Phloem mobility of xenobiotics: tabular review of physicochemical properties governing the output of the Kleier model

The Kleier model of phloem-mobility of xenobiotics combines the intermediate permeability hypothesis with the acid trap mechanism for weak acids. The output of the model is dependent on the lipophilicity of a compound, for which octanol/water partition coefficients (log K_ow) have been used as a measure. The membrane permeability of xenobiotics is predicted from these partition coefficients, and the nature of the sieve tube membranes has been modelled using regressions derived from Nitella or potato permeability data. A wide range of log K_ow values for herbicides, fungicides, insecticides and experimental compounds (400) have been tabulated along with the model output for various membrane parameters. The application of the model is in broad agreement with literature and experimental observations on many of the known phloem mobile herbicides and predicts low phloem mobility for the fungicides and insecticides considered here, again in agreement with the literature. The behaviour of herbicides representative of the main chemical families and modes of action are reviewed, along with examples of the few phloem-mobile fungicides and insecticides identified.Abbreviations K_ow octanol-water partition coefficient - pK_a –log₁₀ acid dissociation constant - C_f Concentration factor - P membrane permeability     

The Potential Role of Plastome Copy Number as a Quality Biomarker for Plant Products using Real-time Quantitative Polymerase Chain Reaction

Background: Plastids are plant-specific semi-autonomous self-replicating organelles, containing circular DNA molecules called plastomes. Plastids perform crucial functions, including photosynthesis, stress perception and response, synthesis of metabolites, and storage. The plastome and plastid numbers have been shown to be modulated by developmental stage and environmental stimuli and have been used as a biomarker (identification of plant species) and biosensor (an indicator of abiotic and biotic stresses). However, the determination of plastome sequence and plastid number is a laborious process requiring sophisticated equipment.Methods: This study proposes using plastome copy number (PCN), which can be determined rapidly by real-time quantitative polymerase chain reaction (RT-qPCR) as a plant product quality biomarker. This study shows that the PCN log₁₀ and range PCN log₁₀ values calculated from RT-qPCR data, which was obtained for two years from leaves and lint samples of cotton and seed samples of cotton, rice, soybean, maize, and sesame can be used for assessing the quality of the samples.Results: Observation of lower range PCN log₁₀ values for CS (0.31) and CR (0.58) indicated that the PCN showed little variance from the mean PCN log₁₀ values for CS (3.81) and CR (3.85), suggesting that these samples might have encountered ambient environmental conditions during growth and/ or post-harvest storage and processing. This conclusion was further supported by observation of higher range PCN log₁₀ values for RS (3.09) versus RP (0.05), where rice seeds in the RP group had protective hull covering compared to broken hull-less seeds in the RS group. To further support that PCN is affected by external factors, rice seeds treated with high temperatures and pathogens exhibited lower PCN values when compared to untreated seeds. Furthermore, the range PCN log₁₀ values were found to be high for cotton leaf (CL) and lint (Clt) sample groups, 4.11 and 3.63, respectively, where leaf and lint samples were of different sizes, indicating that leaf samples might be of different developmental stage and lint samples might have been processed differently, supporting that the PCN is affected by both internal and external factors, respectively. Moreover, PCN log₁₀ values were found to be plant specific, with oil containing seeds such as SeS (6.49) and MS (5.05) exhibiting high PCN log₁₀ values compared to non-oil seeds such as SS (1.96).Conclusion: In conclusion, it was observed that PCN log₁₀ values calculated from RT-qPCR assays were specific to plant species and the range of PCN log₁₀ values can be directly correlated to the internal and external factors and, therefore might be used as a potential biomarker for assessing the quality of plant products.     

