Diverse intracellular pathogens activate type III interferon expression from peroxisomes.

Type I interferon responses are considered the primary means by which viral infections are controlled in mammals. Despite this view, several pathogens activate antiviral responses in the absence of type I interferons. The mechanisms controlling type I interferon-independent responses are undefined. We found that RIG-I like receptors (RLRs) induce type III interferon expression in a variety of human cell types, and identified factors that differentially regulate expression of type I and type III interferons. We identified peroxisomes as a primary site of initiation of type III interferon expression, and revealed that the process of intestinal epithelial cell differentiation upregulates peroxisome biogenesis and promotes robust type III interferon responses in human cells. These findings highlight the importance of different intracellular organelles in specific innate immune responses.

Structure of CC Chemokine Receptor 5 with a Potent Chemokine Antagonist Reveals Mechanisms of Chemokine Recognition and Molecular Mimicry by HIV.

CCR5 is the primary chemokine receptor utilized by HIV to infect leukocytes, whereas CCR5 ligands inhibit infection by blocking CCR5 engagement with HIV gp120. To guide the design of improved therapeutics, we solved the structure of CCR5 in complex with chemokine antagonist [5P7]CCL5. Several structural features appeared to contribute to the anti-HIV potency of [5P7]CCL5, including the distinct chemokine orientation relative to the receptor, the near-complete occupancy of the receptor binding pocket, the dense network of intermolecular hydrogen bonds, and the similarity of binding determinants with the FDA-approved HIV inhibitor Maraviroc. Molecular modeling indicated that HIV gp120 mimicked the chemokine interaction with CCR5, providing an explanation for the ability of CCR5 to recognize diverse ligands and gp120 variants. Our findings reveal that structural plasticity facilitates receptor-chemokine specificity and enables exploitation by HIV, and provide insight into the design of small molecule and protein inhibitors for HIV and other CCR5-mediated diseases.

A millimeter water-in-oil droplet as an alternative back exchange prevention strategy for hydrogen/deuterium exchange mass spectrometry of peptides/proteins.

Hydrogen/deuterium exchange mass spectrometry (HDX-MS) is a versatile bioanalytical technique for protein analysis. Since the reliability of HDX-MS analysis considerably depends on the retention of deuterium labels in the post-labeling workflow, deuterium/hydrogen (D/H) back exchange prevention strategies, including decreasing the pH, temperature, and exposure time to protic sources of the deuterated samples, are widely adopted in the conventional HDX-MS protocol. Herein, an alternative and effective back exchange prevention strategy based on the encapsulation of a millimeter droplet of a labeled peptide solution in a water-immiscible organic solvent (cyclohexane) is proposed. Cyclohexane was used to prevent the undesirable uptake of water by the droplet from the atmospheric vapor through the air-water interface. Using the pepsin digest of deuterated myoglobin, our results show that back exchange kinetics of deuterated peptides is retarded in a millimeter droplet as compared to that in the bulk solution. Performing pepsin digestion directly in a water-in-oil droplet at room temperature (18-21 °C) was found to preserve more deuterium labels than that in the bulk digestion with an ice-water bath. Based on the present findings, it is proposed that keeping deuterated peptides in the form of water-in-oil droplets during the post-labelling workflow will facilitate the preservation of deuterium labels on the peptide backbone and thereby enhance the reliability of the H/D exchange data.

Stereochemical inversion at a 1,4-cyclohexyl PROTAC linker fine-tunes conformation and binding affinity.

