have been recognized as key pharmacological targets for pain. A large number of chemically diverse compounds that are able to modulate GlyR function both positively and negatively have been reported, which provides useful information for the development of pharmacological strategies and models for the allosteric modulation of these ion channels. RESULTS: Based on existing literature, we have collected 218 unique chemical entities with documented modulatory activities at homomeric GlyR-α1 and -α3 and built a database named GRALL. This collection includes agonists, antagonists, positive and negative allosteric modulators and a number of experimentally inactive compounds. Most importantly, for a large fraction of them a structural annotation based on their putative binding site on the receptor is provided. This type of annotation, which is currently missing in other drug banks, along with the availability of cooperativity factors from radioligand displacement experiments are expected to improve the predictivity of in silico methodologies for allosteric drug discovery and boost the development of conformation-based pharmacological approaches. AVAILABILITY AND IMPLEMENTATION: The GRALL library is distributed as a web-accessible database at the following link: https://ifm.chimie.unistra.fr/grall. For each molecular entry, it provides information on the chemical structure, the ligand-binding site, the direction of modulation, the potency, the 3D molecular structure and quantum-mechanical charges as determined by our in-house pipeline. CONTACT: mcecchini@unistra.fr. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

In silico identification of noncompetitive inhibitors targeting an uncharacterized allosteric site of falcipain-2.

Falcipain-2 (FP-2) is a Plasmodium falciparum hemoglobinase widely targeted in the search for antimalarials. FP-2 can be allosterically modulated by various noncompetitive inhibitors that have been serendipitously identified. Moreover, the crystal structures of two inhibitors bound to an allosteric site, termed site 6, of the homolog enzyme human cathepsin K (hCatK) suggest that the equivalent region in FP-2 might play a similar role. Here, we conduct the rational identification of FP-2 inhibitors through virtual screenings (VS) of compounds into several pocket-like conformations of site 6, sampled during molecular dynamics (MD) simulations of the free enzyme. Two noncompetitive inhibitors, ZINC03225317 and ZINC72290660, were confirmed using in vitro enzymatic assays and their poses into site 6 led to calculated binding free energies matching the experimental ones. Our results provide strong evidence about the allosteric inhibition of FP-2 through binding of small molecules to site 6, thus opening the way toward the discovery of new inhibitors against this enzyme.

Nanoencapsulation improves the protective effects of a nitric oxide donor on drought-stressed Heliocarpus popayanensis seedlings.

Despite the important role played by nitric oxide (NO) in plants subjected to abiotic stress, NO donors application to induce drought tolerance in neotropical tree seedlings has not yet been tested. It is also worth investigating whether NO bioactivity in drought-stressed seedlings could be potentiated by NO donors nanoencapsulation. The aim of the current study is to evaluate the effects of chitosan nanoparticles (NPs) containing S-nitroso-mercaptosuccinic acid (S-nitroso-MSA) on drought-stressed seedlings of neotropical tree species Heliocarpus popayanensis Kunth in comparison to free NO donor and NPs loaded with non-nitrosated MSA. Nanoencapsulation slowed down NO release from S-nitroso-MSA, and nanoencapsulated S-nitroso-MSA yielded 2- and 1.6-fold higher S-nitrosothiol levels in H. popayanensis roots and leaves, respectively, than the free NO donor. S-nitroso-MSA has prevented drought-induced CO2 assimilation inhibition, regardless of nanoencapsulation, but the nanoencapsulated NO donor has induced earlier ameliorative effect. Both NO and MSA have decreased oxidative stress in H. popayanensis roots, but this effect was not associated with antioxidant enzyme induction, with higher seedling biomass, or with proline and glycine betaine accumulation. Nanoencapsulated S-nitroso-MSA was the only formulation capable of increasing leaf relative water content in drought-stressed plants (from 32.3% to 60.5%). In addition, it induced root hair formation (increase by 36.6% in comparison to well-hydrated plants). Overall, results have evidenced that nanoencapsulation was capable of improving the protective effect of S-nitroso-MSA on H. popayanensis seedlings subjected to drought stress, a fact that highlighted the potential application of NO-releasing NPs to obtain drought-tolerant tree seedlings for reforestation programs.

