Molecular basis for the interactions of eIF2ß with eIF5, eIF2B, and 5MP1 and their regulation by CK2.

The heterotrimeric GTPase eukaryotic translation initiation factor 2 (eIF2) delivers the initiator Met-tRNAi to the ribosomal translation preinitiation complex. eIF2ß has three lysine-rich repeats (K-boxes) in its N-terminal tail, which are important for binding to the GTPase-activating protein (GAP) eIF5, the guanine nucleotide exchange factor (GEF) eIF2B, and the regulator eIF5-mimic protein (5MP). Here, we combine X-ray crystallography with NMR to understand the molecular basis and dynamics of these interactions. The crystal structure of yeast eIF5-CTD in complex with K-box 3 of eIF2ß reveals an extended binding site on eIF2ß, far beyond the K-box. We show that human eIF5, eIF2Bε, and 5MP1 can all bind to each of the three K-boxes, while reducing each other's affinities. Moreover, all these affinities are increased by CK2 phosphomimetic mutations. Our results reveal how eIF5, eIF2B, and 5MP displace each other from eIF2, and elucidate the role of CK2 in remodeling the translation apparatus.

Structural Effects on the Temperature Dependence of Hydride Kinetic Isotope Effects of the NADH/NAD+ Model Reactions in Acetonitrile: Charge-Transfer Complex Tightness Is a Key.

It has recently frequently been found that the kinetic isotope effect (KIE) is independent of temperature (T) in H-tunneling reactions in enzymes but becomes dependent on T in their mutants. Many enzymologists found that the trend is related to different donor-acceptor distances (DADs) at tunneling-ready states (TRSs), which could be sampled by protein dynamics. That is, a more rigid system of densely populated short DADs gives rise to a weaker T dependence of KIEs. Theoreticians have attempted to develop H-tunneling theories to explain the observations, but none have been universally accepted. It is reasonable to assume that the DAD sampling concept, if it exists, applies to the H-transfer reactions in solution, as well. In this work, we designed NADH/NAD+ model reactions to investigate their structural effects on the T dependence of hydride KIEs in acetonitrile. Hammett correlations together with N-CH3/CD3 secondary KIEs were used to provide the electronic structure of the TRSs and thus the rigidity of their charge-transfer complexation vibrations. In all three pairs of reactions, a weaker T dependence of KIEs always corresponds to a steeper Hammett slope on the substituted hydride acceptors. It was found that a tighter/rigid charge-transfer complexation system corresponds with a weaker T dependence of KIEs, consistent with the observations in enzymes.

Medium Optimization and Fermentation Kinetics for Antifungal Compounds Production by an Endophytic Paenibacillus polymyxa DS-R5 Isolated from Salvia miltiorrhiza.

An endophytic bacterium Paenibacillus polymyxa DS-R5 which can effectively inhibit the growth of pathogenic fungi was isolated from Salvia miltiorrhiza in our previous study. By using hydrochloric acid precipitation, methanol extraction, silica gel column isolation, dextran gel chromatography column, and HPLC, 3 compounds with antifungal activity were isolated. To further improve the production of antifungal compounds produced by this strain, fermentation medium was optimized using one-factor-at-a-time, Plackett-Burman design, and Box-Behnken design experiments. Through statistical optimization, the optimal medium composition was determined to be as follows: 14.7 g/l sucrose, 20.0 g/l soluble starch, 7.0 g/l corn steep liquor, 10.0 g/l (NH4)2SO4, and 0.7 g/l KH2PO4. In this optimized medium, the highest titer of antifungal compounds reached 3452 U/ml, which was 123% higher than that in the initial medium. In addition, in order to guide scale-up for production, logistic and Luedeking-Piret equations were proposed to predict the cell growth and antifungal compounds production. The fermentation kinetics and empirical equations of the coefficients (X0, Xm, µm, α, and ß) for the two models were reported, which will aid the design and optimization of industrial processes. The degrees of fit between calculated values of the model and the experimental data were 0.989 and 0.973, respectively. The results show that the cell growth and product synthesis models established in this study may better reflect the dynamic process of antifungal compounds production and provide a theoretical basis for further optimization and on-line monitoring of the fermentation process.

Variational Quantum Algorithm Applied to Collision Avoidance of Unmanned Aerial Vehicles.

Mission planning for multiple unmanned aerial vehicles (UAVs) is a complex problem that is expected to be solved by quantum computing. With the increasing application of UAVs, the demand for efficient conflict management strategies to ensure airspace safety continues to increase. In the era of noisy intermediate-scale quantum (NISQ) devices, variational quantum algorithms (VQA) for optimizing parameterized quantum circuits with the help of classical optimizers are currently one of the most promising strategies to gain quantum advantage. In this paper, we propose a mathematical model for the UAV collision avoidance problem that maps the collision avoidance problem to a quadratic unconstrained binary optimization (QUBO) problem. The problem is formulated as an Ising Hamiltonian, then the ground state is solved using two kinds of VQAs: the variational quantum eigensolver (VQE) and the quantum approximate optimization algorithm (QAOA). We select conditional value-at-risk (CVaR) to further promote the performance of our model. Four examples are given to validate that with our method the probability of obtaining a feasible solution can exceed 90% based on appropriate parameters, and our method can enhance the efficiency of a UAVs' collision avoidance model.