Proteolysis targeting chimeras (PROTACs) are heterobifunctional small-molecule degraders made of a linker connecting a target-binding moiety to a ubiquitin E3 ligase-binding moiety. The linker unit is known to influence the physicochemical and pharmacokinetic properties of PROTACs, as well as the properties of ternary complexes, in turn impacting on their degradation activity in cells and in vivo. Our LRRK2 PROTAC XL01126, bearing a trans-cyclohexyl group in the linker, is a better and more cooperative degrader than its corresponding cis- analogue despite its much weaker binary binding affinities. Here, we investigate how this subtle stereocenter alteration in the linker affects the ligand binding affinity to the E3 ligase VHL. We designed a series of molecular matched pairs, truncating from the full PROTACs down to the VHL ligand, and find that across the series the trans-cyclohexyl compounds showed consistently weaker VHL-binding affinity compared to the cis- counterparts. High-resolution co-crystal structures revealed that the trans linker exhibits a rigid stick-out conformation, while the cis linker collapses into a folded-back conformation featuring a network of intramolecular contacts and long-range interactions with VHL. These observations are noteworthy as they reveal how a single stereochemical inversion within a PROTAC linker impacts conformational rigidity and binding mode, in turn fine-tuning differentiated propensity to binary and ternary complex formation, and ultimately cellular degradation activity.

Configurable Organic Charge Carriers toward Stable Perovskite Photovoltaics.

Due to their solution processability and unique photoelectric characteristics, perovskite solar cells (PSCs) have shown considerable promise in the area of renewable energy. Although their power conversion efficiency (PCE) has risen from 3.8% to 25.7% in only a few years, their short lifetime and high material prices continue to be key roadblocks to commercial viability. Charge transporting materials (CTMs), such as hole/electron transporting materials, are critical components in PSCs because they not only govern hole or electron extraction and transporting from the perovskite layer to the electrodes but also protect the perovskite from direct contact with the ambient environment. CTMs are split into two types: inorganic CTMs (ICTMs) and organic CTMs (OCTMs). Because of their inexpensive prices, well-adjusted energy levels, and low temperature solution-processed features, OCTMs have been more frequently explored and employed than ICTMs. Various forms of OCTMs with more straightforward synthetic pathways and better performance have been thoroughly researched. Recent achievements in the development of OCTMs will be discussed and evaluated on a molecular level in this study, which will include a systematic categorization of OCTMs based on molecular functionalization techniques. In order to achieve highly efficient and stable PSCs, we will present insights on the structure-property relationship in the design of OCTMs as well as device stability. We hope that this analysis will serve as a comprehensive reference to molecular design guidelines for various types of OCTMs, spurring greater research toward designing highly efficient and OCTMs for stable PSCs.

Two-year carcinogenicity study of a novel plasticizer, bis(2-ethylhexyl) cyclohexane-1,4-dicarboxylate (Eco-DEHCH), by oral diet in Han Wistar rats.

Plasticizers are necessary for the usability of various products, including food contact materials. Exposure to plasticizers is most commonly made through the oral route. Several plasticizers have been reported to have adverse effects on humans and the environment. Thus, the present study aimed to determine the long-term toxicity and carcinogenicity of a novel plasticizer called bis(2-ethylhexyl) cyclohexane-1,4-dicarboxylate (Eco-DEHCH), which is an ecofriendly and biologically less harmful replacer. Groups of 50 male and 50 female Han Wistar rats were fed Eco-DEHCH at daily doses of 1,600, 5,000, or 16,000 ppm in their diet for at least 104 weeks. The rats were regularly monitored for mortality, clinical signs, body weight, food consumption, food efficiency, and perceivable mass. All animals were subjected to complete necropsy and histopathological examination. The results indicate that the rats well tolerated chronic exposure to Eco-DEHCH at highest daily doses of 16,000 ppm, with was equivalent to 805.1 mg/kg/day in males and 1060.6 mg/kg/day in females and did not show signs of toxicity or carcinogenicity. In conclusion, Eco-DEHCH could be a safe and promising alternative plasticizer.

Click-to-lead design of a picomolar ABA receptor antagonist with potent activity in vivo.

