G2, G3, and complete basis set calculations on the thermodynamic properties of triazane

As a follow-up study to our study on tetrazane (N₄H₆), we present computed thermodynamic properties of triazane (N₃H₅). Calculated properties include optimized geometries, infrared vibrations, enthalpy of formation, enthalpy of combustion, and proton affinities. We have also mapped the potential energy surface as the molecule is rotated about the N-N bond. We have predicted a specific enthalpy of combustion for triazane of about -20 kJ g⁻¹. Figure Schematic diagram of the dielectric barrier discharge (left) and typical temporal profiles of voltage and current, as obtained from the simulations (right)     

Ab initio calculations on the thermodynamic properties of azaborospiropentanes

Following our recent studies of the thermodynamic properties of azaspiropentane and borospiropentane, in consideration of their usefulness as new potential high energy materials, we follow up with ab initio calculations on the thermodynamic properties of azaborospiropentanes. Properties reported in this study include optimized structural parameters, vibrational frequencies, enthalpies of formation, specific enthalpies of combustion, proton affinities, and hydride affinities. Our results indicate that azatriborospiropentane gives off most energy when combusted, as evidenced by its specific enthalpy of combustion of about −52 kJ per gram. Figure Optimized geometry for R-azatriborospiropentane (10) Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Structural,thermodynamic, and phosphatidylinositol 3‐phosphate binding properties of Phafin2

Phafin2 is a phosphatidylinositol 3‐phosphate (PtdIns(3)P) binding protein involved in the regulation of endosomal cargo trafficking and lysosomal induction of autophagy. Binding of Phafin2 to PtdIns(3)P is mediated by both its PH and FYVE domains. However, there are no studies on the structural basis, conformational stability, and lipid interactions of Phafin2 to better understand how this protein participates in signaling at the surface of endomembrane compartments. Here, we show that human Phafin2 is a moderately elongated monomer of ～28 kDa with an intensity‐average hydrodynamic diameter of ～7 nm. Circular dichroism (CD) analysis indicates that Phafin2 exhibits an α/β structure and predicts ～40% random coil content in the protein. Heteronuclear NMR data indicates that a unique conformation of Phafin2 is present in solution and dispersion of resonances suggests that the protein exhibits random coiled regions, in agreement with the CD data. Phafin2 is stable, displaying a melting temperature of 48.4°C. The folding‐unfolding curves, obtained using urea‐ and guanidine hydrochloride‐mediated denaturation, indicate that Phafin2 undergoes a two‐state native‐to‐denatured transition. Analysis of these transitions shows that the free energy change for urea‐ and guanidine hydrochloride‐induced Phafin2 denaturation in water is ～4 kcal mol^?1. PtdIns(3)P binding to Phafin2 occurs with high affinity, triggering minor conformational changes in the protein. Taken together, these studies represent a platform for establishing the structural basis of Phafin2 molecular interactions and the role of the two potentially redundant PtdIns(3)P‐binding domains of the protein in endomembrane compartments.     

Conformational behaviours of 2-substituted cyclohexanones: a complete basis set,hybrid-DFT study and NBO interpretation

The generalised anomeric effect (GAE) and gauche effect (GE) associated with donor–acceptor delocalisations, dipole–dipole interactions and total steric exchange energies (TSEE) on the conformational properties of 2-methoxy- (1), 2-methylthio- (2), 2-methylseleno- (3), 2-fluoro- (4), 2-chloro- (5) and 2-bromocyclohexanone (6) have been studied by means of ab initio and hybrid density functional theory methods and natural bond orbital (NBO) analysis. All methods used showed that the axial conformation stability increased from 2-methoxy- (1) to 2-methylselenocyclohexanone (3) and also from 2-fluoro- (4) to 2-bromocyclohexanone (6), which is in agreement with reported NMR data. The results obtained by complete basis set 4 (CBS-4), B3LYP/6-311+G** and HF/6-311+G** levels for compounds 1, 5 and 6 are very similar, but the CBS-4 results for compound 4 are not in agreement with the reported experimental data (vapour phase). The NBO analysis showed that the GAE increases from compounds 1 to 3 and also from compounds 4 to 6. The low axial conformer populations of compounds 1 and 4 can be reasonably explained by their small GAE. GE does not have significant impact on the conformational behaviours of compounds 1–6 and GAE succeeds in accounting qualitatively for the increase in the axial preferences in both series of compounds. The results showed that the calculated Δ(TSEE_eq–ax) values decrease from compounds 4 to 6 which contradicts the suggested arguments in the literature about these compounds. On the other hand, the calculated differences between the dipole moment values of the axial and equatorial conformations, Δ(μ_eq ? μ_ax), increase from compounds 1 to 2, but decrease from compounds 2 to 3 and also decrease from compounds 4 to 6. The calculated GAE values are more significant for the explanation of the conformational preferences of compounds 1–6 than the dipole–dipole repulsion effects. The correlations between the GAE, GE, dipole–dipole interactions, Wiberg Bond Index, TSEE, donor and acceptor orbital energies and occupancies, structural parameters and conformational behaviour of compounds 1–6 have been investigated.     

