Quantum mechanics/molecular mechanics studies of triosephosphate isomerase-catalyzed reactions: effect of geometry and tunneling on proton-transfer rate constants

The role of tunneling for two proton-transfer steps in the reactions catalyzed by triosephosphate isomerase (TIM) has been studied. One step is the rate-limiting proton transfer from Calpha in the substrate to Glu 165, and the other is an intrasubstrate proton transfer proposed for the isomerization of the enediolate intermediate. The latter, which is not important in the wild-type enzyme but is a useful model system because of its simplicity, has also been examined in the gas phase and in solution. Variational transition-state theory with semiclassical ground-state tunneling was used for the calculation with potential energy surface determined by an AM1 method specifically parametrized for the TIM system. The effect of tunneling on the reaction rate was found to be less than a factor of 10 at room temperature; the tunneling becomes more important at lower temperature, as expected. The imaginary frequency (barrier) mode and modes that have large contributions to the reaction path curvature are localized on the atoms in the active site, within 4 A of the substrate. This suggests that only a small number of atoms that are close to the substrate and their motions (e.g., donor-acceptor vibration) directly determine the magnitude of tunneling. Atoms that are farther away influence the effect of tunneling indirectly by modulating the energetics of the proton transfer. For the intramolecular proton transfer, tunneling was found to be most important in the gas phase, to be similar in the enzyme, and to be the smallest in water. The major reason for this trend is that the barrier frequency is substantially lower in solution than in the gas phase and enzyme; the broader solution barrier is caused by the strong electrostatic interaction between the highly charged solute and the polar solvent molecules. Analysis of isotope effects showed that the conventional Arrenhius parameters are more useful as experimental criteria for determining the magnitude of tunneling than the widely used Swain-Schaad exponent (SSE). For the primary SSE, although values larger than the transition-state theory limit (3.3) occur when tunneling is included, there is no clear relationship between the calculated magnitudes of tunneling and the SSE. Also, the temperature dependence of the primary SSE is rather complex; the value of SSE tends to decrease as the temperature is lowered (i.e., when tunneling becomes more significant). For the secondary SSE, the results suggest that it is more relevant for evaluating the "coupled motion" between the secondary hydrogen and the reaction coordinate than the magnitude of tunneling. Although tunneling makes a significant contribution to the rate of proton transfer, it appears not to be a major aspect of the catalysis by TIM at room temperature; i.e., the tunneling factor of 10 is "small" relative to the overall rate acceleration by 10(9). For the intramolecular proton transfer, the tunneling in the enzyme is larger by a factor of 5 than in solution.     

Thermo-Responsive ZnPc-g-TiO2-g-PNIPAM Photocatalysts Sensitized with Phthalocyanines for Water Purification under Visible Light

A novel thermo-responsive 2,9(10),16(17),23(24)-tetrakis[(3-carboxyacrylamide) phthalocyaninato] zinc (ZnPc)-g-TiO₂-g-poly(N-isopropylacrylamide) (PNIPAM) photocatalyst modified with phthalocyanines was prepared. The photocatalyst exhibited thermo-responsive properties due to the introduction of PNIPAM, which performed recovery for reuse above the lower critical solution temperature (LCST, about 26 °C). ZnPc-g-TiO₂-g-PNIPAM effectively expanded the light response range to the visible light region and inhibited the recombination of electron–hole pairs, which enhanced the performance of the photocatalyst. As expected, ZnPc-g-TiO₂-g-PNIPAM (0.3 g/L) exhibited excellent photocatalytic performance for the removal of Rhodamine B (RhB, 1.0 × 10⁻⁵ mol/L) and methylene blue (MB, 1.0 × 10⁻⁵ mol/L) under visible light, which reached 97.2% and 88.6% at 20 °C within 40 min, respectively. Furthermore, the influence of temperature upon photocatalytic performance was also investigated. When the temperature increased from 20 °C to 45 °C, the removal of RhB decreased by approximately 53.8%. The stability of the photocatalyst demonstrated that the photocatalytic activity was still above 80% for the removal of RhB after 3 cycles. Above all, this work provided an intelligent thermally responsive photocatalyst based on phthalocyanine for water purification under visible light.     

