Effect of enzyme concentration on the dynamic behavior of a membrane-bound enzyme system

The dynamic behavior of the reaction-diffusion system, composed of glucose oxidase (EC 1.1.3.4) immobilized at a uniform concentration in a membrane, used as a glucose electrode is represented by a diffusion equation with a nonlinear reaction-term in one-dimensional space. The mathematical model is analyzed by computer simulation, that is, numerical integration of the equation under various initial and boundary conditions, to examine the effect of enzyme concentration on the response characteristics (responsiveness and linearity in response) of the electrode. The analysis of the responses of the system to stepwise changes in the boundary value (glucose concentration in simple solution) infers that the enzyme concentration governs the patterns of the spatial distributions of the substrates (glucose and dissolved oxygen) in steady states and transient responses. It is also revealed that the response characteristics of the electrode are optimized with concentration of immobilized enzyme and that the system establishes the steady states at the same spatial distributions of the substrates, regardless of the boundary value. The diffusion of the substrates and the oxygen concentration also have significant effects on the response characteristics of the electrode.     

静电和疏水效应对TGEV主蛋白酶二聚体稳定性的影响

从TGEV 3CL蛋白酶二聚体结构出发,研究了TGEV 3CL蛋白酶二聚体单体之间的静电和疏水相互作用.蛋白质的静电相互作用通过有限差分方法求解Poisson-Boltzmann方程得到,疏水相互作用通过分析溶剂可及性表面模型得到.考察了不同pH值对TGEV 3CL蛋白酶二聚体静电和疏水相互作用的影响,在pH值为5.5～8.5时,二聚体静电相互作用能、静电去溶剂化能和疏水自由能都较小,表明在该条件下静电和疏水相互作用有利于二聚体的稳定存在,这符合实验结晶所需条件.pH值对静电去溶剂化能的影响大于疏水自由能,表明静电作用是造成强酸或强碱条件下二聚体不能稳定存在的主要原因.     

Computational studies of carbon nanotube-hydrocarbon bond strengths at nanotube ends: effect of link heteroatom and hydrocarbon structure

Semiempirical and density functional electronic structure theory methods were used to study SWNT-X--R bond strengths, where the single-walled carbon nanotube (SWNT) had an armchair or zigzag structure, the link heteroatom X was O, N(H), or S and the hydrocarbon chain R was CH(2)CH(3), CH(OH)CH(3), CHCH(2), or CH(CF(3))CH(3). In all systems the hydrocarbon was bonded to the end of the nanotube. The SWNT-X--R bond (that is, the bond joining the link atom to the hydrocarbon) is more than 0.4 eV stronger for armchair than for zigzag nanotubes with the same diameters, irrespective of whether O, N, or S are used as link atoms or whether OH, C==C, or CF(3) groups are present in the hydrocarbon chain. This raises the possibility for selective manipulation of armchair/zigzag nanotubes using a variety of link atoms and hydrocarbon structures. The SWNT-O--CH(CF(3))CH(3) bond is weaker than the SWNT-O--CH(2)CH(3) bond (for both armchair and zigzag nanotubes), while inclusion of a double bond in the ethyl chain increases the bond strengths. Also, SWNT-S--CH(2)CH(3) and SWNT-N(H)--CH(2)CH(3) bonds are stronger than SWNT-O--CH(2)CH(3) bonds.     

Clusters,metastability, and nucleation: Kinetics of first-order phase transitions

We describe and interpret computer simulations of the time evolution of a binary alloy on a cubic lattice, with nearest neighbor interactions favoring like pairs of atoms. Initially the atoms are arranged at random; the time evolution proceeds by random interchanges of nearest neighbor pairs, using probabilities compatible with the equilibrium Gibbs distribution at temperatureT. For temperatures 0.59T_c, 0.81 T_c, and 0.89T _c, with density of A atoms equal to that in the B-rich phase at coexistence, the density C₁ of clusters ofl A atoms approximately satisfies the following empirical formulas: C₁ w(1 –)³ andC ₁, (1 –)⁴Q₁w¹ (2 l 10). Herew is a parameter and we defineQ _l = _K e ^–E(K) , where the sum goes over all translationally nonequivalentl-particle clusters andE(K) is the energy of formation of the clusterK. Forl > 10,Q ₁ is not known exactly; so we use an extrapolation formulaQ _l Aw _s ^–l l ^– exp(–bl ), wherew _s is the value ofw at coexistence. The same formula (withw > w _s) also fits the observed values of C, (for small values ofl) at densities greater than the coexistence density (forT=0.59T_c): When the supersaturation is small, the simulations show apparently metastable states, a theoretical estimate of whose lifetime is compatible with the observations. For higher supersaturation the system is observed to undergo a slow process of segregation into two coexisting phases (andw therefore changes slowly with time). These results may be interpreted as a more quantitative formulation (and confirmation) of ideas used in standard nucleation theory. No evidence for a spinodal transition is found.Supported by AFOSR Grant No. 73-2430D and by ERDA Contract No. EY-76-C-02-3077*000.     

Computer Simulation of the Structure of Porous Electrodes with an Immobilized Enzyme and Nanosized Support Particles

The efficiency of the operation of a porous electrode with an immobilized enzyme is defined, in particular, by a lucky structure of its active layer, which can contain nanosized particles of the support. The composites of such a kind are prepared with the aid of methods of colloidal chemistry. The aim of this particular investigation is to perform a computer simulation of processes of coagulation of particles of the support and their possible heterocoagulation with molecules of the enzyme. Algorithms of the formation of nanocomposite structures in solution are suggested. Calculations show that the concentration of the enzyme molecules in the nanocomposite structures cannot exceed a certain critical value. On the other hand, at a fixed value of the concentration of the enzyme molecules, the concentration of the support particles must not fall below a certain threshold quantity, which provides for the passing of current through the active layer. In order for all the enzyme molecules, rather than for a fraction of these, in the composite to take part in the process of bioelectrocatalysis, the concentration of support particles must be increased even higher, to an optimum value.__________Translated from Elektrokhimiya, Vol. 41, No. 6, 2005, pp. 738–747.Original Russian Text Copyright © 2005 by Chirkov, Rostokin.     