Diethylstilbestrol potentiates and testosterone antagonizes the action of 3-methylcholanthrene on benzo(a) pyrene metabolism in hep G2 cells

We have used the human hepatoma cell line, Hep G2, to examine the ability of hormones and xenobiotics to modulate the hepatic induction of benzo(a)pyrene hydroxylase and epoxide hydrolase. Hep G2 cells were cultured in Eagle's Minimum Essential Medium supplemented with 10% fetal calf serum. 3-Methylcholanthrene, diethylstilbestrol, testosterone propionate, and combinations of 3-meth-ylcholanthrene, and each of the hormones were added directly to the culture media. We subsequently studied the metabolism of benzo(a)pyrene using cell lysates of the Hep G2 cells. Metabolites were quantitated by high-performance liquid chromatography (HPLC) using fluorodetection. Exposure to 3-methyl-cholanthrene alone resulted in an eightfold increase in total benzo(a)pyrene metabolites with a change of the predominant metabolite from the 3-hydroxy-benzo(a)pyrene to the carcinogenic pathway of the benzo(a)pyrene-7,8-diol. Diethylstilbestrol and testosterone propionate resulted in small, but significant, decreases in metabolism of benzo(a)pyrene. When exposed in combination with 3-methyl-cholanthrene, testosterone propionate antagonized and diethylstilbestrol potentiated the metabolism of benzo(a)pyrene. 3-Methylcholanthrene, diethylstilbestrol, and combinations of 3-methylcholanthrene and diethylstilbestrol or testosterone propionate resulted in increased epoxide hydrolase activity as compared to controls. These results, carried out in a human hepatoma cell line, lend support to a concern for potentiated toxicity and carcinogenicity following exposure to complex chemical mixtures.     

In silico identification of MicroRNAs targeting the key nucleator of stress granules,G3BP: Promising therapeutics for SARS-CoV-2 infection

Stress granules (SGs) are non-membrane ribonucleoprotein condensates formed in response to environmental stress conditions via liquid–liquid phase separation (LLPS). SGs are involved in the pathogenesis of aging and aging-associated diseases, cancers, viral infection, and several other diseases. GTPase-activating protein (SH3 domain)-binding protein 1 and 2 (G3BP1/2) is a key component and commonly used marker of SGs. Recent studies have shown that SARS-CoV-2 nucleocapsid protein via sequestration of G3BPs inhibits SGs formation in the host cells. In this study, we have identified putative miRNAs targeting G3BP in search of modulators of the G3BP expression. These miRNAs could be considered as new therapeutic targets against COVID-19 infection via the regulation of SG assembly and dynamics.     

