Thermodynamic Constraints in Kinetic Modeling: Thermodynamic‐Kinetic Modeling in Comparison to Other Approaches

Kinetic models of reaction networks may easily violate the laws of thermodynamics and the principle of detailed balance. In large network models, the constraints that are imposed by these laws are particularly difficult to address. This hinders modeling of biochemical reaction networks. Thermodynamic‐kinetic modeling is a method that provides a thermodynamically sound and formally appealing way for deriving dynamic model equations of reaction systems. State variables of this approach are thermokinetic potentials that describe the ability of compounds to drive a reaction. A compound has a parameter called capacity, which is the ratio of its concentration and thermokinetic potential. A reaction is described by its resistance which is the ratio of the thermokinetic driving force and flux. In these aspects, the formalism is similar to the modeling formalism for electrical networks and an analogous graphical representation is possible. The thermodynamic‐kinetic modeling formalism is equivalent to the traditional kinetic modeling formalism with the exception that it is not possible to build thermodynamically infeasible models. Here, the thermodynamic‐kinetic modeling formalism is reviewed, compared to other approaches, and some of its advantages are worked out. In contrast to other approaches, thermodynamic‐kinetic modeling does not rely on an explicit enumeration of stoichiometric cycles. It is capable of describing rate laws far from equilibrium. Further, the parameterization by capacities and resistances is particularly intuitive and powerful.     

Solubility properties of alkaline phosphatase from matrix vesicles

Alkaline phosphatase has been extracted from matrix vesicles of a calcifying cartilage with 0.15 M KCl, 0.4 M guanidinium chloride and 0.05 M deoxycholate/50% butanol mixture. The catalytic properties of the three extracts have been compared. Although the highest amount of enzyme activity is extracted with the latter reagent (55%), some of it is also extracted with KCl (11%) and guanidinium (7%). By submitting isolated matrix vesicles to a short time sonication the distribution pattern of the alkaline phosphatase activity in the extracts is clearly modified, as the amount extracted with KCl increases from 14 to 50% and the portion extracted with deoxycholate decreases from 55 to 27% of the total enzyme activity of matrix vesicles. The enzymatic preparations were comparable on the basis of specific activities, affinity for the substrates (p-nitrophenylphosphate, ATP), thermostability, sensitivity to inhibitors and activators. By electrofocusing a value of pI = 4.15 was found for the alkaline phosphatase of matrix vesicles independently of the extraction medium. These results contradict the concept that alkaline phosphatase is exclusively an intrinsic membrane protein.     

Kinetic analysis of unpurified native antigens available in very low quantities and concentrations

Affinity measurements of antigen–antibody interactions are generally performed using known concentrations of purified or recombinant materials. In addition, many technologies that measure affinity require the interacting components to be present in at least microgram quantities. Specifically, if the antigen is either available only in low quantities or unable to be purified, or if the quantity is unknown, then the measurement of affinity can be very difficult. Using the Kinetic Exclusion Assay (KinExA) technology, here we describe a method that overcomes the requirement for large amounts of purified and known quantities of antigen. We used this method to precisely measure the affinity of fully human anti-human interleukin 13 (IL13) monoclonal antibodies to IL13 produced in native form from primary T cells derived from a variety of species, including human. These antigens were available only in the limited quantities present in the conditioned cell culture medium, and the affinity was measured directly without further purification.     

Imidacloprid and Related Compounds: Structure and Water Solubility of N-Alkyl Derivatives of Imidacloprid

An intramolecular hydrogen bond between NH???O₂N in insecticide, imidacloprid (1), and its nitromethylene analog 15 was proved by NMR and IR spectra. That electron delocalization over their planar moieties was disrupted by alkylation at the imidazolidine nitrogen atom is demonstrated by the hypsochromic shifts in UV and deshielding effect in NMR spectra. Interestingly, the N-alkyl derivatives (C1-5) had greater water solubility than 1, although increasing alkyl chain length decreased the solubility. The hydrophilicity of the alkyl derivatives would result from remote charge heads being formed as a result of the conjugation disruption by alkylation, while the hydrophobicity of 1 could be ascribed to the charge distribution over the conjugated system coupled with the intramolecular H-bonding. The greater water solubility of 15 than 1 and contrastively small solubility of the cyanoimine analogue are discussed based on the difference in their steric crowding.     