Structural Characteristics,Antioxidant and Hypoglycemic Activities of Polysaccharide from Siraitia grosvenorii

The structural characterization, the in vitro antioxidant activity, and the hypoglycemic activity of a polysaccharide (SGP-1-1) isolated from Siraitia grosvenorii (SG) were studied in this paper. SGP-1-1, whose molecular weight is 19.037 kDa, consisted of Gal:Man:Glc in the molar ratio of 1:2.56:4.90. According to the results of methylation analysis, GC–MS, and NMR, HSQC was interpreted as a glucomannan with a backbone composed of 4)-β-D-Glcp-(1→4)-, α-D-Glcp-(1→4)-, and 4)-Manp-(1 residues. α-1,6 linked an α-D-Galp branch, and α-1,6 linked an α-D-Glcp branch. The study indirectly showed that SGP-1-1 has good in vitro hypoglycemic and antioxidant activities and that these activities may be related to the fact that the SGP-1-1’s monosaccharide composition (a higher proportion of Gal and Man) is the glycosidic-bond type (α- and β-glycosidic bonds). SGP-1-1 could be used as a potential antioxidant and hypoglycemic candidate for functional and nutritional food applications.     

Mulberry Ethanol Extract and Rutin Protect Alcohol-Damaged GES-1 Cells by Inhibiting the MAPK Pathway

Mulberry extract has been proven to have the effect of resisting alcohol damage, but its mechanism is still unclear. In this study, the composition of mulberry ethanol extract (MBE) was identified by LC-MS/MS and the main components of MBE were ascertained by measuring. Gastric mucosal epithelial (GES-1) cells were used to elucidate the mechanism of MBE and rutin (the central part of MBE) helped protect against alcohol damage. The results revealed that phenolics accounted for the majority of MBE, accounting for 308.6 mg/g gallic acid equivalents and 108 substances were identified, including 37 flavonoids and 50 non-flavonoids. The treatment of 400 μg/mL MBE and 320 μM rutin reduced early cell apoptosis and the content of intracellular reactive oxygen species, malondialdehyde and increased glutathione. The qPCR results indicated that the MBE inhibits the expression of genes in the mitogen-activated protein kinase (MAPK) pathway, including p38, JNK, ERK and caspase-3; rutin inhibits the expression of p38 and caspase-3. Overall, MBE was able to reduce the oxidative stress of GES-1 cells and regulated apoptosis-related genes of the MAPK pathway. This study provides information for developing anti-ethanol injury drugs or functional foods.     

Racemic Norlignans as Diastereoisomers from Ferula sinkiangensis Resins with Antitumor and Wound-Healing Promotion Activities

Ferulasinkins A–D (1–4), four new norlignans, were isolated from the resins of Ferula sinkiangensis, a medicinal plant of the Apiaceae family. All of them were obtained as racemic mixtures, chiral HPLC was used to produce their (+)- and (−)-antipodes. The structures of these new compounds, including their absolute configurations, were elucidated by spectroscopic and computational methods. This isolation provides new insight into the chemical profiling of F. sinkiangensis resins beyond the well-investigated structure types such as sesquiterpene coumarins and disulfides. Compounds 2a and 3a were found to significantly inhibit the invasion and migration of triple-negative breast cancer (TNBC) cell lines via CCK-8 assay. On the other hand, the wound-healing assay also demonstrated that compounds 4a and 4b could promote the proliferation of human umbilical vein endothelial cells (HUVECs). Notably, the promoting effects of 4a and 4b were observed as more significant versus a positive control using basic fibroblast growth factor (bFGF).     