Multicolor BiFC analysis of competition among G protein β and γ subunit interactions

We have applied multicolor BiFC to study the association preferences of G protein β and γ subunits in living cells. Cells co-express multiple isoforms of β and γ subunits, most of which can form complexes. Although many βγ complexes exhibit similar properties when assayed in reconstituted systems, knockout experiments in vivo suggest that individual isoforms have unique functions. BiFC makes it possible to correlate βγ complex formation with functionality in intact cells by comparing the amounts of fluorescent βγ complexes with their abilities to modulate effector proteins. The relative predominance of specific βγ complexes in vivo is not known. To address this issue, multicolor BiFC can determine the association preferences of β and γ subunits by simultaneously visualizing the two fluorescent complexes formed when β or γ subunits fused to amino terminal fragments of yellow fluorescent protein (YFP-N) and cyan fluorescent protein (CFP-N) compete to interact with limiting amounts of a common γ or β subunit, respectively, fused to a carboxyl terminal fragment of CFP (CFP-C). Multicolor BiFC also makes it possible to determine the roles of interacting proteins in the subcellular targeting of complexes, study the formation of protein complexes that are unstable under isolation conditions, determine the roles of co-expressed proteins in regulating the association preferences of interacting proteins, and visualize dynamic events affecting multiple protein complexes. These approaches can be applied to studying the assembly and functions of a wide variety of protein complexes in the context of a living cell.     

C3G mediated suppression of malignant transformation involves activation of PP2A phosphatases at the subcortical actin cytoskeleton

In previous work, we demonstrated that C3G suppresses Ras oncogenic transformation by a mechanism involving inhibition of ERK phosphorylation. Here we present evidences indicating that this suppression mechanism is mediated, at least in part, by serine/threonine phosphatases of the PP2A family. Thus: (i) ectopic expression of C3G or C3GDeltaCat (mutant lacking the GEF activity) increases specific ERK-associated PP2A phosphatase activities; (ii) C3G and PP2A interact, as demonstrated by immunofluorescence and co-immunoprecipitation experiments; (iii) association between PP2A and MEK or ERK increases in C3G overexpressing cells; (iv) phosphorylated-inactive PP2A level decreases in C3G expressing clones and, most importantly, (v) okadaic acid reverts the inhibitory effect of C3G on ERK phosphorylation. Moreover, C3G interacts with Ksr-1, a scaffold protein of the Ras-ERK pathway that also associates with PP2A. The fraction of C3G involved in transformation suppression is restricted to the subcortical actin cytoskeleton where it interacts with actin. Furthermore, the association between C3G and PP2A remains stable even after cytoskeleton disruption with cytochalasin D, suggesting that the three proteins form a complex at this subcellular compartment. Finally, C3G- and C3GDeltaCat-mediated inhibition of ERK phosphorylation is reverted by incubation with cytochalasin D. We hypothesize that C3G triggers PP2A activation and binding to MEK and ERK at the subcortical actin cytoskeleton, thus favouring ERK dephosphorylation.     

3-Silaoxetane and 3-silathietane: structure and reactivity studies on the basis of spectroscopic data and theoretical calculations

The ab initio and DFT calculations (structural parameters, electron localization function (ELF)) on 3-silaoxetane 3,3-dimethyl-2,2,4,4-tetraphenyl-1-oxa-3-silacyclobutane (1) and 3-silathietane 3,3-dimethyl-2,2,4,4-tetraphenyl-1-sila-3-thiacyclobutane (2) show the cyclobutane ring in 2 as being non-planar with a C-Si-C angle of 89.2° and a C-S-C angle of 93.3°, whereas the cyclobutane ring in 1 is planar with an unusual small bond angle at the silicon atom of 74.7°, which can only be explained by bent bonds. Since the synthesis was performed in water, small bent angles cannot be indicative for high reactivity. The Raman spectra of 1 and 2 were then recorded and analyzed in the 1800-200 cm⁻¹ spectral region at various temperatures (300-10 K) with the help of the DFT calculation results (harmonic vibrational wavenumbers, Raman scattering activities). Although the wavenumber shifts are quite small, the subtle changes in the spectral features of the 3-silaoxetane and phenyl rings vibrational modes may indicate a loss of symmetry in 1 (between 200 and 150 K) and a possible phase transition in 2 (at about 200 K). Furthermore, the Raman spectra of 1 and 2 confirmed the ELF calculation results, excluding any bond interaction between the silicon and the oxygen or sulfur atom.     