Kinetic and Thermodynamic Characterization of Glucoamylase from Colletotrichum sp. KCP1

Extracellular glucoamylase of Colletotrichum sp. KCP1 produced through solid state fermentation was purified by two steps purification process comprising ammonium sulphate precipitation followed by gel permeation chromatography (GPC). The Recovery of glucoamylase after GPC was 50.40 % with 19.3-fold increase in specific activity. The molecular weight of enzyme was found to be 162.18 kDa by native-PAGE and was dimeric protein of two sub-units with molecular weight of 94.62 and 67.60 kDa as determined by SDS-PAGE. Activation energy for starch hydrolysis was 26.45 kJ mol⁻¹ while temperature quotient (Q₁₀) was found to be 1.9. The enzyme was found to be stable over wide pH range and thermally stable at 40–50 °C up to 120 min while exhibited maximum activity at 50 °C with pH 5.0. The pKa₁ and pKa₂ of ionisable groups of active site controlling V_max were 3.5 and 6.8, respectively. V_max, K_m and K_cat for starch hydrolysis were found to be 58.82 U ml⁻¹, 1.17 mg (starch) ml⁻¹ and 449 s⁻¹, respectively. Activation energy for irreversible inactivation (E_a(d)) of glucoamylase was 74.85 kJ mol⁻¹. Thermodynamic parameters of irreversible inactivation of glucoamylase and starch hydrolysis were also determined.     

Kinetic analysis of simultaneously occurring proton-sorbose symport and passive sorbose transport in Saccharomyces fragilis

Sorbose transport in Saccharomyces fragilis takes place both via an active sugar-H⁺ symport system and via facilitated diffusion.To establish whether the two modes of transport proceed via the same transporter or via two different carriers, the kinetic consequences of both models were investigated. The kinetic equations for initial transport were derived for three possible reaction sequences with respect to sugar and H⁺ binding to the symport carrier: random binding and obligatory ordered binding with either sugar or H⁺ binding first, yielding six sets of kinetic parameters.Analysis of experimental data of sorbose transport in S. fragilis showed the existence of separate carriers for active, sorbose-H⁺ symport and facilitated diffusion. Furthermore, it could be concluded that the symport carrier shows random binding of sugar and H⁺.In recent literature, a similar combination of active and passive sugar transport in Rhodotorula gracilis and Chlorella vulgaris was interpreted as two modes of action of the same carrier, viz., active symport via the protonated, and facilitated diffusion via the unprotonated carrier. Analysis of the experimental data according to the criteria presented in this paper showed, however, that this supposition is untenable and that two different carriers must also be involved in these micro-organisms.     

ZK-I菌发酵液中抗真菌活性化合物的纯化与部分特性研究

芽孢杆菌属(Bacillus sp．)菌株ZK-I对甜瓜疫霉病、棉花枯萎病等多种作物真菌病害以及啤酒酵母都有很强的抑制作用。报道了ZK-I菌发酵液中抗真菌化合物的分离纯化及其部分特性。该菌株发酵液经过酸沉淀、正相硅胶层析以及C_(18)相硅胶层析等步骤,得到四个化合物,经HPLC检测均为单峰,通过质谱测定分子量并结合高效液相检测结果确定它们为同系物,其中A为捷安肽素A,并推测其余化合物为捷安肽素A的结构类似物。     

The Influence of Organic Matter and pH on DDT Aqueous Solubility

We have studied the concentrations of DDT in ground water samples at field locations with DDT-polluted topsoil and concentrations and solubility in samples prepared from deionized water with different types and concentration of organic acids. The solubility of DDT increased with increasing concentration of humic acid when the pH of the samples was low (adjusted to about 5.5). The effect flutters in the humic acid concentration range from 200 to 300?mg/L, in accordance with humic acid hydrophobicity, operationally measured as liquid surface tension. The findings correspond to trends previously reported in the literature. The trend of increasing solubility was not found using fulvic acid or low-molecular-weight aliphatic acids. No trend was found adding humic acid without adjusting the pH. The mechanism of enhanced solubility due to humic compounds can explain relatively high levels of DDT in ground water. The ground water samples, however, had a moderately high concentration of maximum 6?µg/L compared with a maximum of about 2300?µg/L in the water samples with humic acid in pure water.     