Rapid Identification for the Pterocarpus Bracelet by Three-Step Infrared Spectrum Method

In order to explore a rapid identification method for the anti-counterfeit of commercial high value collections, a three-step infrared spectrum method was used for the pterocarpus collection identification to confirm whether a commercial pterocarpus bracelet (PB) was made from the precious species of Pterocarpus santalinus (P. santalinus). In the first step, undertaken by Fourier transform infrared spectroscopy (FTIR) spectrum, the absorption peaks intensity of PB was slightly higher than that of P. santalinus only at 1594 cm⁻¹, 1205 cm⁻¹, 1155 cm⁻¹ and 836 cm⁻¹. In the next step of second derivative IR spectra (SDIR), the FTIR features of the tested samples were further amplified, and the peaks at 1600 cm⁻¹, 1171 cm⁻¹ and 1152 cm⁻¹ become clearly defined in PB. Finally, by means of two-dimensional correlation infrared (2DIR) spectrum, it revealed that the response of holocellulose to thermal perturbation was stronger in P. santalinus than that in PB mainly at 977 cm⁻¹, 1008 cm⁻¹, 1100 cm⁻¹, 1057 cm⁻¹, 1190 cm⁻¹ and 1214 cm⁻¹, while the aromatic functional groups of PB were much more sensitive to the thermal perturbation than those of P. santalinus mainly at 1456 cm⁻¹, 1467 cm⁻¹, 1518 cm⁻¹, 1558 cm⁻¹, 1576 cm⁻¹ and 1605 cm⁻¹. In addition, fluorescence microscopy was used to verify the effectiveness of the above method for wood identification and the results showed good consistency. This study demonstrated that the three-step IR method could provide a rapid and effective way for the anti-counterfeit of pterocarpus collections.     

Molecular Simulation to Explore the Dissolution Behavior of Sulfur in Carbon Disulfide

Soluble sulfur (S₈) and insoluble sulfur (IS) have different application fields, and molecular dynamics simulation can reveal their differences in solubility in solvents. It is found that in the simulated carbon disulfide (CS₂) solvent, soluble sulfur in the form of clusters mainly promotes the dissolution of clusters through van der Waals interaction between solvent molecules (CS₂) and S₈, and the solubility gradually increases with the increase in temperature. However, the strong interaction between polymer chains of insoluble sulfur in the form of polymer hinders the diffusion of IS into CS₂ solvent, which is not conducive to high-temperature dissolution. The simulated solubility parameter shows that the solubility parameter of soluble sulfur is closer to that of the solvent, which is consistent with the above explanation that soluble sulfur is easy to dissolve.     

Electrochemical Immunoassay for Tumor Marker CA19-9 Detection Based on Self-Assembled Monolayer

A CA19-9 electrochemical immunosensor was constructed using a hybrid self-assembled membrane modified with a gold electrode and applied to detect real samples. Hybrid self-assembled membranes were selected for electrode modification and used to detect antigens. First, the pretreated working electrodes were placed in a 3-mercaptopropionic acid (MPA)/β-mercaptoethanol (ME) mixture for 24 h for self-assembly. The electrodes were then placed in an EDC/NHS mixture for 1 h. Layer modification was performed by stepwise dropwise addition of CA19-9 antibody, BSA, and antigen. Differential pulse voltammetry was used to characterize this immunosensor preparation process. The assembled electrochemical immunosensor enables linear detection in the concentration range of 0.05–500 U/mL of CA19-9, and the detection limit was calculated as 0.01 U/mL. The results of the specificity measurement test showed that the signal change of the interfering substance was much lower than the response value of the detected antigen, indicating that the sensor has good specificity and strong anti-interference ability. The repeatability test results showed that the relative standard deviations were less than 5%, showing good accuracy and precision. The CA19-9 electrochemical immunosensor was used for the actual sample detection, and the experimental results of the standard serum addition method showed that the RSD values of the test concentrations were all less than 10%. The recoveries were 102.4–115.0%, indicating that the assay has high precision, good accuracy, and high potential application value.     