Molecular simulations of porous coordination network-based mixed matrix membranes for CO2/N2 separations

In this study, the challenge of selecting porous coordination networks (PCNs) as filler particles in mixed matrix membranes (MMMs) was examined using molecular simulations. PCNs are promising nanoporous materials in gas separations because of their tunable pore sizes, high porosities, good thermal and mechanical stabilities. Gas permeability and selectivity of 200 new MMMs composed of 20 different PCNs and 10 different polymers were calculated for CO₂/N₂ separation. We showed that selecting the appropriate PCN as filler particles in polymers results in MMMs that have high CO₂/N₂ selectivities and high CO₂ permeabilities compared with pure polymer membranes. Several PCN/polymer MMMs were identified to exceed the upper bound established for CO₂/N₂ separation. Effect of framework flexibility of PCNs on the performance of MMMs was also examined. Results showed that considering the flexibility of PCNs is important for predicting gas permeability of pure PCNs but has less significance for predicting gas permeability of PCN-filled MMMs whenever the PCN volume fraction is low. For rapid screening of PCN/polymer MMMs, flexibility of the fillers can be neglected as a reasonable approximation if the filler volume fraction is < 0.3. The methods introduced in this study will create many opportunities for selecting PCN/polymer combinations for MMMs with useful properties in CO₂ separation applications.     

Shortcomings in USEPA's Approach for Predicting Risk Due to Consumption of Animal Food Products Impacted by Air Emissions from Hazardous Waste Combustion Facilities: A Case Study Involving Phthalates

As a part of the permitting process for hazardous waste combustion facilities, regulatory agencies are now conducting site-specific, multipathway risk assessments. In accordance with the approach established by the USEPA, the Texas Natural Resource Conservation Commission uses a prospective risk assessment paradigm whereby site-specific activity pattern and land use information is used to determine plausible exposure scenarios and pathways. A set of exposure scenarios defined as receptors (i.e., resident adult, resident child, farmer adult, farmer child, fisher adult and fisher child) is then assumed to be exposed via multiple applicable exposure pathways. In conducting such risk assessments, modeled air emissions of di-n-octyl phthalate (DNOP), at concentrations near or below detectable levels, have been observed to produce an unacceptable hazard in the farmer exposure scenario. Sensitivity analyses indicated that two key parameters affected hazard estimates for DNOP in the farmer scenario: the octanol-water partition coefficient (K_ow), which is used to predict bioaccumulation in animal tissue, and the metabolism factor, which is used to account for metabolism and elimination. Evidence indicates that K_ow values for highly lipophillie compounds are accurately determined using a slow-stir method. In addition, evidence indicates that the phthalates of interest are extensively metabolized and eliminated. However, current USEPA guidance includes geometric mean K_ow values for highly lipophillie compounds derived in part on methods that are outdated and no longer considered accurate. In addition, USEPA guidance only considers metabolism for bis-% ethylhexyl phthalate (BEHP). Collectively, these two shortcomings in the USEPA approach result in a 38-fold underestimation of hazard for BEHP and a 172,000-fold overestimation of hazard for DNOP.     

Evaluating controllability of pharmaceuticals and metabolites in biologically engineered processes,using corresponding octanol–water distribution coefficient

The efficiency of removing 9 different pharmaceuticals, 5 carbamazepine metabolites, and 1 personal care product through wastewater treatment plants and constructed wetlands was investigated. The compound concentrations were measured using solid phase extraction followed by liquid chromatography quadrupole tandem mass spectrometry. For extraction confirmation and better accuracy, isotopic dilution and standards addition methods were employed. The reporting limits for the investigated compounds were less than 10 ng/L except TCEP (24 ng/L). The removal efficiencies were found to be inversely proportional to the octanol–water partition coefficients (log K_ow) after modification with ionizable functional groups (log D_ow); compounds with a higher hydrophilicity were more efficiently removed in the engineered processes through biological treatment mechanisms. Carbamazepine metabolites that were formed in the early stages of certain metabolic reactions exhibited enhanced removal efficiencies due to a decreased log D_ow values. However, the removal efficiency of those formed in later stages did not increase, but rather fluctuated with large standard deviations. The removal behaviors of metabolites in biologically operating engineered systems need to be more extensively examined.     

