Product Complex Research Articles

Control of 3' splice site selection by the yeast splicing factor Fyv6.

Pre-mRNA splicing is catalyzed in two steps: 5' splice site (SS) cleavage and exon ligation. A number of proteins transiently associate with spliceosomes to specifically impact these steps (1st and 2nd step factors). We recently identified Fyv6 (FAM192A in humans) as a 2nd step factor in S. cerevisiae; however, we did not determine how widespread Fyv6's impact is on the transcriptome. To answer this question, we have used RNA-seq to analyze changes in splicing. These results show that loss of Fyv6 results in activation of non-consensus, branch point (BP) proximal 3' SS transcriptome-wide. To identify the molecular basis of these observations, we determined a high-resolution cryo-EM structure of a yeast product complex spliceosome containing Fyv6 at 2.3 Å. The structure reveals that Fyv6 is the only 2nd step factor that contacts the Prp22 ATPase and that Fyv6 binding is mutually exclusive with that of the 1st step factor Yju2. We then use this structure to dissect Fyv6 functional domains and interpret results of a genetic screen for fyv6Δ suppressor mutations. The combined transcriptomic, structural, and genetic studies allow us to propose a model in which Yju2/Fyv6 exchange facilitates exon ligation and Fyv6 promotes usage of consensus, BP distal 3' SS.

What is the Origin of the Regioselective C3-Hydroxylation of L-Arg by the Nonheme Iron Enzyme Capreomycin C?

The nonheme iron dioxygenase capreomycin C (CmnC) hydroxylates a free L-arginine amino acid regio- and stereospecifically at the C3-position as part of the capreomycin antibiotics biosynthesis. Little is known on its structure, catalytic cycle and substrate specificity and, therefore, a comprehensive computational study was performed. A large QM cluster model of CmnC was created of 297 atoms and the mechanisms for C3-H, C4-H and C5-H hydroxylation and C3-C4 desaturation were investigated. All low-energy pathways correspond to radical reaction mechanisms with an initial hydrogen atom abstraction followed by OH rebound to form alcohol product complexes. The work is compared to alternative L-Arg hydroxylating nonheme iron dioxygenases and the differences in active site polarity are compared. We show that a tight hydrogen bonding network in the substrate binding pocket positions the substrate in an ideal orientation for C3-H activation, whereby the polar groups in the substrate binding pocket induce an electric field effect that guides the selectivity.

Some rigid results on doubly twisted product complex Finsler manifolds

Some rigid results on doubly twisted product complex Finsler manifolds

Construction of a Bifunctional Nanoelectrode for Intracellular Natural Product Delivery and Monitoring Anticancer Efficiency in Single Cells.

Natural products play a significant role in new drug discovery and anticancer therapy, making the evaluation of their anticancer efficiency crucial for clinical application. However, delivering natural products to single cells and in situ monitoring of induced signaling molecule fluctuation to evaluate anticancer efficiency remain significant challenges. Hence, we proposed a universal and straightforward strategy to construct a bifunctional nanoelectrode that integrates drug loading and monitoring of signal molecule fluctuations at the single-cell level. Platinum (Pt) nanoparticles/reduced graphene oxide (rGO) composites were first electrochemically deposited on the carbon fiber nanoelectrode (CFNE@Pt/rGO) to serve as electrocatalytic materials for the monitoring of natural-product-induced reactive oxygen species (ROS) generation. The GO/natural product complex, formed by π-π stacking and hydrophobic interactions, was further electrochemically reduced on the surface of CFNE@Pt/rGO to enable the CFNE drug-loading function. Using this bifunctional functional nanoelectrode, a series of natural products (such as capsaicin, curcumin, and chrysin) were delivered into single cancer cells, and their anticancer efficiency was evaluated by measuring ROS generation. The results showed that intracellular ROS production induced by chrysin was 1.5-fold greater than that of curcumin and 2.1-fold greater than that of capsaicin. This work proposes an effective tool to evaluate the anticancer efficiency of various natural products. Additionally, this nanotool can be expanded to monitor the fluctuation of other biomolecules (such as RNS, GSH, NADH, etc.) by replacing Pt nanoparticles with other electrocatalytic materials, which is significant for comprehensively exploring the anticancer efficiency of new drugs and for the clinical treatment of various diseases.

Hydroxyl radical-induced C1'-H abstraction reaction of different artificial nucleotides.