Abscisic acid (ABA) is a key plant hormone that mediates both plant biotic and abiotic stress responses and many other developmental processes. ABA receptor antagonists are useful for dissecting and manipulating ABA's physiological roles in vivo. We set out to design antagonists that block receptor-PP2C interactions by modifying the agonist opabactin (OP), a synthetically accessible, high-affinity scaffold. Click chemistry was used to create an ∼4,000-member library of C4-diversified opabactin derivatives that were screened for receptor antagonism in vitro. This revealed a peptidotriazole motif shared among hits, which we optimized to yield antabactin (ANT), a pan-receptor antagonist. An X-ray crystal structure of an ANT-PYL10 complex (1.86 Å) reveals that ANT's peptidotriazole headgroup is positioned to sterically block receptor-PP2C interactions in the 4' tunnel and stabilizes a noncanonical closed-gate receptor conformer that partially opens to accommodate ANT binding. To facilitate binding-affinity studies using fluorescence polarization, we synthesized TAMRA-ANT. Equilibrium dissociation constants for TAMRA-ANT binding to Arabidopsis receptors range from ∼400 to 1,700 pM. ANT displays improved activity in vivo and disrupts ABA-mediated processes in multiple species. ANT is able to accelerate seed germination in Arabidopsis, tomato, and barley, suggesting that it could be useful as a germination stimulant in species where endogenous ABA signaling limits seed germination. Thus, click-based diversification of a synthetic agonist scaffold allowed us to rapidly develop a high-affinity probe of ABA-receptor function for dissecting and manipulating ABA signaling.

Comparative analysis of diisononyl phthalate and di(isononyl)cyclohexane-1,2 dicarboxylate plasticizers in regulation of lipid metabolism in 3T3-L1 cells.

Diisononyl phthalate (DINP) and di(isononyl)cyclohexane-1,2-dicarboxylate (DINCH) are plasticizers introduced to replace previously used phthalate plasticizers in polymeric products. Exposure to DINP and DINCH has been shown to impact lipid metabolism. However, there are limited studies that address the mechanisms of toxicity of these two plasticizers. Here, a comparative toxicity analysis has been performed to evaluate the impacts of DINP and DINCH on 3T3-L1 cells. The preadipocyte 3T3-L1 cells were exposed to 1, 10, and 100 µM of DINP or DINCH for 10 days and assessed for lipid accumulation, gene expression, and protein analysis. Lipid staining showed that higher concentrations of DINP and DINCH can induce adipogenesis. The gene expression analysis demonstrated that both DINP and DINCH could alter the expression of lipid-related genes involved in adipogenesis. DINP and DINCH upregulated Pparγ, Pparα, C/EBPα Fabp4, and Fabp5, while both compounds significantly downregulated Fasn and Gata2. Protein analysis showed that both DINP and DINCH repressed the expression of FASN. Additionally, we analyzed an independent transcriptome dataset encompassing temporal data on lipid differentiation within 3T3-L1 cells. Subsequently, we derived a gene set that accurately portrays significant pathways involved in lipid differentiation, which we subsequently subjected to experimental validation through quantitative polymerase chain reaction. In addition, we extended our analysis to encompass a thorough assessment of the expression profiles of this identical gene set across 40 discrete transcriptome datasets that have linked to diverse pathological conditions to foreseen any potential association with DINP and DINCH exposure. Comparative analysis indicated that DINP could be more effective in regulating lipid metabolism.

Comparing the EU and Chinese carbon trading market operations and their spillover effects.

A carbon trading market (CTM) policy for trading carbon dioxide emission rights as a commodity was created to reduce greenhouse gas emissions. CTMs operate differently in different countries and regions, and their interactions deserve an in-depth study. This study focused on the world's largest CTM, the European Union (EU), and the CTM of China, largest carbon-emitting country. First, we evaluate the liquidity and volatility of the two CTMs. Subsequently, the VAR model is used to explore the mean spillover effect between the two markets and the BEKK-GARCH model is used to explore the volatility spillover effect between the two markets. The study concludes that: (1) The liquidity of China's CTM is better than that of the EU's CTM. (2) Both the EU and Chinese CTMs are unstable, but the volatility of the Chinese CTM is lower than that of the EU CTM. (3) Price changes in the EU and Hubei CTMs have a mutual influence. (4) There are interactions between the market fluctuations of the EU CTM and the Shanghai CTM and those of the EU CTM and the Hubei CTM. The results of this study have implications for the construction and development of CTMs in the EU and China.