A stochastic model for the synthesis and degradation of natural organic matter part II: molecular property distributions

A stochastic biogeochemical model has been developed to simulate the transformation and degradation of natural organic matter (NOM) using an agent-based algorithm which treats each molecule as a separate and potentially unique entity. Molecules react when a pseudo-random number is lower than the calculated reaction probability in a given time step; repeated time steps simulate the transformation of precursor molecules into a complex NOM assemblage. The data for each molecule—elemental and functional group composition—can be used to calculate many properties directly and exactly for each molecule in the assemblage, e.g., molecular weight (MW), fraction of aromatic C (Ar), and charge at pH 7 (Z). Empirical quantitative structure activity relationships (QSARs) are developed which permit the estimation of thermodynamic quantities K _ow (the octanol–water partition coefficient) and pK _a (acidity) for each molecule. Root mean square errors for these QSARs are 0.39 log units for log K _ow and 0.45 log units for pK _a. Distributions of both exactly calculated (MW, Ar, Z) and estimated thermodynamic (K _ow, pK _a) properties are examined and compared with published experimental data. Molecular weight distributions from size exclusion HPLC experiments on aquatic NOM are quantitatively similar to simulation results. pH titrations and polarity distributions from reversed-phase HPLC are qualitatively similar to simulation results. This agreement suggests that the agent-based model can be used to explore hypotheses regarding both compositional and thermodynamic properties of NOM. Robert Wetzel—deceased.     

Na<Superscript>+</Superscript> Modulates Anion Permeation and Block of P2X<Subscript>7</Subscript> Receptors from Mouse Parotid Glands

Experiments were conducted to test the hypothesis that aliphatic hydrocarbons bind to pockets/crevices of sodium (Na⁺) channels to cause action potential (AP) block. Aliphatic solutes exhibiting successively greater octanol/water partitition coefficients (K _ow) were studied. Each solute blocked Na⁺ channels. The 50% effective concentration (EC₅₀) to block APs could be mathematically predicted as a function of the solute’s properties. The solutes studied were methyl ethyl ketone (MEK), cyclohexanone, dichloromethane, chloroform and triethylamine (TriEA); the K _ow increased from MEK to TriEA. APs were recorded from frog nerves, and test solutes were added to Ringer’s solution bathing the nerve. When combined with EC₅₀s for solutes with log K _ows < 0.29 obtained previously, the solute EC₅₀s could be predicted as a function of the fractional molar volume (dV/dm = [dV/dn]/100), polarity (P) and the hydrogen bond acceptor basicity (β) by the following equation: Fluidity changes cannot explain the EC₅₀s. Each of the solutes blocks Na⁺ channels with little or no change in kinetics. Na⁺ channel block explains much of the EC₅₀ data. EC₅₀s are produced by a combination of effects including ion channel block, fluidity changes and osmotically induced structural changes. As the solute log K _ow increases to values near 1 or greater, Na⁺ channel block dominates in determining the EC₅₀. The results are consistent with the hypothesis that the solutes bind to channel crevices to cause Na⁺ channel and AP block.     

Rapid determination of logarithmic partition coefficients between n-octanol and water using micellar electrokinetic capillary chromatography

Micellar electrokinetic capillary chromatography (MECC) was evaluated as a rapid screening tool for the determination of logarithmic partition coefficients between n-octanol-water (logP_ow). The technique is performed by electrochromatographing a mixture of standards of known log P_ow. The logarithmic capacity factor of each standard was plotted against its log P_ow to form a linear calibration curve for a given set of chromatographic conditions. The log P_ow of an unknown is calculated by using its chromatographically determined capacity factor and extracting the log P_ow value from the calibration curve. The method was evaluated with a set of model compounds with known log P_ow. The accuracy of the method was examined and found to be within the limits required for screening purposes. The correlation of log P_ow values determined using HPLC and MECC for some novel compounds was examined. This technique allows the screening of log P_ow at a rate of four samples per hour with minimal sample requirements (<μg) and with extremely small solvent waste generated.     