Stimulation action of mefenpyr-diethyl on soybean, wheat, and signal grass plants.

Mefenpyr-diethyl is a safener used for protection of cereal plants under applications of ACCase and ALS inhibitor herbicides. Current studies are describing safeners using a new approach, relating these products to stimulation action on plants. The objective of this work was to evaluate the stimulation action of mefenpyr-diethyl on soybean, wheat, and signal grass plants. The experiment was conducted in a greenhouse, under a completely randomized design, with four replications, in two seasons. Mefenpyr-diethyl (50 g a.i. ha-1) was applied on soybean plants (at V4 stage), and wheat and signal grass plants (both with 15 cm height). The variables evaluated were plant height, dry matter, and lipid content of the three species, and number of tillers of wheat and signal grass plants. The application of mefenpyr-diethyl in the first season increased the number of tillers of wheat and height of soybean plants. The soybean presented 24 and 14% more dry matter than the control in the first and second season, respectively, and 0.5% more lipid content in plants treated with mefenpyr-diethyl. These results show the stimulation action of mefenpyr-diethyl on wheat and soybean plants, denoting its potential for growth promotion and indicating the need for studies with this approach. No effect was found for the signal grass plants.

Effects of copper oxide nanoparticles on growth of lettuce (Lactuca sativa L.) seedlings and possible implications of nitric oxide in their antioxidative defense.

Copper oxide nanoparticles (CuO NPs) have been extensively explored for use in agriculture. Previous studies have indicated that application of CuO NPs might be promising for development and conservation of plants, pest control, and for the recovery of degraded soils. However, depending on the applied concentration copper can cause phytotoxic effects. In this work, biosynthesized CuO NPs (using green tea extract) were evaluated on their effects on lettuce (Lactuca sativa L.) seedling growth, which were exposed at concentrations ranged between 0.2 and 300 µg mL-1. From the biosynthesized were obtained ultra-small CuO NPs (~ 6.6 nm), with high stability in aqueous suspension. Toxicity bioassays have shown that at low concentrations (up to 40 µg mL-1), CuO NPs did not affect or even enhanced the seed germination. At higher concentrations (higher than 40 µg mL-1), inhibition of seed germination and radicle growth ranging from 35 to 75% was observed. With the increase of CuO NPs concentrations, nitrite and S-nitrosothiols levels in radicles increased, whereas superoxide dismutase and total antioxidant activities decreased. The nitrite and S-nitrosothiols levels in lettuce radicles showed a direct dose response to CuO NP application, which may indicate nitric oxide-dependent signaling pathways in the plant responses. Therefore, the results demonstrated that at low concentrations (≤ 20 µg mL-1) of CuO NPs, beneficial effects are obtained from seedlings, enhancing plant growth, and the involvement of nitric oxide signaling in the phytotoxic effects induced by high concentration of this formulation. Graphical abstract.

Dynamics of (total and methyl) mercury in sediment, fish, and crocodiles in an Amazonian Lake and risk assessment of fish consumption to the local population.

Increasing concerns have been raised about the toxicity of mercury (Hg) to humans, especially for those that consume a great amount of fish. High Hg concentrations have previously been measured in Amazonian waterbodies, both resulting from natural and anthropogenic sources. However, few studies have been conducted so far in Amazonian lakes that are fished by local populations. In addition, few of those studies included methylmercury (MeHg), the most toxic and bioaccumulative Hg form, and evaluated the influence of physico-chemical conditions and season on Hg dynamics. In the present study, total Hg (THg) and MeHg concentrations were measured in bottom sediment as well as in two fish and two crocodile species of the Amazonian Cuniã Lake. Bottom sediment MeHg concentrations were higher in the dry season than in the wet season, which is related to differences in physico-chemical (pH and electrical conductivity) conditions. Diet appeared to be related with animal tissue MeHg concentrations, with the herbivorous fish having lower MeHg levels than the predatory fish and crocodiles. Based on the measured tissue concentrations and published data on local person weight and fish consumption, MeHg risk to Cuniã Lake populations was estimated. Although the MeHg fish tissue concentrations did not exceed national and international standards, a significant risk to the local population is anticipated due to their high fish consumption rates. Graphical abstract.