Addition of (bio)surfactants in the biofiltration of hydrophobic volatile organic compounds in air.

The removal of volatile organic compounds (VOCs) in air is of utmost importance to safeguard both environmental quality and human well-being. However, the low aqueous solubility of hydrophobic VOCs results in poor removal in waste gas biofilters (BFs). In this study, we evaluated the addition of (bio)surfactants in three BFs (BF1 and BF2 mixture of compost and wood chips (C + WC), and BF3 filled with expanded perlite) to enhance the removal of cyclohexane and hexane from a polluted gas stream. Experiments were carried out to select two (bio)surfactants (i.e., Tween 80 and saponin) out of five (sodium dodecyl sulfate (SDS), Tween 80, surfactin, rhamnolipid and saponin) from a physical-chemical (i.e., decreasing VOC gas-liquid partitioning) and biological (i.e., the ability of the microbial consortium to grow on the (bio)surfactants) point of view. The results show that adding Tween 80 at 1 critical micelle concentration (CMC) had a slight positive effect on the removal of both VOCs, in BF1 (e.g., 7.0 ± 0.6 g cyclohexane m-3 h-1, 85 ± 2% at 163 s; compared to 6.7 ± 0.4 g cyclohexane m-3 h-1, 76 ± 2% at 163 s and 0 CMC) and BF2 (e.g., 4.3 ± 0.4 g hexane m-3 h-1, 27 ± 2% at 82 s; compared to 3.1 ± 0.7 g hexane m-3 h-1, 16 ± 4% at 82 s and 0 CMC), but a negative effect in BF3 at either 1, 3 and 9 CMC (e.g., 2.4 ± 0.4 g hexane m-3 h-1, 30 ± 4% at 163 s and 1 CMC; compared to 4.6 ± 1.0 g hexane m-3 h-1, 43 ± 8% at 163 s and 0 CMC). In contrast, the performance of all BFs improved with the addition of saponin, particularly at 3 CMC. Notably, in BF3, the elimination capacity (EC) and removal efficiency (RE) doubled for both VOCs (i.e., 9.1 ± 0.6 g cyclohexane m-3 h-1, 49 ± 3%; 4.3 ± 0.3 g hexane m-3 h-1, 25 ± 3%) compared to no biosurfactant addition (i.e., 4.5 ± 0.4 g cyclohexane m-3 h-1, 23 ± 3%; hexane 2.2 ± 0.5 g m-3 h-1, 10 ± 2%) at 82 s. Moreover, the addition of the (bio)surfactants led to a shift in the microbial consortia, with a different response in BF1-BF2 compared to BF3. This study evaluates for the first time the use of saponin in BFs, it demonstrates that cyclohexane and hexane RE can be improved by (bio)surfactant addition, and it provides recommendations for future studies in this field.

Concentration and non-dietary human health risk assessment of pesticide residues in soil of farms in Golestan province, Iran.

Detection of pesticide residues in soil samples was conducted using UHPLC-MS/MS. Non-dietary health risk assessment was conducted using calculate chronic daily intake (CDI) from ingestion, inhalation and dermal contact pathways and following non-carcinogenic and carcinogenic risks in the adults and adolescent. The rank order of pesticide in soil based on their concentration was malathion (0.082 mg kg-1)> cyproconazole (0.019 mg kg-1)> propargite (0.018 mg kg-1)> butachlor (0.016 mg kg-1) > chlorpyrifos (0.0067 mg kg-1)> diazinon (0.0014 mg kg-1)> imidacloprid (0.0007 mg kg-1). Hazard index (HI) values obtained of exposure to pesticides in soil in adults and adolescent were 0.0012 and 0.0035, respectively. Hence, exposed population are at the acceptable range of non-carcinogenic risk (HI < 1). Cancer risk (CR) values due to propargite in soil via ingestion pathway in adults and adolescent were 2.03E-09 and 2.08E-09, respectively; therefore, carcinogenic risk due to the exposure to pesticide contaminated soil was safe range (CR < 1E-06).