A QTL for broad-spectrum resistance to cyst nematode species (Globodera spp.) maps to a resistance gene cluster in potato

 Broad-spectrum resistance in potato to the potato cyst nematode (PCN) species Globodera rostochiensis and G. pallida is commonly regarded as a polygenically inherited trait. Yet, by use of QTL analysis and a selected set of PCN populations, resistance to both PCN species could be ascribed to the action of locus Grp1. Grp1 confers major resistance to G. rostochiensis line Ro₅-22 and G. pallida population Pa₂-D383 and partial resistance to G. pallida population Pa₃-Rookmaker. Grp1 was mapped on chromosome 5 using previously characterized AFLP markers. Cleaved amplified polymorphic sequence (CAPS) markers available for RFLP loci GP21 and GP179 revealed that Grp1 maps on a genomic region harboring other resistance factors to viral, fungal and nematodal pathogens. The present data indicate that Grp1 is a compound locus which contains multiple genes involved in PCN resistance. Received: 10 September 1997 / Accepted: 6 October 1997     

Quantitative structure-activity relationship by CoMFA for cyclic urea and nonpeptide-cyclic cyanoguanidine derivatives on wild type and mutant HIV-1 protease

Abstact 3D-QSAR studies using the Comparative Molecular Field Analysis (CoMFA) methodology were conducted to predict the inhibition constants, K_i, and the inhibitor concentrations, IC₉₀ of 127 symmetrical and unsymmetrical cyclic urea and cyclic cyanoguanidine derivatives containing different substituent groups such as: benzyl, isopropyl, 4-hydroxybenzyl, ketone, oxime, pyrazole, imidazole, triazole and having anti-HIV-1 protease activities. A significant cross-validated correlation coefficient (q²) of 0.63 and a fitted correlation coefficient r² of 0.70 were obtained, indicating that the models can predict the anti-protease activity from poorly to highly active compounds reliably. The best predictions were obtained for: XV643 (predicted log 1/K_i=9.86), a 3,5-dimethoxy-benzyl cyclic urea derivate (molec60, predicted log 1/K_i=8.57) and a benzyl cyclic urea derivate (molec 61, predicted log 1/IC₉₀=6.87). Using the CoMFA method, we also predicted the biological activity of 14 cyclic urea derivatives that inhibit the HIV-1 protease mutants V82A, V82I and V82F. The predicted biological activities of the: (i) XNO63 (inhibitory activity on the mutant HIV-1 PR V82A), (ii) SB570 (inhibiting the mutant HIV-1 PR V82I) and also (iii) XV652 (during the interaction with the mutant HIV-1 PR V82F) were in good agreement with the experimental values.Figure Stereoview of the contour plots of the CoMFA steric and electrostatic fields. The favorable (indicated by blue polyhedra) and unfavorable (represented by red polyhedra) electrostatic areas and also the favorable (shown by green polyhedra) and unfavorable (shown by yellow polyhedra) steric areas formed around the most active molecule, 6a.     

Determination of plasmid copy number reveals the total plasmid DNA amount is greater than the chromosomal DNA amount in Bacillus thuringiensis YBT-1520

Bacillus thuringiensis is the most widely used bacterial bio-insecticide, and most insecticidal crystal protein-coding genes are located on plasmids. Most strains of B. thuringiensis harbor numerous diverse plasmids, although the plasmid copy numbers (PCNs) of all native plasmids in this host and the corresponding total plasmid DNA amount remains unknown. In this study, we determined the PCNs of 11 plasmids (ranging from 2 kb to 416 kb) in a sequenced B. thuringiensis subsp. kurstaki strain YBT-1520 using real-time qPCR. PCNs were found to range from 1.38 to 172, and were negatively correlated to plasmid size. The amount of total plasmid DNA (∼8.7 Mbp) was 1.62-fold greater than the amount of chromosomal DNA (∼5.4 Mbp) at the mid-exponential growth stage (OD₆₀₀ = 2.0) of the organism. Furthermore, we selected three plasmids with different sizes and replication mechanisms to determine the PCNs over the entire life cycle. We found that the PCNs dynamically shifted at different stages, reaching their maximum during the mid-exponential growth or stationary phases and remaining stable and close to their minimum after the prespore formation stage. The PCN of pBMB2062, which is the smallest plasmid (2062 bp) and has the highest PCN of those tested, varied in strain YBT-1520, HD-1, and HD-136 (172, 115, and 94, respectively). These findings provide insight into both the total plasmid DNA amount of B. thuringiensis and the strong ability of the species to harbor plasmids.     