Recently, a few antiviral drugs viz Molnupiravir (EIDD-1931), Favipiravir, Ribavirin, Sofosbuvir, Galidesivir, and Remdesivir are shown to be beneficial against COVID-19 disease. These drugs bind to the viral RNA single strand to inhibit the virus genome replication. Similarly, recently, some artificial nucleotides, such as P, J, B, X, Z, V, S, and K were proposed to behave as potent antiviral candidates. However, their activity in the presence of the most reactive hydroxyl (OH) radical is not yet known. Here, the possibility of RNA strand break due to the OH radical-induced C1'-hydrogen (H) abstraction reaction of the above molecules (except Remdesivir) is studied in detail by considering their nucleotide conformation. The results are compared with those of the natural RNA nucleotides (G, C, A, and U). Due to low Gibbs barrier-free energy and high exothermicity,all these nucleotides (except Remdesivir) are prone to OH radical-inducedC1'-H abstraction reaction.As Remdesivir contains a C1'-CN bond,the OH radical substitution reactions at theCN and C1' siteswould likely liberate the catalytically important CN group, thereby downgrading its activity. Initially, the B3LYP-D3 dispersion-corrected density functional theory method and 6-31 + G* basis set were used to optimize all reactant, transition state, and product complexes in the implicit aqueous medium. Subsequently, the structures of these complexes were further optimized by using the ωB97X-D dispersion-corrected density functional theory method and cc-PVTZ basis set in the aqueous medium. The IEFPCM method was used to model the aqueous medium.

Dioxygenase Chemistry in Nucleophilic Aldehyde Deformylations Utilizing Dicopper O2-Derived Peroxide Complexes.

The chemistry of copper-dioxygen complexes is relevant to copper enzymes in biology as well as in (ligand)Cu-O2 (or Cu2-O2) species utilized in oxidative transformations. For overall energy considerations, as applicable in chemical synthesis, it is beneficial to have an appropriate atom economy; both O-atoms of O2(g) are transferred to the product(s). However, examples of such dioxygenase-type chemistry are extremely rare or not well documented. Herein, we report on nucleophilic oxidative aldehyde deformylation reactivity by the peroxo-dicopper(II) species [Cu2II(BPMPO-)(O22-)]1+ {BPMPO-H = 2,6-bis{[(bis(2-pyridylmethyl)amino]methyl}-4-methylphenol)} and [Cu2II(XYLO-)(O22-)]1+ (XYLO- = a BPMPO- analogue possessing bis(2-{2-pyridyl}ethyl)amine chelating arms). Their dicopper(I) precursors are dioxygenase catalysts. The O2(g)-derived peroxo-dicopper(II) intermediates react rapidly with aldehydes like 2-phenylpropionaldehyde (2-PPA) and cyclohexanecarboxaldehyde (CCA) in 2-methyltetrahydrofuran at -90 °C. Warming to room temperature (RT) followed by workup results in good yields of formate (HC(O)O-) along with ketones (acetophenone or cyclohexanone). Mechanistic investigation shows that [Cu2II(BPMPO-)(O22-)]1+ species initially reacts reversibly with the aldehydes to form detectable dicopper(II) peroxyhemiacetal intermediates, for which optical titrations provide the Keq (at -90 °C) of 73.6 × 102 M-1 (2-PPA) and 10.4 × 102 M-1 (CCA). In the reaction of [Cu2II(XYLO-)(O22-)]1+ with 2-PPA, product complexes characterized by single-crystal X-ray crystallography are the anticipated dicopper(I) complex, [Cu2I(XYLO-)]1+ plus a mixed-valent Cu(I)Cu(II)-formate species. Formate was further identified and confirmed by 1H NMR spectroscopy and electrospray ionization mass spectrometry (ESI-MS) analysis. Using 18O2(g)-isotope labeling the reaction produced a high yield of 18-O incorporated acetophenone as well as formate. The overall results signify that true dioxygenase reactions have occurred, supported by a thorough mechanistic investigation.

