Alternative Pathway for the Reaction Catalyzed by DNA Dealkylase AlkB from Ab Initio QM/MM Calculations

AlkB is the title enzyme of a family of DNA dealkylases that catalyze the direct oxidative dealkylation of nucleobases. The conventional mechanism for the dealkylation of N¹-methyl adenine (1-meA) catalyzed by AlkB after the formation of Fe^IV–oxo is comprised by a reorientation of the oxo moiety, hydrogen abstraction, OH rebound from the Fe atom to the methyl adduct, and the dissociation of the resulting methoxide to obtain the repaired adenine base and formaldehyde. An alternative pathway with hydroxide as a ligand bound to the iron atom is proposed and investigated by QM/MM simulations. The results show OH^– has a small impact on the barriers for the hydrogen abstraction and OH rebound steps. The effects of the enzyme and the OH^– ligand on the hydrogen abstraction by the Fe^IV–oxo moiety are discussed in detail. The new OH rebound step is coupled with a proton transfer to the OH^– ligand and results in a novel zwitterion intermediate. This zwitterion structure can also be characterized as Fe–O–C complex and facilitates the formation of formaldehyde. In contrast, for the pathway with H₂O bound to iron, the hydroxyl product of the OH rebound step first needs to unbind from the metal center before transferring a proton to Glu136 or other residue/substrate. The consistency between our theoretical results and experimental findings is discussed. This study provides new insights into the oxidative repair mechanism of DNA repair by nonheme Fe^II and α-ketoglutarate (α-KG) dependent dioxygenases and a possible explanation for the substrate preference of AlkB

Dicationic Ionic Liquids as Environmentally Benign Catalysts for Biodiesel Synthesis

Some dicationic ionic liquids, N,N,N′,N′-tetramethyl-N,N′-dipropanesulfonic acid ethylenediammonium hydrogen sulfate, N,N,N′,N′-tetramethyl-N,N′-dipropanesulfonic acid 1,3-propanediammonium hydrogen sulfate, N,N,N′,N′-tetramethyl-N,N′-dipropanesulfonic acid 1,6-hexanediammonium hydrogen sulfate, were prepared. These ionic liquids could be used as efficient and recyclable catalysts for the synthesis of biodiesel from free long-chain fatty acids or their mixtures with low-molecular-weight alcohols as substrates. the reaction was accomplished in a monophase at 70 °C for 6 h, while the products was separated from the catalyst system by liquid/liquid biphase separation at room temperature with good yields of 93−96%. The post processing was simple, and after removal of water, the catalysts could be reused at least six times and the decrease in the yield was 3%. The novel and clean procedure offers advantages including short reaction time, good yield, operational simplicity, and environmentally benign characteristics

DataSheet1_High-efficiency adsorption of Cd2+ and Cr3+ by sodium vanadate nanowire arrays.docx

With the development of economy, the problem of heavy metal pollution in water environment is becoming more and more serious, so it is urgent to find a kind of efficient water purification material. The current work aimed to investigate the potential power of sodium vanadate nanowire arrays (Na5V12O32) to remove cadmium (Cd2+) and chromium (Cr3+) from simulated aqueous solutions. The adsorption effects of Na5V12O32 on Cd2+ and Cr3+ under different adsorption conditions were analyzed. The products before and after adsorption were compared by XRD, SEM, TEM, FTIR and XPS. The results showed that the irregular grass-like structure of Na5V12O32 nanowire arrays provided more active sites for the ion exchange reaction, and the maximum adsorption capacity of Cd2+ and Cr3+ was 541.2 and 251.8 mg·g-1, respectively. The pseudo-second-order kinetic model was more suitable to describe the adsorption behavior by kinetic study. The research demonstrated that Na5V12O32 nanowire arrays exhibited excellent adsorption performance, which provided an effective parameter basis for the future adsorption of heavy metal ions.</p

<i>Ab Initio</i> QM/MM Calculations Show an Intersystem Crossing in the Hydrogen Abstraction Step in Dealkylation Catalyzed by AlkB