Phloem Mobility of Xenobiotics: II. Bioassay Testing of the Unified Mathematical Model

Two bioassays were used to test phloem mobility of selected xenobiotic compounds: (a) excised bean leaf assay; (b) rooted bean leaf assay. Compounds assayed were N-alkylpyridiniums with systematic variation in octanol-water partition coefficients (log K_ow), substituted benzoic acids with about the same log K_ow value but variable acidities. Results of the assays strongly conform, quantitatively, to the predictions of the unified mathematical model. Results also indicate that the membrane permeability value of a compound, which depends directly on log K_ow value, is the overriding factor in determining phloem mobility. When the weak acid functionality of a compound confers increased phloem mobility, it does so principally by making the log K_ow value, and consequently the membrane permeability of the compound more optimal.     

Organophosphorus and Organochlorine Pesticides Bioaccumulation by Eichhornia crassipes in Irrigation Canals in an Urban Agricultural System

A natural wetland in Mexico City Metropolitan Area is one of the main suppliers of crops and flowers, and in consequence its canals hold a high concentration of organochlorine (OC) and organophosphorus (OP) pesticides. There is also an extensive population of water hyacinth (Eichhornia crassipes), which is considered a plague; but literature suggests water hyacinth may be used as a phytoremediator. This study demonstrates bioaccumulation difference for the OC in vivo suggesting their bioaccumulation is ruled by their log K_ow, while all the OP showed bioaccumulation regardless of their log K_ow. The higher bioaccumulation factors (BAF) of the accumulated OC pesticides cannot be explained by their log K_ow, suggesting that the OC pesticides may also be transported passively into the plant. Translocation ratios showed that water hyacinth is an accumulating plant with phytoremediation potential for all organophosphorus pesticides studied and some organochlorine pesticides. An equation for free water surface wetlands with floating macrophytes, commonly used for the construction of water-cleaning wetlands, showed removal of the pesticides by the wetland with room for improvement with appropriate management.     

Retention of xenobiotics along the phloem path

Detached leaves of Cyclamen persicum Mill. can be used as a simple source-sink system. Phloem transport in the excised material was monitored by the noninvasive ¹¹C-technique. Assimilate movement stopped immediately when the petiole was cut off. However, within 20 min a recovery of transport was observed. The translocation rate in the detached leaf was only 13% of that in the intact plant. ¹⁴C-Xenobiotics and [³H]sucrose were injected into the upper petiole parenchyma (source). They moved downstream by a symplastic route. The stump of the petiole was inserted into a buffer solution containing ethylenediaminetetraacetic acid (sink). After 3 h, the distribution of sucrose and xenobiotics was determined in five subsequent segments of the petiole (path). The retention coefficient (r) was calculated from the ratio of radioactivity in the vascular bundle to that in the petiole parenchyma. The distribution along the vascular path was given by a geometric progression, whereas its constant was the transport coefficient (q). Values of r and q corresponded with the degree of phloem mobility and ambimobility. Four groups of compounds were classified: (i) acidic substances with log K_ow = — 2 to — 2.4 (K_ow is the partition coefficient octanol/water) at pH 8 (pH of sieve tube sap), retained by ion trapping and exhibiting small lateral efflux (q0.7; maleic hydrazide, dalapon); (ii) acidic substances with log K_ow = — 0.7 to — 0.8 at pH 8, retained by ion trapping and subjected to a moderate lateral efflux (0.7>q> 0.5; 2,4-dichlorophenoxyacetic acid, 2-methyl-4-chlorophenoxyacetic acid, bromoxynil); (iii) nonionised substances retained by optimum permeability, exhibiting a considerable lateral leakage (q<0.5; glyphosate, amitrole); (iv) substances without basipetal transport in the phloem (atrazine, diuron). Retention of sucrose corresponded quantitatively with that shown in group (i). This classification was also supported by results of uptake and efflux experiments using the isolated conducting tissue. Theoretical translocation profiles were calculated from the determined transport coefficients (q).Abbreviations 2,4-D 2,4-dichlorophenoxyacetic acid - K_ow partition coefficient octanol/water - MCPA 2-methyl-4-chloro-phenoxyacetic acid - q transport coefficient in the vascular bundle - r retention coefficient in the vascular bundle The authors gratefully acknowledge the assistance of H. Fiedler and M. Neugebauer. We are particularly grateful to K. Dutschka, G. Hudepokl, and Dr. J. Knust for producing ¹¹CO₂.     