Methodology for the calculation of the potential of mean force for a cation-pi complex in water.

We report potential of mean force (PMF) calculations on the interaction between the p-sulfonatocalix[4]arene and a monovalent cation (Cs(+)). It has been recently shown from microcalorimetry and (133)Cs NMR experiments that the association with Cs(+) is governed by favourable cation-pi interactions and is characterized by the insertion of the cation into the cavity of the macrocycle. We show that the PMF calculation based upon a classical model is not able to reproduce both the thermodynamic properties of association and the insertion of the cation. In order to take into account the different contributions of the cation-pi interactions, we develop a new methodology consisting of changing the standard PMF by an additional contribution resulting from quantum calculations. The calculated thermodynamic properties of association are thus in line with the microcalorimetry and (133)Cs NMR experiments and the structure of the complex at the Gibbs free-energy minimum shows the insertion of the cation into the cavity of the calixarene.     

Detection of TMV with ODA-H(2)O(2)-HRP voltammetric enzyme-linked immunoassay system

o-Dianisidine (ODA)-H₂O₂-horseradish peroxidase (HRP) voltammetric enzyme-linked immunoassay system has firstly been used for the detection of tobacco mosaic virus (TMV). HRP catalyzes strongly the oxidation reaction of ODA by H₂O₂, the product of which produces a sensitive second order derivative linear sweep voltammetric peak at potential of −0.56 V (versus SCE) in Britton–Robinson (BR) buffer. HRP activity has been measured with this voltammetric peak and TMV detected through immunoreaction. The detection limit for HRP is 9.25×10^-7 mU l⁻¹ and the linear range is 2.5×10⁻⁶–5.0×10⁻⁴ mU l⁻¹. The detection limit for the clarified TMV is 0.25 ng ml⁻¹ and the highest dilution ratio detected for the infected leaf sap is 1:8×10⁵. The sensitivity for TMV detection with this method is higher than that with the enzyme-linked immunosorbent spectrophotometric assay (ELISA) using ODA-H₂O₂-HRP system. The processes of the enzyme-catalyzed reaction and the electro-reduction of the product of the enzyme-catalyzed reaction have been described.     

Computing the Kekulé structure count for alternant hydrocarbons

A fast computer algorithm brings computation of the permanents of sparse matrices, specifically, molecular adjacency matrices. Examples and results are presented, along with a discussion of the relationship of the permanent to the Kekulé structure count. A simple method is presented for determining the Kekulé structure count of alternant hydrocarbons. For these hydrocarbons, the square of the Kekulé structure count is equal to the permanent of the adjacency matrix. In addition, for alternant structures the adjacency matrix for N atoms can be written in such a way that only an N/2 × N/2 matrix need be evaluated. The Kekulé structure count correlates with topological indices. The inclusion of the number of cycles improves the fit. When comparing with previous results, the variance decreases 74%. The calculated standard heat of formation correlates with the logarithm of the Kekulé structure count. This heat increments 349 kJ/mol each time the Kekulé structure count increases by one order of magnitude. © 2002 Wiley Periodicals, Inc. Int J Quantum Chem, 2002     

Topologies of capillary condensation

Calculations are presented to illustrate the dependence of capillary adsorption upon the interactions present in model pores. The sequence of phase transitions at zero temperature is determined for a Lennard-Jones lattice gas in a pore consisting of 4 × 4 × sites. The dependence of the specific filling sequence upon the comparative strength of the gas-pore wall and the gas-gas interaction well-depths is determined. Grand canonical Monte Carlo simulations of sorption at finite temperature in the continuum version of the same model pore are also reported. Both the theory and the simulations were performed with variable gas-solid and gas-gas energy well-depths. At a temperature of 90 K, the gas-solid heterogeneity associated with atoms adsorbed in the corners, on the walls and in the interior pore volume gives rise to sequential adsorption similar to that observed in the lattice gas calculation at 0 K. A gradual approach to non-wetting behavior is observed as the gas-solid well-depth decreases. Values of the gas-solid well-depth needed to produce pore filling at saturation (i.e., pore-wetting) are discussed.     

The Biological Effects of Forsythia Leaves Containing the Cyclic AMP Phosphodiesterase 4 Inhibitor Phillyrin

Forsythia fruit (Forsythia suspensa Vahl (Oleaceae)) is a common component of Kampo medicines for treating the common cold, influenza, and allergies. The main polyphenolic compounds in the leaves of F. suspensa are pinoresinol β-d-glucoside, phillyrin and forsythiaside, and their levels are higher in the leaves of the plant than in the fruit. It is known that polyphenolic compounds stimulate lipid catabolism in the liver and suppress dyslipidemia, thereby attenuating diet-induced obesity and polyphenolic anti-oxidants might attenuate obesity in animals consuming high-fat diets. Recently, phillyrin was reported as a novel cyclic AMP phosphodiesterase 4 (PDE4) inhibitor derived from forsythia fruit. It was expected that the leaves of F. suspensa might display anti-obesity effects and serve as a health food material. In this review, we summarized our studies on the biological effects of forsythia leaves containing phillyrin and other polyphenolic compounds, particularly against obesity, atopic dermatitis, and influenza A virus infection, and its potential as a phytoestrogen.