Development of a robust method for Cd(II) ions analysis using CeO2- and CeO2-Cu-BTC-based electrochemical sensors.

Simple and sensitive electrochemical sensors were fabricated from cerium oxide (CeO2) and copper-benzene tricarboxylic acid-modified cerium oxide (CeO2-Cu-BTC) materials for differential pulse voltammetric analysis of toxic cadmium (Cd) ions in aqueous solutions. The materials were prepared by hydrothermal method and structurally characterized by Fourier transform infrared spectroscopy (FTIR), scanning electron microscopy with energy-dispersive X-ray (SEM-EDX), thermogravimetric analysis (TGA), and X-ray diffraction analysis (XRD). The CeO2-modified carbon paste electrode (CeCPE) and the CeO2-Cu-BTC-modified carbon paste electrode (CeBCPE) were electrochemically characterized by their cyclic voltammetry and electrochemical impedance study in standard K3[Fe(CN)6] single-electron redox process. Their electrochemical surface areas, electrode surface coverages, and charge transfer resistances were calculated to be 1.46 cm2, 2.338 × 10-5 mol∙cm-2, and 2790 Ω and 5.48 cm2, 2.476 × 10-5 mol∙cm-2, and 1254.65 Ω for CeCPE and CeBCPE, respectively. These fabricated electrodes were used as electrochemical sensors for cadmium ion estimation by optimizing the experimental parameters through differential pulse voltammetry. The optimized conditions included 10% modifier for CeCPE and 5% modifier for CeBCPE in 0.12 M HCl solution of pH 5 as supporting electrolyte at - 1.2 V deposition for 30 s in 0.01 to 10 mg L-1 linear cadmium solution range. Under these conditions, the limit of quantification (LOQ) of 0.368 mg L-1 and 0.005 mg L-1 was calculated for CeCPE and CeBCPE electrodes, respectively. The limit of detection (LOD) was calculated to be 0.121 mg L-1 and 0.002 mg L-1 for CeCPE and CeBCPE, respectively. All the experimental results indicated that electrodes fabricated from CeO2-Cu-BTC show better performance as compared to CeO2-based electrodes. Both these types of electrochemical sensors presented good repeatability and performance in the presence of interfering ions as well. From these findings, it can also be inferred that these electrochemical sensors can provide a simple and very sensitive method for approximation of toxic cadmium ions in aqueous solutions.

Stereoselective Borylcupration/Michael Addition on Symmetrical Dienones.

An efficient cascade protocol for the stereoselective synthesis of borylated carbocycles via copper-catalyzed borylative Michael/Michael cyclization is presented. Using this mild approach, up to 24 new boronic ester substituted indanes, cyclohexanes, and cyclopentanes were prepared in good yields with excellent diasteroselectivities and exceptional functional group tolerance. Furthermore, carbacyclic boronates were oxidized successfully through synthetic transformation. Gram-scale synthesis of the present protocol was also carried out effectively.

The effects of thymol, oxalic acid (Api-Bioxal) and hops extract (Nose-Go) on viability, the Nosema sp. spore load and the expression of vg and sod-1 genes in infected honey bees.

This study was done to investigate the effects of thymol, fumagillin, oxalic acid (Api-Bioxal) and hops extract (Nose-Go) on Nosema sp. spore load, the expression of vitellogenin (vg) and superoxide-dismutase-1 (sod-1) genes and mortality of bees infected with N. ceranae. Five healthy colonies were assigned as the negative control, and 25 Nosema sp. infected colonies were assigned to five treatment groups including: the positive control: no additive to sirup; fumagillin 26.4 mg/L, thymol 0.1 g/L, Api-Bioxal 0.64 g/L and Nose-Go 5.0 g/L sirup. The reduction in the number of Nosema sp. spores in fumagillin, thymol, Api-Bioxal and Nose-Go compared to the positive control was 54, 25, 30 and 58%, respectively. Nosema sp. infection in all infected groups increased (p < .05) Escherichia coli population compared to the negative control. Nose-Go had a negative effect on lactobacillus population compared to other substances. Nosema sp. infection decreased vg and sod-1 genes expression in all infected groups compared to the negative control. Fumagillin and Nose-Go increased the expression of vg gene, and Nose-Go and thymol increased the expression of sod-1 gene than the positive control. Nose-Go has the potential to treat nosemosis if the necessary lactobacillus population is provided in the gut.