Kinetic studies on the reversible ring opening-closure reaction of the triazine ligand and structural properties of palladium(II) complexes

A Pd(II) complex containing didentate triazine ligand L¹ (2-(2-methylphenyl)-3-(2-pyridyl)-2,3-dihydronaphtho[2,1-e][1,2,4]triazine) [PdCl₂(L¹)] (1) was prepared, and the structure was determined by X-ray crystallography. The absorption spectrum of complex 1 in dichloromethane changed gradually with isosbestic points when methanol was added to the solution, and [PdCl(L²)] (2) (L² = N-[methoxy(2-pyridyl)methyl]-1-(2-methylphenylazo)-2-naphthylamide) was obtained from the resulting solution after the reaction was completed. Addition of hydrogen chloride to the solution of complex 2 led to the recovery of complex 1. Thus, a reversible ring opening and closure reaction of the triazine ligand was observed. The progress of the ring opening reaction was monitored by observing the absorbance changes at several wavelengths of the visible spectra as a function of the concentration of methanol. The absorbance plots were fitted successfully with a mechanism that includes the consumption of two methanol molecules and the release of HCl, whose concentration is equivalent to that of the produced Pd complex . In dichloromethane with a low dielectric constant, the polar HCl molecule will be stabilized by forming an adduct with methanol. The equilibrium constant was determined as at T = 25.0 °C. The kinetics of the reaction of [PdCl₂(L¹)] with methanol was investigated by monitoring the absorbance change of the reacting solution with time. We obtained rate constant values of k₁ = (2.40 ± 0.07) × 10⁻³ s⁻¹ and k₂ = (5.8 ± 0.1) × 10⁻³ M⁻¹ s⁻¹ at T = 25.0 °C on the observed pseudo-first-order rate constant of the forward reaction, k_f = k₁ + k₂ [CH₃OH].     

Thermodynamic, kinetic, and operational stabilities of yeast alcohol dehydrogenase in sugar and compatible osmolyte solutions

Thermodynamic, kinetic, and operational stabilities of yeast alcohol dehydrogenase (YADH) were measured and compared in aqueous solutions containing various sugars (sucrose, glucose, and ribose) and compatible osmolytes (betaine and sarcosine). In the measurement of operational stability, native YADH was entrapped and physically immobilized in an ultrafiltration hollow fiber tube to retain the native characteristics of the enzyme. All the additives tested increased thermodynamic stability and kinetic stability of YADH. The order of the magnitude of stabilization effect among additives was different between thermodynamic and kinetic stabilities. Compared to the thermodynamic and kinetic stabilities, the effects of additives were much different in operational stability. Sucrose, glucose, and betaine stabilized YADH substantially while ribose and sarcosine destabilized the enzyme. These results show that the thermodynamic and kinetic stabilities do not necessarily guarantee the operational stability of YADH. The coexistence of stabilizing solute was proved effective to increase the productivity of the bioreactor with immobilized YADH.     

Kinetic and structural features of betaine aldehyde dehydrogenases: Mechanistic and regulatory implications

The betaine aldehyde dehydrogenases (BADH; EC 1.2.1.8) are so-called because they catalyze the irreversible NAD(P)⁺-dependent oxidation of betaine aldehyde to glycine betaine, which may function as (i) a very efficient osmoprotectant accumulated by both prokaryotic and eukaryotic organisms to cope with osmotic stress, (ii) a metabolic intermediate in the catabolism of choline in some bacteria such as the pathogen Pseudomonas aeruginosa, or (iii) a methyl donor for methionine synthesis. BADH enzymes can also use as substrates aminoaldehydes and other quaternary ammonium and tertiary sulfonium compounds, thereby participating in polyamine catabolism and in the synthesis of γ-aminobutyrate, carnitine, and 3-dimethylsulfoniopropionate. This review deals with what is known about the kinetics and structural properties of these enzymes, stressing those properties that have only been found in them and not in other aldehyde dehydrogenases, and discussing their mechanistic and regulatory implications.     