汉滩病毒囊膜糖蛋白G1、G2腺病毒载体的表达及免疫分析

为了研究利用腺病毒载体表达汉滩病毒囊膜糖蛋白G1、G2的可行性及免疫原性。通过克隆76-118株G1、G2基因至腺病毒表达载体pAdTrackCMV,得到阳性克隆padTrackCMV-G1、G2。PmeI线性化的阳性克隆与腺病毒骨架载体pAdeasy-1共转化BJ5183宿主菌,经同源重组后得到重组病毒rAdeasy-G1、rAdeasy-G2。重组病毒经PacI线性化后,脂质体介导转染293细胞,使重组病毒得到扩增。将重组病毒免疫Balb／c小鼠,并通过ELISA和间接免疫荧光对免疫小鼠血清进行了分析。结果表明,rAdeasy—G1组六只免疫小鼠、rAdeasy—G2组4只免疫小鼠均产生了能与汉滩病毒抗原发生反应的特异抗体。该研究为进一步研制以腺病毒为活载体的汉坦病毒工程疫苗奠定了基础。     

汉滩病毒囊膜糖蛋白G1、G2腺病毒载体的表达及免疫分析

为了研究利用腺病毒载体表达汉滩病毒囊膜糖蛋白G1、G2的可行性及免疫原性.通过克隆76-118株G1、G2基因至腺病毒表达载体pAdTrackCMV,得到阳性克隆pAdTrackCMV-G1、G2.PmeI线性化的阳性克隆与腺病毒骨架载体pAdeasy-1共转化BJ5183宿主菌,经同源重组后得到重组病毒rAdeasy-G1、rAdeasy-G2.重组病毒经PacI线性化后,脂质体介导转染293细胞,使重组病毒得到扩增.将重组病毒免疫Balb/c小鼠,并通过ELISA和间接免疫荧光对免疫小鼠血清进行了分析.结果表明,rAdeasy-G1组六只免疫小鼠、rAdeasy-G2组4只免疫小鼠均产生了能与汉滩病毒抗原发生反应的特异抗体.该研究为进一步研制以腺病毒为活载体的汉坦病毒工程疫苗奠定了基础.     

Extensive mutagenesis experiments corroborate a structural model for the DNA deaminase domain of APOBEC3G

APOBEC3G is a single-strand DNA cytosine deaminase capable of blocking retrovirus and retrotransposon replication. APOBEC3G has two conserved zinc-coordinating motifs but only one is required for catalysis. Here, deletion analyses revealed that the minimal catalytic domain consists of residues 198-384. Size exclusion assays indicated that this protein is monomeric. Many (31/69) alanine substitution derivatives of APOBEC3G198-384 retained significant to full levels of activity. These data corroborated an APOBEC2-based structural model for the catalytic domain of APOBEC3G indicating that most non-essential residues are solvent accessible and most essential residues cluster within the protein core.     

Rheological properties of barley β-glucan

Health benefits of cereal β-glucan are linked to its high viscosity. Although viscosity of β-glucan gum solutions has been reported previously, there are conflicting reports about its behavior at elevated temperatures. Therefore, the viscosity behavior of barley β-glucan gum obtained in a pilot plant (PP) or in a laboratory (LAB) was determined at different shear rates (1.29–129 s⁻¹) and temperatures (0.1–75 °C) in this study. Viscosity decrease with temperature was demonstrated for both gums and activation energy E_a was calculated from the Arrhenius equation. None of the fresh gum solutions exhibited thixotropic behavior at ≤1% (w/w) concentration, but the measurement demonstrated that increased shear rate is not applicable to polymer solutions of low viscosity. Information about rheological properties of β-glucan will lead to better understanding of its behavior under physiological and processing conditions.     

Association of the PIK3C2G gene polymorphisms with type 2 DM in a Japanese population

The associations of five SNPs (SNPs1-5: A-5468G, A-3333G, C-1794T, C437T and T9148C) of the class II phosphoinositide 3-kinase γ-subunit (PIK3C2G) gene with type 2 diabetes were examined using a population of the Takahata Study (n (M/W): 2930 (1328/1602); age: 63.3 ± 10.2 years), a Japanese community-based study. Quantitative association study of the SNPs with HbA1c levels showed significant association for SNPs 2 and 4 (p = 0.018 and 0.004, respectively). A case-control association study of SNP 4 with diabetes by multiple logistic regression analysis showed a significant association of the genotype TT of the SNP with an odds ratio of 2.21 (p = 0.001) independently of age, gender and BMI. In the NGT subjects, serum fasting insulin levels in the at-risk genotype group of SNP 4 were significantly lower than those in the others (TT, TC, and CC, 4.9 ± 2.6, 5.4 ± 3.0, and 5.6 ± 3.4 μU/ml, respectively; p = 0.029).     