AlkB is a bacterial enzyme that catalyzes the dealkylation of alkylated DNA bases. The rate-limiting step is known to be the abstraction of an H atom from the alkyl group on the damaged base by a Fe^IV-oxo species in the active site. We have used hybrid <i>ab initio</i> quantum mechanical/molecular mechanical methods to study this step in AlkB. Instead of forming an Fe^III-oxyl radical from Fe^IV-oxo near the C–H activation transition state, the reactant is found to be an Fe^III-oxyl with an intermediate-spin Fe (<i>S</i> = 3/2) ferromagnetically coupled to the oxyl radical, which we explore in detail using molecular orbital and quantum topological analyses. The minimum energy pathway remains on the quintet surface, but there is a transition between ^ISFe^III-oxyl and the state with a high-spin Fe (<i>S</i> = 5/2) antiferromagnetically coupled to the oxyl radical. These findings provide clarity for the evolution of the well-known π and σ channels on the quintet surface in the enzyme environment. Additionally, an energy decomposition analysis reveals nine catalytically important residues for the C–H activation step, some of which are conserved in two human homologues. These conserved residues are proposed as targets for experimental mutagenesis studies

<i>Ab Initio</i> QM/MM Calculations Show an Intersystem Crossing in the Hydrogen Abstraction Step in Dealkylation Catalyzed by AlkB

AlkB is a bacterial enzyme that catalyzes the dealkylation of alkylated DNA bases. The rate-limiting step is known to be the abstraction of an H atom from the alkyl group on the damaged base by a Fe^IV-oxo species in the active site. We have used hybrid <i>ab initio</i> quantum mechanical/molecular mechanical methods to study this step in AlkB. Instead of forming an Fe^III-oxyl radical from Fe^IV-oxo near the C–H activation transition state, the reactant is found to be an Fe^III-oxyl with an intermediate-spin Fe (<i>S</i> = 3/2) ferromagnetically coupled to the oxyl radical, which we explore in detail using molecular orbital and quantum topological analyses. The minimum energy pathway remains on the quintet surface, but there is a transition between ^ISFe^III-oxyl and the state with a high-spin Fe (<i>S</i> = 5/2) antiferromagnetically coupled to the oxyl radical. These findings provide clarity for the evolution of the well-known π and σ channels on the quintet surface in the enzyme environment. Additionally, an energy decomposition analysis reveals nine catalytically important residues for the C–H activation step, some of which are conserved in two human homologues. These conserved residues are proposed as targets for experimental mutagenesis studies

Toward a Deeper Understanding of Enzyme Reactions Using the Coupled ELF/NCI Analysis: Application to DNA Repair Enzymes

The combined Electron Localization Funtion (ELF)/ Noncovalent Interaction (NCI) topological analysis (Gillet et al. <i>J. Chem. Theory Comput.</i> <b>2012</b>, <i>8</i>, 3993) has been extended to enzymatic reaction paths. We applied ELF/NCI to the reactions of DNA polymerase λ and the ε subunit of DNA polymerase III. ELF/NCI is shown to provide insights on the interactions during the evolution of enzymatic reactions including predicting the location of TS from structures located earlier along the reaction coordinate, differential metal coordination, and on barrier differences with two different cations

Toward a Deeper Understanding of Enzyme Reactions Using the Coupled ELF/NCI Analysis: Application to DNA Repair Enzymes

The combined Electron Localization Funtion (ELF)/ Noncovalent Interaction (NCI) topological analysis (Gillet et al. <i>J. Chem. Theory Comput.</i> <b>2012</b>, <i>8</i>, 3993) has been extended to enzymatic reaction paths. We applied ELF/NCI to the reactions of DNA polymerase λ and the ε subunit of DNA polymerase III. ELF/NCI is shown to provide insights on the interactions during the evolution of enzymatic reactions including predicting the location of TS from structures located earlier along the reaction coordinate, differential metal coordination, and on barrier differences with two different cations

DataSheet_1_Transcriptome Analysis Reveal Candidate Genes and Pathways Responses to Lactate Dehydrogenase Inhibition (Oxamate) in Hyperglycemic Human Renal Proximal Epithelial Tubular Cells.zip