First Organic–Inorganic Hybrid Compounds Formed by Ge-V-O Clusters and Transition Metal Complexes of Aromatic Organic Ligands

Three compounds based on Ge-V-O clusters were hydrothermally synthesized and characterized by IR, UV-Vis, XRD, ESR, elemental analysis and X-ray crystal structural analysis. Both [Cd(phen)(en)]₂[Cd₂(phen)₂V₁₂O₄₀Ge₈(OH)₈(H₂O)]∙12.5H₂O (1) and [Cd(DETA)]₂[Cd(DETA)₂]_0.5[Cd₂(phen)₂V₁₂O₄₁Ge₈(OH)₇(0.5H₂O)]∙7.5H₂O (2) (1,10-phen = 1,10-phenanthroline, en = ethylenediamine, DETA = diethylenetriamine) are the first Ge-V-O cluster compounds containing aromatic organic ligands. Compound 1 is the first dimer of Ge-V-O clusters, which is linked by a double bridge of two [Cd(phen)(en)]²⁺. Compound 2 exhibits an unprecedented 1-D chain structure formed by Ge-V-O clusters and [Cd₂(DETA)₂]⁴⁺ transition metal complexes (TMCs). [Cd(en)₃]{[Cd(η₂-en)₂]₃[Cd(η₂-en)(η₂-μ₂-en)(η₂-en)Cd][Ge₆V₁₅O₄₈(H₂O)]}∙5.5H₂O (3) is a novel 3-D structure which is constructed from [Ge₆V₁₅O₄₈(H₂O)]¹²⁻ and four different types of TMCs. We also synthesized [Zn₂(enMe)₃][Zn(enMe)]₂[Zn(enMe)₂(H₂O)]₂[Ge₆V₁₅O₄₈(H₂O)]∙3H₂O (4) and [Cd(en)₂]₂{H₈[Cd(en)]₂Ge₈V₁₂O₄₈(H₂O)}∙6H₂O (5) (enMe = 1,2-propanediamine), which have been reported previously. In addition, the catalytic properties of these five compounds for styrene epoxidation have been assessed.     

The Influence of Tyrosol-Enriched Rhodiola sachalinensis Extracts Bioconverted by the Mycelium of Bovista plumbe on Scopolamine-Induced Cognitive,Behavioral, and Physiological Responses in Mice

Alzheimer’s disease (AD) is an age-related neurodegenerative disorder characterized by cognitive deficits, which are accompanied by memory loss and cognitive disruption. Rhodiola sachalinensis (RSE) is a medicinal plant that has been used in northeastern Asia for various pharmacological activities. We attempted to carry out the bioconversion of RSE (Bio-RSE) using the mycelium of Bovista plumbe to obtain tyrosol-enriched Bio-RSE. The objective of this study was to investigate the effects of Bio-RSE on the activation of the cholinergic system and the inhibition of oxidative stress in mice with scopolamine (Sco)-induced memory impairment. Sco (1 mg/kg body weight, i.p.) impaired the mice’s performance on the Y-maze test, passive avoidance test, and water maze test. However, the number of abnormal behaviors was reduced in the groups supplemented with Bio-RSE. Bio-RSE treatment improved working memory and avoidance times against electronic shock, increased step-through latency, and reduced the time to reach the escape zone in the water maze test. Bio-RSE dramatically improved the cholinergic system by decreasing acetylcholinesterase activity and regulated oxidative stress by increasing antioxidant enzymes (superoxide dismutase (SOD) and catalase (CAT)). The reduction in nuclear factor erythroid 2-related factor 2 (Nrf2)/heme oxygenase-1 (HO-1) signaling in the brain tissue due to scopolamine was restored by the administration of Bio-RSE. Bio-RSE also significantly decreased amyloid-beta 1–42 (Aβ1–42) and amyloid precursor protein (APP) expression. Moreover, the increased malondialdehyde (MDA) level and low total antioxidant capacity in Sco-treated mouse brains were reversed by Bio-RSE, and an increase in Nrf2 and HO-1 was also observed. In conclusion, Bio-RSE protected against Sco-induced cognitive impairment by activating Nrf2/HO-1 signaling and may be developed as a potential beneficial material for AD.