Dose-Dependent Dual Effect of Soil Copper on the Initial Development of Glycine max (L.) Merr. cv. BRS 257 Seedlings.

The aim of this study was to evaluate, through nonlinear regression models, the initial development of soybean (Glycine max L. Merr. cv. BRS 257) in soil supplemented with different copper levels. The experiment was performed in a greenhouse under natural light and temperature conditions. The seeds were sowed in soil containing different copper levels (11.20, 32.28, 52.31, 64.51, 79.42, 117.70, 133.53, 144.32, or 164.00 mg kg- 1). Germination percentage was not affected by the increase of copper content in the soil, but there was a delay in the germination process. There was no influence of copper levels on the seedling emergence speed index until 98.42 mg kg- 1; however, higher copper amounts reduced this parameter. Low copper concentrations increased plant development, but higher concentrations compromised mainly root growth. Overall, these results suggest that copper supplementation in the soil exerted dose-dependent dual effects on soybean seedlings.

Oxidative stress and antioxidant biomarker responses after a moderate-intensity soccer training session.

The present study investigated the effects of a moderate-intensity soccer training session on the production of reactive oxygen species (ROS) and the antioxidant capacity in athletes along with the biomarkers creatine kinase and transaminases for lesions in muscle and liver cells. Twenty-two male soccer players participated in this study. Blood samples were collected 5 min before and after a moderate-intensity game simulation. The results showed a decrease in the concentration of reduced glutathione (GSH) from an elevation in the production of ROS that maintained the redox homeostasis. Although the session promoted an elevated energy demand, observed by an increase in lactate and glucose levels, damage to muscle and/or liver cells was only suggested by a significant elevation in the levels of alanine transaminase (ALT). Of the two biomarkers analysed, the results suggest that measurements of the ALT levels could be adopted as a method to monitor recovery in athletes.

Aerobic exercise training enhances the in vivo cholesterol trafficking from macrophages to the liver independently of changes in the expression of genes involved in lipid flux in macrophages and aorta.

BACKGROUND: Regular exercise prevents and regresses atherosclerosis by improving lipid metabolism and antioxidant defenses. Exercise ameliorates the reverse cholesterol transport (RCT), an antiatherogenic system that drives cholesterol from arterial macrophages to the liver for excretion into bile and feces. In this study we analyzed the role of aerobic exercise on the in vivo RCT and expression of genes and proteins involved in lipid flux and inflammation in peritoneal macrophages, aortic arch and liver from wild type mice. METHODS: Twelve-week-old male mice were divided into sedentary and trained groups. Exercise training was performed in a treadmill (15 m/min, 30 min/day, 5 days/week). Plasma lipids were determined by enzymatic methods and lipoprotein profile by fast protein liquid chromatography. After intraperitoneal injection of J774-macrophages the RCT was assessed by measuring the recovery of (3)H-cholesterol in plasma, feces and liver. The expression of liver receptors was determined by immunoblot, macrophages and aortic mRNAs by qRT-PCR. (14)C-cholesterol efflux mediated by apo A-I and HDL2 and the uptake of (3)H-cholesteryl oleoyl ether ((3)H-COE)-acetylated-LDL were determined in macrophages isolated from sedentary and trained animals 48 h after the last exercise session. RESULTS: Body weight, plasma lipids, lipoprotein profile, glucose and blood pressure were not modified by exercise training. A greater amount of (3)H-cholesterol was recovered in plasma (24 h and 48 h) and liver (48 h) from trained animals in comparison to sedentary. No difference was found in (3)H-cholesterol excreted in feces between trained and sedentary mice. The hepatic expression of scavenger receptor class B type I (SR-BI) and LDL receptor (B-E) was enhanced by exercise. We observed 2.8 and 1.7 fold rise, respectively, in LXR and Cyp7a mRNA in the liver of trained as compared to sedentary mice. Macrophage and aortic expression of genes involved in lipid efflux was not systematically changed by physical exercise. In agreement, (14)C-cholesterol efflux and uptake of (3)H-COE-acetylated-LDL by macrophages was similar between sedentary and trained animals. CONCLUSION: Aerobic exercise in vivo accelerates the traffic of cholesterol from macrophages to the liver contributing to prevention and regression of atherosclerosis, independently of changes in macrophage and aorta gene expression.