Assessment of milk production and processing in the southern regions of the Republic of Kazakhstan

Goal - indicators of production and processing of cow's milk in the region are presented using the construction of multiple regression model and recommendations for the development of dairy market in Kazakhstan are given. In the work methods of logic, statistical analysis, factorial, econometric modeling and systematization are used. Results - it is noted that dairy industry is an integral part of agro-industrial complex. Literary sources containing information on achievements in dairy industry of developed countries are analyzed; current state of the world economy and its importance for ensuring food security are shown: inflation, anti-Russian sanctions, decline in consumer incomes. The productivity of cows, reasons for the decline and increase in milk production, low share of dairy processing, and high depreciation of agricultural machinery are considered. The need to conduct research on the volume of dairy products production is substantiated using the example of Almaty as a large milk-processing regional center. It has been determined that the influx of investment has a significant impact on productivity of the city's dairy enterprises. An econometric assessment of the factors that have the greatest impact on the process of processing raw materials and obtaining finished products was carried out. Conclusions – scientific and practical results of generated regression model for assessing production processes and milk processing are presented. Socioeconomic criteria have been determined: the level of employee salaries, food inflation in dairy industry, increase in the number of dairy product complexes. Recommendations for modernization of dairies based on effective measures of state support, consolidation of small agricultural producers, and introduction of innovative technologies have been developed. Resource conservation is important - mandatory requirement for equipment, technologies, production activities, and economic mechanisms. Accounting of resources, their availability and consumption, careful attitude to the use of energy, water, heat are mandatory components of the rational use of potential.

Computational Insights into Amide Bond Formation Catalyzed by the Condensation Domain of Nonribosomal Peptide Synthetases.

Nonribosomal peptide synthetases (NRPSs) are important enzymes that synthesize an array of nongenetically encoded peptides. The latter have diverse physicochemical properties and roles. NRPSs are modular enzymes in which, for example, the condensation (C-) domain catalyzes the formation of amide bonds. The NRPS tyrocidine synthetase from Brevibacillus brevis is responsible for synthesizing the cyclic-peptide antibiotic tyrocidine. The first step is formation of an amide bond between a proline and phenylalanine which is catalyzed by a C-domain. In this study, a multiscale computational approach (molecular dynamics and QM/MM) has been used to investigate substrate binding and catalytic mechanism of the C-domain of tyrocidine synthetase. Overall, the mechanism is found to proceed through three exergonic steps in which an active site Histidine, His222, acts as a base and acid. First, His222 acts as a base to facilitate nucleophilic attack of the prolyl nitrogen at the phenylalanyl's carbonyl carbon. This is also the rate-limiting step with a free energy barrier of 38.8 kJ mol-1. The second step is collapse of the resulting tetrahedral intermediate with cleavage of the S-C bond between the phenylalanyl and its Ppant arm, along with formation of the above amide bond. Meanwhile, the now protonated His222 imidazole has rotated toward the newly formed thiolate of the Ppant arm. In the final step, His222 acts as an acid, protonating the thiolate and regenerating a neutral His222. The overall mechanism is found to be exergonic with the final product complex being 46.3 kJ mol-1 lower in energy than the initial reactant complex.

Systems metabolic engineering of Escherichia coli for high-yield production of Para-hydroxybenzoic acid

Para-hydroxybenzoic acid (PHBA) is extensively used as an additive in the food and cosmetics industries, significantly enhancing product shelf life and stability. While microbial fermentation offers an environment-friendly and sustainable method for producing PHBA, the titer and productivity are limited due to product toxicity and complex metabolic flux distributions. Here, we initially redesigned a L-phenylalanine-producing Escherichia coli by employing rational metabolic engineering strategies, resulting in the production of PHBA reached the highest reported level of 14.17 g/L. Subsequently, a novel accelerated evolution system was devised comprising deaminase, the alpha subunit of RNA polymerase, an uracil-DNA glycosylase inhibitor, and the PHBA-responsive promoter PyhcN. This system enabled us to obtain a mutant strain exhibiting a 47% increase in the half-inhibitory concentration (IC50) for PHBA within 15 days. Finally, the evolved strain achieved a production of 21.35 g/L PHBA in a 5-L fermenter, with a yield of 0.19 g/g glucose and a productivity rate of 0.44 g/L/h. This engineered strain emerges as a promising candidate for industrial production of PHBA through an eco-friendly approach.

Computational Insights into Protein Aging: Spontaneous Deamidation of Glutamine.