Reduction of Fe(III) (Hydr)oxides with Known Thermodynamic Stability by Geobacter metallireducens

Sulfate-reducing and methanogenic microorganisms become inactive when the concentration of the electron donors drops below a threshold set by the minimum Gibbs free energy required for the bacterial metabolism to be maintained. Thus, their activity is thermodynamically controlled. In this paper we study if the activity of dissimilatory Fe(III) reducing bacteria is also limited by the thermodynamics of the reaction. We synthesized five Fe (III) (hydr)oxides (FHOs) of moderate stability and determined the solubility product (log K _SO (?39.1)-(?41.8)), in order to calculate their standard free energy of formation. K _SO values, estimated from the particle size did not correspond with experimentally determined ones. HCO₃ ^? and PIPES-buffered media, containing 45 mM FHO and either 1, 10, or 100 mM acetate were inoculated with Geobacter metallireducens. At the end of bacterial reduction, the Gibbs free energy of the reaction showed significant differences between the different FHOs. The termination of the bacterial activity was consequently not triggered thermodynamically. However, the non-dissolved Fe(II) (HCl-soluble minus soluble Fe(II)) showed an excellent correlation with the surface of the FHOs (15 μmol m^?2). It is therefore likely that the termination of the reaction was caused by blocking of the FHO surface with insoluble Fe(II), as has been previously reported in the literature. The ecological significance of both thermodynamic limitation and surface availability limitation is discussed for FHOs of different K _SO in environments with approximately neutral pH.     

Kinetic resolution of 1-chloro-3-(1-naphthyloxy)-2-propanol,an intermediate in the synthesis of beta-adrenergic receptor blockers

(R)- and (S)-1-chloro-3-(1-naphthyloxy)-2-propanol are intermediates in the synthesis of β-adrenergic blocking agents and antihypertensive drugs such as propranolol and nadoxolol. Herein, improvement in the preparation of racemic 1-chloro-3-(1-naphthyloxy)-2-propanol generated from 1-naphthol and epichlorohydrin are reported. In addition, kinetic resolution studies have been conducted to obtain both (R) and (S)-1-chloro-3-(1-naphthyloxy)-2-propanol. These compounds were obtained in highly optically pure form by the stereoselective hydrolysis of its acyl derivatives using whole cell preparations containing enzymes from native sources. The results were compared with those obtained using commercial lipases.     

Critical Values and Some Properties of a New Test Statistic for Analyzing Unreplicated Factorial Experiments

Critical values of the test statistic proposed by Al‐Shiha and Yang (1999) for analyzing unreplicated factorials are estimated by fitting an appropriate linear model. Some important properties of the test are also provided.     

Bioactive sulfoximines: syntheses and properties of Vioxx analogs

The syntheses and biological profiles of sulfoximine-based Vioxx® analogs 2 are described. Interesting data have been obtained for 2a, which shows a selective COX-2 inhibition (albeit not as strong as Vioxx® itself) exhibiting reduced hERG activity compare to the parent sulfone Vioxx® (1).     

用R法估计方差组分的原理、方法和应用

综述了R法估计方差组分的原理、方法和应用,目的是使该方法能够得到合理应用。R法是通过计算全数据集对亚数据集随机效应的回归因子（R）来估计方差组分的。利用一种基于一个变换矩阵的多变量迭代算法,结合先决条件的共扼梯度法求解混合模型方程组使R法的计算效率大为改善。R法的主要优点是计算成本低,同时可以得到方差组分估值的抽样误差和近似置信区间。其缺点是对于同样的数据,R法较其他方法的抽样误差大,而且在小样本中估计值往往有偏。做为一种可选方法,R法可以应用到大数据集的方差组分估计中,同时应进一步研究其理论特性,拓宽其应用范围。Abstract: Theory, method and application of Method R on estimation of (co)variance components were reviewed in order to make the method be reasonably used. Estimation requires R values,which are regressions of predicted random effects that are calculated using complete dataset on predicted random effects that are calculated using random subsets of the same data. By using multivariate iteration algorithm based on a transformation matrix,and combining with the preconditioned conjugate gradient to solve the mixed model equations, the computation efficiency of Method R is much improved. Method R is computationally inexpensive,and the sampling errors and approximate credible intervals of estimates can be obtained. Disadvantages of Method R include a larger sampling variance than other methods for the same data,and biased estimates in small datasets. As an alternative method, Method R can be used in larger datasets. It is necessary to study its theoretical properties and broaden its application range further.     