Formation of Nanoporous Gold Studied by Transmission Electron Backscatter Diffraction.

Transmission electron backscatter diffraction (t-EBSD) was used to investigate the effect of dealloying on the microstructure of 140-nm thin gold foils. Statistical and local comparisons of the microstructure between the nonetched and nanoporous gold foils were made. Analyses of crystallographic texture, misorientation distribution, and grain structure clearly prove that during the dealloying manufacturing process of nanoporous materials the crystallographic texture is enhanced significantly with a clear decrease of internal strain, whereas maintaining the grain structure.

Achieving High-Temperature Stable Structural Color through Nanostructuring in Polymer-Derived Ceramics.

Structural colors offer a myriad of advantages over conventional pigment-based colors, which often rely on toxic chemical substances that are prone to UV degradation. To take advantage of these benefits in demanding environments, there is growing interest in producing structural colors from ceramics. Polymer-derived ceramics (PDCs) emerge as a compelling choice, presenting two distinct advantages: their enhanced shape ability in their polymeric state associated with impressive temperature resistance once converted to ceramics. This study pioneers the fabrication of noniridescent structural colors from silicon oxycarbide (SiOC) PDC, enabled by the nanostructuring of an inverse photonic glass within the PDC material. This design, a functionally graded material with an inverse photonic glass (FGM-PhG) structure, leverages the innate light-absorbing properties of SiOC, yielding a vivid structural color that maintains its saturation even in white surroundings. This study elucidates the process-structure-properties relationship for the obtained structural colors by investigating each layer of the functionally graded material (FGM) in a stepwise coating deposition process. To further emphasize the exceptional processing flexibility of PDCs, the three-step process is later transferred to an additive manufacturing approach. Finally, the FGM-PhG structural colors are demonstrated to have remarkable thermal stability up to 1000 °C for 100 h, possibly making them the most thermally stable ceramic structural colors to date.

Integrating Dynamic Network Analysis with AI for Enhanced Epitope Prediction in PD-L1:Affibody Interactions.

Understanding binding epitopes involved in protein-protein interactions and accurately determining their structure is a long standing goal with broad applicability in industry and biomedicine. Although various experimental methods for binding epitope determination exist, these approaches are typically low throughput and cost intensive. Computational methods have potential to accelerate epitope predictions, however, recently developed artificial intelligence (AI)-based methods frequently fail to predict epitopes of synthetic binding domains with few natural homologs. Here we have developed an integrated method employing generalized-correlation-based dynamic network analysis on multiple molecular dynamics (MD) trajectories, initiated from AlphaFold2 Multimer structures, to unravel the structure and binding epitope of the therapeutic PD-L1:Affibody complex. Both AlphaFold2 and conventional molecular dynamics trajectory analysis alone each proved ineffectual in differentiating between two putative binding models referred to as parallel and perpendicular. However, our integrated approach based on dynamic network analysis showed that the perpendicular mode was significantly more stable. These predictions were validated using a suite of experimental epitope mapping protocols including cross linking mass spectrometry and next-generation sequencing-based deep mutational scanning. Our research highlights the potential of deploying dynamic network analysis to refine AI-based structure predictions for precise predictions of protein-protein interaction interfaces.