Spontaneous deamidation of amino acids is a physiologically important process, particularly for protein aging and diseases. Despite its widespread occurrence, the mechanism of glutamine deamidation particularly within proteins remains poorly understood. We have used a multiscale computational approach to investigate glutamine deamidation in the tripeptide Glycine-Glutamine-Glycine (Gly-Gln-Gly) and γS-Crystallin protein. Specifically, both the 5- and 6-membered water-assisted deamidation pathways in the tripeptide have been elucidated and compared. Both are found to occur in three stages: iminol formation, cyclization, and deamination. The rate-limiting step in each mechanism is nucleophilic attack of the backbone iminol nitrogen, formed in the first stage, at the glutamine's side-chain carbonyl carbon. For the 6- and 5-membered mechanisms, this occurs with a free energy cost of 136.4 and 179.5 kJ mol-1, respectively. Thus, overall, in the Gly-Gln-Gly tripeptide, the 6-membered pathway is preferred. Furthermore, the free energies for forming cyclic intermediates and products at selected Gln residues (based on experimentally reported % deamidation) in γS-Crystallin have been obtained. It is found that the 5-membered product complex is exergonic at -25.3 kJ mol-1, while the 6-membered product complex is calculated to be endergonic at 90.7 kJ mol-1. Thus, the deamidation pathway in folded and constrained proteins may not exclusively follow the 6-membered route. Molecular dynamics (MD) simulations of γS-Crystallin indicate that deamidation is more likely to occur when two or more water molecules are in the proximity of the glutamine residue. Consequently, significant conformational changes are found to accompany Gln120 deamidation in γS-Crystallin. This in turn can influence water availability at the other Gln residues considered and hence potentially their deamidation. Collectively, these results provide comprehensive insights into spontaneous water-assisted deamidation of glutamine residues in peptides and into the role and impact of Gln deamidation in proteins.

Apolipoprotein D3 and LOX product play a role in immune-priming of a lepidopteran insect, Spodoptera exigua

Immune-priming occurs in insects after a prior pathogen exposure. However, its underlying mechanism in insects remains elusive. In the present work, immune-priming was detected in a lepidopteran insect, Spodoptera exigua. Specifically, a prior infection with a heat-killed pathogenic bacterium, Escherichia coli, led to increased survival upon the second infection of different pathogens. Plasma collected from larvae with the prior infection possessed the immune-priming factor(s) that significantly up-regulated cellular and humoral immune responses of naïve larvae. Our study also finds that variations in the timing of plasma collection for priming larvae resulted in distinct impacts on both cellular and humoral responses. However, when the active plasma exhibiting the immune-priming was heat-treated, it lost this priming activity, therefore suggesting that protein factor(s) play a role in this immune-priming. An immunofluorescence assay showed that the hemocytes collected from the immune-primed larvae highly reacted to a polyclonal antibody specific to a vertebrate lipocalin, apolipoprotein D (ApoD). Among 27 ApoD genes (Se-ApoD1 ∼ Se-ApoD27) of S. exigua, Se-ApoD3 was found to be highly induced during the immune-priming, in which it was shown to be expressed in hemocytes and fat body from a fluorescence in situ hybridization analysis. RNA interference of Se-ApoD3 expression significantly impaired the immune-priming of S. exigua larvae. Moreover, the inhibition of eicosanoid biosynthesis suppressed the immune-priming, in which treatment with a lipoxygenase (LOX) inhibitor—and not treatment with a cyclooxygenase inhibitor—suppressed immune-priming. Further, an addition of LOX product such as lipoxin A4 or lipoxin B4 significantly rescued the lost immune-priming activity. Taken together, these results suggest that a complex of ApoD3 and LOX product mediates the immune-priming activity of S. exigua.

Dairy-product complex: features of functioning

The goal is to monitor functioning of dairy product complex, including production, management, marketing and economic aspects, on the basis of which the current state and prospects for its development are considered, problems and possible solutions are identified, optimal options for intensifying production processes are shown to increase their efficiency and improving the quality of dairy products. Methods – statistical collection and analysis of data on volumes, productivity levels, consumer demand, prices for dairy products; economic analysis made it possible to study production component, including the study of costs, profits, structure of expenses and income, factors influencing on profitability and competitiveness of dairy enterprises. By familiarizing with technological schemes of the dairy industry, quality level, living conditions of animals, methods of storage and transportation of milk and dairy products were analyzed, and promising directions of production cycle were assessed. Results - recommendations for the effective use of technologies to increase labor productivity and product competitiveness have been prepared. A study of dairy sector of agriculture, which makes a significant contribution to the country’s economy, made it possible to identify problematic segments: high costs, instability of prices for raw materials and products, as well as insufficient demand in foreign trade. It is recommended to develop a strategy for promoting domestic products and meeting the needs of domestic and foreign markets. Conclusions - regular updating of equipment, constant training of personnel and adaptation to changing market requirements are the key to success in increasing the volume of the dairy industry.