Thermodynamic and structural analysis of interactions between peptide ligands and SEB

Staphylococcal enterotoxin B (SEB) is an exotoxin produced by Staphylococcus aureus and commonly associated with food poisoning. In this study, SEB‐binding peptides were identified by screening a phage displayed peptide library. The binding of peptides to SEB was tested with isothermal titration calorimetry (ITC) and of the five selected peptides, three showed affinity to SEB, with one measured to have the highest affinity constant (10⁵ M^?1). ITC revealed that the interaction of peptide ligands with SEB was driven entropically and the binding was dominated by hydrophobic interactions. Circular dichroism (CD) measurements and molecular dynamics (MD) simulations, together, give a structural insight into the interaction of peptides with SEB. While SEB binding peptides showed random coil structure before binding, after complex formation they had more ordered structures. The peptide with highest affinity to SEB showed stable conformation during MD simulation. Taken together, our approach about thermodynamic and structural characterization of peptide ligands can be used to develop aptamers, with high affinity and selectivity, for biosensor applications. Copyright © 2009 John Wiley & Sons, Ltd.     

Inhibition of Jack Bean Urease by N-(n-butyl)thiophosphorictriamide and N-(n-butyl)phosphorictriamide: Determination of the Inhibition Mechanism

N-(n-butyl)thiophosphorictriamide (NBPT) and its oxygen analogue N-(n-butyl)phosphorictriamide (NBPTO) were studied as inhibitors of jack bean urease. NBPTO was obtained by spontaneous conversion of NBPT into NBPTO. The conversion under laboratory conditions was slow and did not affect NBPT studies. The mechanisms of NBPT and NBPTO inhibition were determined by analysis of the reaction progress curves in the presence of different inhibitor concentrations. The obtained plots were time-dependent and characteristic of slow-binding inhibition. The effects of different concentration of NBPT and NBPTO on the initial and steady-state velocities as well as the apparent first-order velocity constants obeyed the relationships for a one-step enzyme-inhibitor interaction, qualified as mechanism A. The inhibition constants of urease by NBPT and NBPTO were found to be 0.15 μM and 2.1 nM, respectively. The inhibition constant for NBPT was also calculated by steady-state analysis and was found to be 0.13 μM. NBPTO was found to be a very strong inhibitor of urease in contrast to NBPT.     

Synthesis,DNA Binding,and Oxidative Cleavage Studies of Fe(II) and Co(III) Complexes Containing Bioactive Ligands

The two complexes containing bioactive ligands of the type and [Fe(L)] (PF₆)₂ (1) (where L = [1-{[2-{[2-hydroxynaphthalen-1-yl)methylidine]amino}phenyl)imino] methyl}naphthalene-2-ol]) and [Co(L₁L₂)] (PF₆)₃ (2) (where L₁L₂ = mixed ligand of 2-seleno-4-methylquinoline and 1,10-phenanthroline in the ratio 1:2, respectively) were synthesized and structurally characterized. The DNA binding property of the complexes with calf thymus DNA has been investigated using absorption spectra, viscosity measurements, and thermal denaturation experiments. Intrinsic binding constant K_b has been estimated at room temperature. The absorption spectral studies indicate that the complexes intercalate between the base pairs of the CT-DNA tightly with intrinsic DNA binding constant of 2.8 × 10⁵ M^?1 for (1) and 4.8 × 10⁵ M^?1 for (2) in 5 mM Tris-HCl/50 mM NaCl buffer at pH 7.2, respectively. The oxidative cleavage activity of (1) and (2) were studied by using gel electrophoresis and the results show that complexes have potent nuclease activity.