Endothelium-Derived Semaphorin 3G Regulates Hippocampal Synaptic Structure and Plasticity via Neuropilin-2/PlexinA4

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The MAPK1/3 pathway is essential for the deregulation of autophagy observed in G2019S LRRK2 mutant fibroblasts

The link between the deregulation of autophagy and cell death processes can be essential in the development of several neurodegenerative diseases, such as Parkinson disease (PD). However, the molecular mechanism of deregulation of this degradative process in PD patients is unknown. The leucine-rich repeat kinase 2 (LRRK2) gene is related to PD and its implication in autophagy regulation has been described. Our recent work shows that the presence of the G2019S LRRK2 mutation, one of the most prevalent in LRRK2, is accompanied by a deregulation of autophagy basal levels dependent on the MAPK1/3 (ERK2/1) pathway.     

The MAPK1/3 pathway is essential for the deregulation of autophagy observed in G2019S LRRK2 mutant fibroblasts

The link between the deregulation of autophagy and cell death processes can be essential in the development of several neurodegenerative diseases, such as Parkinson disease (PD). However, the molecular mechanism of deregulation of this degradative process in PD patients is unknown. The leucine-rich repeat kinase 2 (LRRK2) gene is related to PD and its implication in autophagy regulation has been described. Our recent work shows that the presence of the G2019S LRRK2 mutation, one of the most prevalent in LRRK2, is accompanied by a deregulation of autophagy basal levels dependent on the MAPK1/3 (ERK2/1) pathway.     

G9a/GLP-sensitivity of H3K9me2 Demarcates Two Types of Genomic Compartments

In the nucleus, chromatin is folded into hierarchical architecture that is tightly linked to various nuclear functions. However, the underlying molecular mechanisms that confer these architectures remain incompletely understood. Here, we investigated the functional roles of H3 lysine 9 dimethylation (H3K9me2), one of the abundant histone modifications, in three-dimensional (3D) genome organization. Unlike in mouse embryonic stem cells, inhibition of methyltransferases G9a and GLP in differentiated cells eliminated H3K9me2 predominantly at A-type (active) genomic compartments, and the level of residual H3K9me2 modifications was strongly associated with B-type (inactive) genomic compartments. Furthermore, chemical inhibition of G9a/GLP in mouse hepatocytes led to decreased chromatin-nuclear lamina interactions mainly at G9a/GLP-sensitive regions, increased degree of genomic compartmentalization, and up-regulation of hundreds of genes that were associated with alterations of the 3D chromatin. Collectively, our data demonstrated essential roles of H3K9me2 in 3D genome organization.     

Competing G protein‐coupled receptor kinases balance G protein and β‐arrestin signaling

Seven‐transmembrane receptors (7TMRs) are involved in nearly all aspects of chemical communications and represent major drug targets. 7TMRs transmit their signals not only via heterotrimeric G proteins but also through β‐arrestins, whose recruitment to the activated receptor is regulated by G protein‐coupled receptor kinases (GRKs). In this paper, we combined experimental approaches with computational modeling to decipher the molecular mechanisms as well as the hidden dynamics governing extracellular signal‐regulated kinase (ERK) activation by the angiotensin II type 1A receptor (AT_1AR) in human embryonic kidney (HEK)293 cells. We built an abstracted ordinary differential equations (ODE)‐based model that captured the available knowledge and experimental data. We inferred the unknown parameters by simultaneously fitting experimental data generated in both control and perturbed conditions. We demonstrate that, in addition to its well‐established function in the desensitization of G‐protein activation, GRK2 exerts a strong negative effect on β‐arrestin‐dependent signaling through its competition with GRK5 and 6 for receptor phosphorylation. Importantly, we experimentally confirmed the validity of this novel GRK2‐dependent mechanism in both primary vascular smooth muscle cells naturally expressing the AT_1AR, and HEK293 cells expressing other 7TMRs.