Solvent Effects on the Temperature Dependence of Hydride Kinetic Isotope Effects: Correlation to the Donor-Acceptor Distances.

Protein structural effects on the temperature (T) dependence of kinetic isotope effects (KIEs) in H-tunneling reactions have recently been used to discuss about the role of enzyme thermal motions in catalysis. Frequently observed nearly T-independent KIEs in the wild-type enzymes and T-dependent KIEs in variants suggest that H-tunneling in the former is assisted by the naturally evolved protein constructive vibrations that help sample short donor-acceptor distances (DADs) needed. This explanation that correlates the T-dependence of KIEs with DAD sampling has been highly debated as simulations following other H-tunneling models sometimes gave alternative explanations. In this paper, solvent effects on the T-dependence of KIEs of two hydride tunneling reactions of NADH/NAD+ analogues (represented by ΔEa = EaD - EaH) were determined in attempts to replicate the observations in enzymes and test the protein vibration-assisted DAD sampling concept. Effects of selected aprotic solvents on the DADPRC's of the productive reactant complexes (PRCs) and the DADTRS's of the activated tunneling ready states (TRSs) were obtained through computations and analyses of the kinetic data, including 2° KIEs, respectively. A weaker T-dependence of KIEs (i.e., smaller ΔEa) was found in a more polar aprotic solvent in which the system has a shorter average DADPRC and DADTRS. Further results show that a charge-transfer (CT) complexation made of a stronger donor/acceptor gives rise to a smaller ΔEa. Overall, the shorter and less broadly distributed DADs resulting from the stronger CT complexation vibrations give rise to a smaller ΔEa. Our results appear to support the explanation that links the T-dependence of KIEs to the donor-acceptor rigidity in enzymes.

Isolation and identification of a new biocontrol bacteria against Salvia miltiorrhiza root rot and optimization of culture conditions for antifungal substance production using response surface methodology.

BACKGROUND: S. miltiorrhiza root rot is a soil-borne disease mainly caused by Fusarium solani and Fusarium oxysporum, which has spread rapidly in China in recent years. To reduce the amount of pesticides to control this plant fungal disease, biological control using endophytic bacteria is a promising method. Many endophytic bacteria show good biocontrol potential against various plant fungal diseases. The aims of this study were to isolate and identify endophytic bacteria with antifungal activity from Salvia miltiorrhiza plant tissue. In order to increase antifungal substances production, the culture conditions of the isolated DS-R5 strain were optimized through response surface methodology. RESULTS: Thirteen endophytic bacteria with antifungal activity against the target pathogenic fungus were successfully screened. The DS-R5 strain that had the strongest antifungal activity was identified based on morphological, physiological and biochemical characteristics, 16S rRNA and gyrB sequence analysis.The results of response surface methodology experiments showed that the optimal values of the three significant factors were as follows: medium volume, 51.0 ml; initial pH, 6.7; fermentation temperature, 33.1 °C. Under these optimal culture conditions, the titer of antifungal substances produced by the DS-R5 strain was 77.6% higher than that under the initial culture conditions. CONCLUSIONS: The antifungal activity of endophytic bacteria from Salvia miltiorrhiza has been demonstrated for the first time, which may benefit future crop quality and production. In addition, response surface methodology can be well applied the optimization of culture conditions for antifungal substance, which lays the foundation for further research on strain DS-R5.

Synthesis of Heterobiaryl 4-Aryl Furans through a Base-Promoted Decarboxylative Propargylation/Cycloisomerization Annulation.

A transition-metal-free synthesis of heterobiaryl 4-aryl furans through a base-promoted decarboxylative propargylation/cycloisomerization annulation of ethynyl benzoxazinanones and readily accessible ß-keto esters or 1,3-diketones has been developed. A series of novel heterobiaryl 4-aryl furans were accessed efficiently in the presence of base under mild reaction conditions. This protocol is significant for probing the reaction mechanism of ethynyl benzoxazinanones and even other propargylic compounds.

On some binomial [Formula: see text]-difference sequence spaces.

In this paper, we introduce the binomial sequence spaces [Formula: see text], [Formula: see text] and [Formula: see text] by combining the binomial transformation and difference operator. We prove the BK-property and some inclusion relations. Furthermore, we obtain Schauder bases and compute the α-, ß- and γ-duals of these sequence spaces. Finally, we characterize matrix transformations on the sequence space [Formula: see text].

Some normed binomial difference sequence spaces related to the [Formula: see text] spaces.

The aim of this paper is to introduce the normed binomial sequence spaces [Formula: see text] by combining the binomial transformation and difference operator, where [Formula: see text]. We prove that these spaces are linearly isomorphic to the spaces [Formula: see text] and [Formula: see text], respectively. Furthermore, we compute Schauder bases and the α-, ß- and γ-duals of these sequence spaces.