Identification of 2,4-Di-tert-butylphenol as a Novel Agonist for Insect Odorant Receptors.

Odorant molecules interact with odorant receptors (ORs) lining the pores on the surface of the sensilla on an insect's antennae and maxillary palps. This interaction triggers an electrical signal that is transmitted to the insect's nervous system, thereby influencing its behavior. Orco, an OR coreceptor, is crucial for olfactory transduction, as it possesses a conserved sequence across the insect lineage. In this study, we focused on 2,4-di-tert-butylphenol (DTBP), a single substance present in acetic acid bacteria culture media. We applied DTBP to oocytes expressing various Drosophila melanogaster odor receptors and performed electrophysiology experiments. After confirming the activation of DTBP on the receptor, the binding site was confirmed through point mutations. Our findings confirmed that DTBP interacts with the insect Orco subunit. The 2-heptanone, octanol, and 2-hexanol were not activated for the Orco homomeric channel, but DTBP was activated, and the EC50 value was 13.4 ± 3.0 µM. Point mutations were performed and among them, when the W146 residue changed to alanine, the Emax value was changed from 1.0 ± 0 in the wild type to 0.0 ± 0 in the mutant type, and all activity was decreased. Specifically, DTBP interacted with the W146 residue of the Orco subunit, and the activation manner was concentration-dependent and voltage-independent. This molecular-level analysis provides the basis for novel strategies to minimize pest damage. DTBP, with its specific binding to the Orco subunit, shows promise as a potential pest controller that can exclusively target insects.

Calix[4]pyrrole-Based Azo-Bridged Porous Organic Polymer for Bromine Capture.

The toxicity, corrosiveness, and volatility of elemental bromine presents challenges for its safe storage and transportation. Purification from other halogens is also difficult. Here, we report an easy-to-prepare calix[4]pyrrole-based azo-bridged porous organic polymer (C4P-POP) that supports efficient bromine capture. C4P-POP was found to capture bromine as a vapor and from a cyclohexane source phase with maximum uptake capacities of 3.6 and 3.4 g·g-1, respectively. Flow-through adsorption experiments revealed that C4P-POP removes 80% of the bromine from a 4.0 mM cyclohexane solution at a flow rate of 45 mL·h-1. C4P-POP also allowed the selective capture of bromine from a 1:1 mixture of bromine and iodine in cyclohexane.

Chloride Oxidation by One- or Two-Photon Excitation of N-Phenylphenothiazine.

Chloride oxidation has tremendous utility in the burgeoning field of chlorine-mediated C-H activation, yet it remains a challenging process to initiate with light because of the exceedingly positive one-electron reduction potential, E° (Cl•/-), beyond most common transition-metal photooxidants. Herein, two photocatalytic chloride oxidation pathways that involve either one- or consecutive two-photon excitation of N-phenylphenothiazine (PTH) are presented. The one-photon pathway generates PTH•+ by oxidative quenching that subsequently disproportionates to yield PTH2+ that oxidizes chloride; this pathway is also accessed by the electrochemical oxidation of PTH. The two-photon pathway, which proceeded through the radical cation excited state, 2PTH•+*, was of particular interest as this super-photooxidant was capable of directly oxidizing chloride to chlorine atoms. Laser flash photolysis revealed that the photooxidation by the doublet excited state proceeded on a subnanosecond timescale through a static quenching mechanism with an ion-pairing equilibrium constant of 0.36 M-1. The PTH photoredox chemistry was quantified spectroscopically on nanosecond and longer time scales, and chloride oxidation chemistry was revealed by reactivity studies with model organic substrates. One- and two-photon excitation of PTH enabled chlorination of unactivated C(sp3)-H bonds of organic compounds such as cyclohexane with substantial yield enhancement observed from inclusion of the second excitation wavelength. This study provides new mechanistic insights into chloride oxidation catalyzed by an inexpensive and commercially available organic photooxidant.