Transformer-Empowered Multi-Modal Item Embedding for Enhanced Image Search in E-commerce

Over the past decade, significant advances have been made in the field of image search for e-commerce applications. Traditional image-to-image retrieval models, which focus solely on image details such as texture, tend to overlook useful semantic information contained within the images. As a result, the retrieved products might possess similar image details, but fail to fulfil the user's search goals. Moreover, the use of image-to-image retrieval models for products containing multiple images results in significant online product feature storage overhead and complex mapping implementations. In this paper, we report the design and deployment of the proposed Multi-modal Item Embedding Model (MIEM) to address these limitations. It is capable of utilizing both textual information and multiple images about a product to construct meaningful product features. By leveraging semantic information from images, MIEM effectively supplements the image search process, improving the overall accuracy of retrieval results. MIEM has become an integral part of the Shopee image search platform. Since its deployment in March 2023, it has achieved a remarkable 9.90% increase in terms of clicks per user and a 4.23% boost in terms of orders per user for the image search feature on the Shopee e-commerce platform.

ОБЕСПЕЧЕНИЕ ПРОДОВОЛЬСТВЕННОЙ БЕЗОПАСНОСТИ ЗА СЧЕТ ИМПОРТОЗАМЕЩЕНИЯ МОЛОКА

The scientific article conducts a theoretical and economic study of the problems of ensuring food security through import substitution, import and export of milk. A review of the scientific literature showed the relevance of the study; many domestic and foreign scientists are directing their scientific interests to the development of an effective mechanism for ensuring the development of agricultural production sectors, and in particular the dairy product complex. In the field of interest of scientists are the problems of ensuring growth in production volumes, the prospects for reducing and completely eliminating the import of milk, as well as the possibility of increasing milk exports in certain regions. For the period from 2013 to 2022, according to official statistics, we observe an increase in milk production volumes, while in 2015 a decrease of 0.4% was detected, and in 2016 by 0.3%. Over the past three years, milk imports do not exceed 18% of the total dairy resource, which indicates food security at the level of 83%. The growth rate of milk exports significantly exceeds the growth rate of its imports; their value has crossed the mark of 114%. It was revealed that the growth of milk volumes was significantly influenced by the annual increase in cow productivity in the ten-year study period; a decrease in milk production volumes was observed in those periods when the number of animals decreased significantly. A slight decrease in milk production volumes in 2015 and 2016 did not have a detrimental effect on milk sales volumes; milk sales volumes, according to official statistics, have been trending upward over the past 10 years.

Multireference and Coupled-Cluster Study of Dimethyltetroxide (MeO4Me) Formation and Decomposition.

Peroxyl radicals (RO2) are important intermediates in the atmospheric oxidation processes. The RO2 can react with other RO2 to form reactive intermediates known as tetroxides, RO4R. The reaction mechanisms of RO4R formation and its various decomposition channels have been investigated in multiple computational studies, but previous approaches have not been able to provide a unified methodology that is able to connect all relevant reactions together. An apparent difficulty in modeling the RO4R formation and its decomposition is the involvement of open-shell singlet electronic states along the reaction pathway. Modeling such electronic states requires multireference (MR) methods, which we use in the present study to investigate in detail a model reaction of MeO2 + MeO2 → MeO4Me, and its decomposition, MeO4Me → MeO + O2 + MeO, as well as the two-body product complexes MeO···O2 + MeO and MeO···MeO + O2. The used MR methods are benchmarked against relative energies of MeO2 + MeO2, MeO4Me, and MeO + MeO + O2, calculated with CCSD(T)/CBS, W2X, and W3X-L methods. We found that the calculated relative energies of the overall MeO2 + MeO2 → MeO4Me → MeO + O2 + MeO reaction are very sensitive to the chosen MR method and that the CASPT2(22e,14o)-IPEA method is able to reproduce the relative energies obtained by the various coupled-cluster methods. Furthermore, CASPT2(22e,14o)-IPEA and W3X-L results show that the MeO···O2 product complex + MeO is lower in energy than the MeO···MeO complex + O2. The formation of MeO4Me is exothermic, and its decomposition is endothermic, relative to the tetroxide. Both the formation and decomposition reactions appear to follow pathways with no saddle points. According to potential energy surface scans of the decomposition pathway, the concerted cleavage of both MeO···O bonds in MeO4Me is energetically preferred over the corresponding sequential decomposition.