Calculations of the φ -ψ Conformational Contour Maps for N-Acetyl Alanine N'-Methyl Amide and of the Characteristic Ratios of Poly-L-alanine Using Various Molecular Mechanics Forcefields

Abstract

We generated φ -ψ conformational energy contour maps for the of N-acetyl alanine N'-methyl amide using the molecular mechanics forcefields AMBER, AMBER3, BI085, CFF91, CVFF, MM2, MM3, MM+, and SYBYL. With MM2, MM3, and MM+, we used a dielectric constant of ? = 1.5, the default effective value for these forcefields. With the other forcefields we used ? = 1 and 4, except with SYBYL, which, in Spartan 3.1, has no electrostatic term. All forcefields yielded the C^eq ₇ conformation as a low-energy minimum or the global minimum. Most of the forcefields also yielded a minimum-energy conformation in the C₅,α_R, and α_t. regions of the φ -ψ contour map. Fewer of the forcefields yielded a minimum in the C^ax ₇ region; however, adiabatic relaxation frequently lowered the relative energy of this region. Based on the appearance of the φ -ψ maps, the following pairs of forcefields were broadly similar (but not identical) to each other but dissimilar to the other pairs: AMBER3 and AMBER, BI085 and CHARMM, MM+ and MM2, SYBYL and ECEPP, and CFF91 and MM3. We used the data from the φ -ψ contour maps to compute the characteristic ratio of poly-L-alanine. Most of the computed values deviated significantly from the experimental value. Only the computed characteristic ratio of CFF91 without adiabatic relaxation at ? = 4 and MM3 without adiabatic relaxation at ? = 1.5 agreed with the experimental value.     

Identification of reactive toxicants: Structure–activity relationships for amides

A diverse series of amides were evaluated for aquatic toxicity (IGC₅₀) assessed in the Tetrahymena pyriformis population growth impairment assay and for reactivity (EC₅₀) with the model soft nucleophile thiol in the form of the cysteine residue of the tripeptide glutathione. All alkylamides along with some halo-substituted amides are well predicted by the simple hydrophobicity (log K _ow)–electrophilicity (E _lumo) response-surface model [log(IGC⁻¹ ₅₀) = 0.45(log K _ow) − 0.342(E _lumo) − 1.11]. However, 2-halo amides with the halogen at the end of the molecule and α,β-unsaturated primary amides are among those derivatives identified as being more toxic than predicted by the model. Amides, which exhibit excess toxicity, were capable of forming covalent bonds through an S_N2 displacement or a Michael addition. Moreover, only those amides exhibiting excess toxicity were reactive with thiol, suggesting that the reactivity with model nucleophiles such as the thiol group may provide a means of accurately defining reactive toxicants.     

Effects of temperature and CO2 enrichment on kinetic properties of NADP+-malate dehydrogenase in two ecotypes of Barnyard grass (Echinochloa crus-galli (L.) Beauv.) from contrasting climates

Summary The apparent energy of activation (E _a), Michaelis-Menten constant (K _mfor oxaloacetate), V _max/K _mratios and specific activities of NADP⁺-malate dehydrogenase (NADP⁺-MDH; EC 1.1.1.82) were analyzed in plants of Barnyard grass from Québec (QUE) and Mississippi (MISS) acclimated to two thermoperiods 28/22°C, 21/15°C, and grown under two CO₂ concentrations, 350 l l^-1 and 675 l l^-1. E _avalues of NADP⁺-MDH extracted from QUE plants were significantly lower than those of MISS plants. K _mvalues and V _max/K _mratios of the enzyme from both ecotypes were similar over the range of 10–30°C but reduced V _max/K _mratios were found for the enzyme of QUE plants at 30 and 40°C assays. MISS plants had higher enzyme activities when measured on a chlorophyll basis but this trend was reversed when activities were expressed per fresh weight leaf or per leaf surface area. Activities were significantly higher in plants of both populations acclimated to 22/28°C. CO₂ enrichment did not modify appreciably the catalytic properties of NADP⁺-MDH and did not have a compensatory effect upon catalysis or enzyme activity under cool acclimatory conditions. NADP⁺-MDH activities were always in excess of the amount required to support observed rates of CO₂ assimilation and these two parameters were significantly correlated. The enhanced photosynthetic performance of QUE plants under cold temperature conditions, as compared to that of MISS plants, cannot be attributed to kinetic differences of NADP⁺-malate dehydrogenase among these ecotypes.     