1,6;2,3-Bis-BN Cyclohexane: Synthesis, Structure, and Hydrogen Release.

BN/CC isosterism has been widely investigated as a strategy to expand carbon-based compounds. The introduction of BN units in organic molecules always results in novel properties. In this work, we reported the first synthesis and characterization of 1,6;2,3-bis-BN cyclohexane, an isostere of cyclohexane with two adjacent BN pairs. Its ring flipping barrier is similar to that of cyclohexane. Protic hydrogens on N in 1,6;2,3-bis-BN cyclohexane show higher reactivity than its isomeric bis-BN cyclohexane. This compound exhibits an appealing hydrogen storage capability of >9.0 wt %, nearly twice as much as the 1,2;4,5-bis-BN cyclohexane.

Genetic characterization of the cyclohexane carboxylate degradation pathway in the denitrifying bacterium Aromatoleum sp. CIB.

The alicyclic compound cyclohexane carboxylate (CHC) is anaerobically degraded through a peripheral pathway that converges with the central benzoyl-CoA degradation pathway of aromatic compounds in Rhodopseudomonas palustris (bad pathway) and some strictly anaerobic bacteria. Here we show that in denitrifying bacteria, e.g. Aromatoleum sp. CIB strain, CHC is degraded through a bad-ali pathway similar to that reported in R. palustris but that does not share common intermediates with the benzoyl-CoA degradation pathway (bzd pathway) of this bacterium. The bad-ali genes are also involved in the aerobic degradation of CHC in strain CIB, and orthologous bad-ali clusters have been identified in the genomes of a wide variety of bacteria. Expression of bad-ali genes in strain CIB is under control of the BadR transcriptional repressor, which was shown to recognize CHC-CoA, the first intermediate of the pathway, as effector, and whose operator region (CAAN4 TTG) was conserved in bad-ali clusters from Gram-negative bacteria. The bad-ali and bzd pathways generate pimelyl-CoA and 3-hydroxypimelyl-CoA, respectively, that are metabolized through a common aab pathway whose genetic determinants form a supraoperonic clustering with the bad-ali genes. A synthetic bad-ali-aab catabolic module was engineered and it was shown to confer CHC degradation abilities to different bacterial hosts.

Orientation and Conformation of Hydrophobin at the Oil-Water Interface: Insights from Molecular Dynamics Simulations.

Hydrophobins, a new class of potential protein emulsifiers, have been extensively employed in the food, pharmaceutical, and chemical industries. However, the knowledge of the underlying molecular mechanism of protein adsorption at the oil-water interface remains elusive. In this study, all-atom molecular dynamics simulations were performed to probe the adsorption orientation and conformation change of class II hydrophobin HFBI at the cyclohexane-water interface. It was proposed that a hydrophobic dipole of the protein could be used to quantitatively predict the orientation of the adsorbed HFBI. Simulation results revealed that HFBI adsorbed at the interface with the patch-up orientation toward the oil phase, regardless of its initial orientations. HFBI's secondary structure was maintained to be intact in the course of simulations despite relatively significant variations in the tertiary structure observed, which could well preserve the bioactivity of HFBI. From the energy analysis, the driving force for interface adsorption was primarily determined by van der Waals interactions between HFBI and cyclohexane. Further analysis indicated that the adsorption orientation and conformation of HFBI at the oil-water interface were typically regulated by the hydrophobic patch and some key residues. This study provides some insights into the orientation, conformation, and adsorption mechanism of proteins at the oil-water interface and theoretical guidelines for the design and development of novel biological emulsifiers involved in the food, pharmaceutical, and chemical industries.