Centers of responsibility for the formation of effective activities of enterprises of the grain product complex

Introduction. To ensure the efficiency of enterprises, it is important to form responsibility centers. They will be responsible for the performance of enterprises. These processes are intensified under the influence of the war in Ukraine and due to the negative consequences of the Covid-19 pandemic. Global changes that have occurred in the external environment require a revision of approaches to the formation of efficiency of enterprises in general, as well as their structural divisions. The purpose of the paper is to research the centers of responsibility in the enterprise management system of the grain production complex. Results. The authors defend the thesis that responsibility centers solve the tasks of coordinating, distributing responsibilities and stimulating all units to achieve the strategic goals of the enterprise. It is necessary to consider the centers of responsibility as structural divisions of the enterprise, since the transformation of the organizational system of the enterprise is constant. That is, the allocation of responsibility centers occurs within a specially created structure that does not coincide with the organizational structure of the enterprise. The authors will give on a concrete example the performance indicators of the enterprise of the grain production complex for Volyn-Zerno-Product LLC. On this basis, conclusions are drawn about positive or negative trends that affect the efficiency of enterprises. In particular, positive changes are the growth of current and non-current assets, receivables, and negative ones are the increase in production costs, payables, a decrease in cash, a slowdown in asset turnover, low liquidity indicators, and financial stability. To overcome negative trends, it is necessary to develop measures to improve performance. One of the areas of increasing the effectiveness of Volyn-Grain-Product LLC is the formation of responsibility centers: costs, revenues, profits, investments. Conclusion. The use of responsibility centers will distinguish between the main functions, powers, rights and responsibilities through which the activities of enterprises of the grain production complex are carried out. Departments or business processes in this situation are independent units of the process, and managers are responsible for the implementation of planned indicators.

Redox reactions of a pyrazine-bridged RuIII(edta) binuclear complex: spectrochemical, spectroelectrochemical and theoretical studies.

The redox reactions of a pyrazine-bridged binuclear [(edta)RuIIIpzRuIII(edta)]2- (edta4- = ethylenediaminetetraacetate; pz = pyrazine) have been investigated spectrochemically and spectroelectrochemically for the first time. The kinetics of the reduction of [(edta)RuIIIpzRuIII(edta)]2- (RuIII-RuIII) with the ascorbic acid anion (HA-) was studied as a function of ascorbic concentration and temperature at a fixed pH 6.0. The overall reaction of RuIII-RuIII was found to consist of two-steps involving the initial formation of the mixed-valence [(edta)RuIIpzRuIII(edta)]3- (RuII-RuIII) intermediate complex (λmax = 462 nm, εmax = 10 000 M-1 cm-1), which undergoes further reduction by ascorbic acid to produce the [(edta)RuIIpzRuII(edta)]4-(RuII-RuII) ultimate product complex (λmax = 540 nm, εmax = 20 700 M-1 cm-1). Our studies further revealed that the RuII-RuIII and RuII-RuII species are formed in the electrochemical reduction of the RuIII-RuIII complex at 0.0 and -0.4 V (vs. SHE), respectively. Formation of RuII-RuIII and RuII-RuII was further corroborated by magnetic moment measurements and DFT calculations. Kinetic data and activation parameters are interpreted in terms of a mechanism involving rate-determining outer-sphere electron transfer between Ru(III) and the ascorbate monoanion (HA-) at pH 6.0. A detailed reaction mechanism in agreement with the spectral, spectro-electrochemical and kinetic data is presented. The results of the spectral and kinetic studies of the reaction of the RuII-RuII complex with molecular oxygen (O2) reveal the ability of the RuII-RuII species to effect the oxygen reduction reaction (ORR) leading to the formation of H2O2, a partial reduction product of dioxygen (O2).

Large Computational Survey of Intrinsic Reactivity of Aromatic Carbon Atoms with Respect to a Model Aldehyde Oxidase.