An efficient method for the determination of K m values for HCO 3 - of phosphoenolpyruvate carboxylase

One of the most serious problems in obtaining estimates of the K _m values for HCO ₃ ^- of phosphoenolpyruvate carboxylase (PEPCase; EC 4.1.1.31) by measurement of initial rates at varying HCO ₃ ^- is the impossibility of completely excluding any contaminating HCO ₃ ^- . A method is proposed which has no need for the careful control of HCO ₃ ^- /CO₂ contamination. The kinetic data are obtained by the evaluation of progress curves of HCO ₃ ^- consumption. The method is discussed and the K _m values for HCO ₃ ^- of PEPCase from several C₄-species are presented.Abbreviations C₃, C₄ assimilated CO₂ initially found in 3-phosphoglycerate (C₃) or malate and aspartate (C₄) - OAA oxaloacetic acid - PEP phosphoenolpyruvate - PEPCase phosphoenolpyruvate carboxylase     

Interaction Mode between Inclusion Complex of Vitamin K3 with γ- Cyclodextrin and Herring-Sperm DNA

Methods including spectroscopy, electronic chemistry and thermodynamics were used to study the inclusion effect between γ-cyclodextrin (CD) and vitamin K₃(K₃), as well as the interaction mode between herring-sperm DNA (hsDNA) and γ-CD-K₃ inclusion complex. The results from ultraviolet spectroscopic method indicated that VK₃ and γ-CD formed 1:1 inclusion complex, with the inclusion constant K_f = 1.02 × 10⁴ L/mol, which is based on Benesi–Hildebrand's viewpoint. The outcomes from the probe method and Scatchard methods suggested that the interaction mode between γ-CD-K₃ and DNA was a mixture mode, which included intercalation and electrostatic binding effects. The binding constants were K ^θ_25°C = 2.16 × 10⁴ L/mol, and K^θ_37°C = 1.06 × 10⁴ L/mol. The thermodynamic functions of the interaction between γ-CD-K₃ and DNA were Δ_rH_m^θ = ?2.74 × 10⁴ J/mol, Δ_rS_m^θ = 174.74 J·mol^?1K^?1, therefore, both Δ_rH_m^θ (enthalpy) and Δ_rS_m^θ (entropy) worked as driven forces in this action.     

Molecular docking and 3D-QSAR studies on β-phenylalanine derivatives as dipeptidyl peptidase IV inhibitors

Three-dimensional quantitative structure-activity relationship (3D-QSAR) and molecular docking studies were carried out to explore the binding of 73 inhibitors to dipeptidyl peptidase IV (DPP-IV), and to construct highly predictive 3D-QSAR models using comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA). The negative logarithm of IC₅₀ (pIC₅₀) was used as the biological activity in the 3D-QSAR study. The CoMFA model was developed by steric and electrostatic field methods, and leave-one-out cross-validated partial least squares analysis yielded a cross-validated value (r_cv² {\hbox{r}}_{{\rm{cv}}}^{\rm{2}} ) of 0.759. Three CoMSIA models developed by different combinations of steric, electrostatic, hydrophobic and hydrogen-bond fields yielded significant r_cv² {\hbox{r}}_{{\rm{cv}}}^{\rm{2}} values of 0.750, 0.708 and 0.694, respectively. The CoMFA and CoMSIA models were validated by a structurally diversified test set of 18 compounds. All of the test compounds were predicted accurately using these models. The mean and standard deviation of prediction errors were within 0.33 and 0.26 for all models. Analysis of CoMFA and CoMSIA contour maps helped identify the structural requirements of inhibitors, with implications for the design of the next generation of DPP-IV inhibitors for the treatment of type 2 diabetes.