Diabetic kidney disease (DKD) is the leading cause of both chronic kidney disease (CKD) and end-stage renal disease (ESRD). Previous studies showed that oxamate could regulate glycemic homeostasis and impacted mitochondria respiration in a hyperglycemia-dependent manner in the rat proximal tubular cells. To explore the transcriptome gene expression profiling of kidney tissues in human renal proximal epithelial tubular cell line (HK-2), we treated HK-2 cells with high D-glucose (HG) for 7 days before the addition of 40 mM oxamate for a further 24 hours in the presence of HG in this study. Afterwards, we identified 3,884 differentially expressed (DE) genes based on adjusted P-value ≤ 0.05 and investigated gene relationships based on weighted gene co-expression network analysis (WGCNA). After qRT-PCR validations, MAP1LC3A, MAP1LC3B (P-value -75 and log2(FC) = 2.64) interacted with 6 up-regulated and 12 down-regulated DE genes in the network that were enriched in the p53 signaling pathway. This is the first study reporting co-expression patterns of a gene network after lactate dehydrogenase inhibition in HK-2 cells. Our results may contribute to our understanding of the underlying molecular mechanism of in vitro reprogramming under hyperglycemic stress that orchestrates the survival and functions of HK-2 cells.</p

The Preliminary Experiences with Three-Dimensional Heads-Up Display Viewing System for Vitreoretinal Surgery under Various Status

Statement: The current article has not been published elsewhere and has not been submitted simultaneously for publication elsewhere. Purpose: To investigate the preliminary use of three-dimensional (3D) heads-up display (HUD) viewing system for vitreoretinal surgery under various status. Materials and Methods: Nonrandomized case–control study. Consecutive cases to have vitreoretinal surgery under various status were prospectively recruited. Twenty-five-gauge vitrectomy platform and 3D viewing system were used. Main outcomes included: luminous emittance (lux) of endoillumination pipe, surgical duration, the surgeon and residents’ preference and ergonomics. Consecutive patients to have vitreoretinal surgery with the conventional viewing system were recruited as control group following the same inclusion and exclusion criteria and underwent surgeries by the same surgeon with the same microscope and vitrectomy platform. Results: Thirty-one patients (31 eyes; Group Study) and twenty-eight patients (28 eyes; Group Control) were included; without significantly statistical difference in terms of age, gender, main diagnosis, surgical duration, and difficulty rating between both groups (all P > 0.05). Lower endoillumination intensity was needed in Group Study than that in Group Control (10% vs. 35%; 598.7 ± 5.4 vs. 1913.0 ± 12.9 lux, P P  Conclusion: Vitreoretinal surgery under various status can be well finished with the HUD platform by novice at the system. Main benefits included lower endoillumination intensity, enhanced users’ preference, and improved ergonomics. Some further refinements of the system are expected.</p

Combined Selective Hydrogenation and Catalytic Cracking Process for Efficient Conversion of Heavy Cycle Oil to High Octane Number Gasoline

Heavy cycle oil (HCO) is difficult to be converted into gasoline via fluid catalytic cracking (FCC) or hydrotreating. Abundant polycyclic aromatic hydrocarbons in HCO lead to condensation coke and high H2 consumption. To efficiently convert HCO, in this work, HCO was selectively hydrogenated first and then cracked in an FCC unit. For the ideal molecular structure of naphthenoaromatics cracking after HCO selective hydrogenation, tetralin-type naphthenoaromatics were the desired products by the FCC test of model compounds. The effect of hydrogenation extent on structural composition was analyzed to confirm the optimal hydrogenation extent of HCO. The catalytic cracking results of hydro-HCO (Hy-HCO) indicated that the research octane number of FCC gasoline from selective hydrogenation is up to 96.5. Compared with HCO, the conversion and gasoline yield increased significantly, and the yields of heavy oil and coke decreased. Finally, the FCC operation conditions of Hy-HCO were investigated to enhance cracking efficiency