Aldehyde oxidase (AOX) and other related molybdenum-containing enzymes are known to oxidize the C-H bonds of aromatic rings. This process contributes to the metabolism of pharmaceutical compounds and, therefore, is of vital importance to drug pharmacokinetics. The present work describes an automated computational workflow and its use for the prediction of intrinsic reactivity of small aromatic molecules toward a minimal model of the active site of AOX. The workflow is based on quantum chemical transition state searches for the underlying single-step oxidation reaction, where the automated protocol includes identification of unique aromatic C-H bonds, creation of three-dimensional reactant and product complex geometries via a templating approach, search for a transition state, and validation of reaction end points. Conformational search on the reactants, products, and the transition states is performed. The automated procedure has been validated on previously reported transition state barriers and was used to evaluate the intrinsic reactivity of nearly three hundred heterocycles commonly found in approved drug molecules. The intrinsic reactivity of more than 1000 individual aromatic carbon sites is reported. Stereochemical and conformational aspects of the oxidation reaction, which have not been discussed in previous studies, are shown to play important roles in accurate modeling of the oxidation reaction. Observations on structural trends that determine the reactivity are provided and rationalized.

Possible Roles of Transition Metal Cations in the Formation of Interstellar Benzene via Catalytic Acetylene Cyclotrimerization.

Polycyclic aromatic hydrocarbons (PAHs) are ubiquitous interstellar molecules. However, the formation mechanisms of PAHs and even the simplest cyclic aromatic hydrocarbon, benzene, are not yet fully understood. Recently, we reported the statistical and dynamical properties in the reaction mechanism of Fe+-catalyzed acetylene cyclotrimerization, whereby three acetylene molecules are directly converted to benzene. In this study, we extended our previous work and explored the possible role of the complex of other 3d transition metal cations, TM+ (TM = Sc, Ti, Mn, Co, and Ni), as a catalyst in acetylene cyclotrimerization. Potential energy profiles for bare TM+-catalyst (TM = Sc and Ti), for TM+NC--catalyst (TM = Sc, Ti, Mn, Co, and Ni), and for TM+-(H2O)8-catalyst (TM = Sc and Ti) systems were obtained using quantum chemistry calculations, including the density functional theory levels. The calculation results show that the scandium and titanium cations act as efficient catalysts in acetylene cyclotrimerization and that reactants, which contain an isolated acetylene and (C2H2)2 bound to a bare (ligated) TM cation (TM = Sc and Ti), can be converted into a benzene-metal-cation product complex without an entrance barrier. We found that the number of electrons in the 3d orbitals of the transition metal cation significantly contributes to the catalytic efficiency in the acetylene cyclotrimerization process. On-the-fly Born-Oppenheimer molecular dynamics (BOMD) simulations of the Ti+-NC- and Ti+-(H2O)8 complexes were also performed to comprehensively understand the nuclear dynamics of the reactions. The computational results suggest that interstellar benzene can be produced via acetylene cyclotrimerization reactions catalyzed by transition metal cation complexes.

Structural basis for Tpt1-catalyzed 2'-PO4 transfer from RNA and NADP(H) to NAD.

Tpt1 is an essential agent of fungal and plant tRNA splicing that removes an internal RNA 2'-phosphate generated by tRNA ligase. Tpt1 also removes the 2'-phosphouridine mark installed by Ark1 kinase in the V-loop of archaeal tRNAs. Tpt1 performs a two-step reaction in which the 2'-PO4 attacks NAD+ to form an RNA-2'-phospho-(ADP-ribose) intermediate, and transesterification of the ADP-ribose O2″ to the RNA 2'-phosphodiester yields 2'-OH RNA and ADP-ribose-1″,2″-cyclic phosphate. Here, we present structures of archaeal Tpt1 enzymes, captured as product complexes with ADP-ribose-1″-PO4, ADP-ribose-2″-PO4, and 2'-OH RNA, and as substrate complexes with 2',5'-ADP and NAD+, that illuminate 2'-PO4 junction recognition and catalysis. We show that archaeal Tpt1 enzymes can use the 2'-PO4-containing metabolites NADP+ and NADPH as substrates for 2'-PO4 transfer to NAD+. A role in 2'-phospho-NADP(H) dynamics provides a rationale for the prevalence of Tpt1 in taxa that lack a capacity for internal RNA 2'-phosphorylation.