Flavin-photosensitized reactions of retinal and stilbene

1. Retinol and stilbene are both isomerized when they are illuminated anaerobically in the presence of flavins. 2. Triplet quenchers (e.g. oxygen, potassium iodide and paramagnetic ions) inhibit the reaction more efficiently than they quench flavin fluorescence. At 77 degrees C in a diethyl ether-isopentane-ethanol (5:5:2) glass retinol quenches flavin phosphorescence, but not its fluorescence. 3. For the stilbene reaction cis/trans photostationary-state mixtures are obtained with different flavins and these are linearly related to the phosphorescence transition energies of the flavins used. 4. The reaction involves the triplet state of flavin and a scheme for the reaction is suggested. 5. The dependence of the rate of reaction on substrate concentration is explicable in terms of this scheme. 6. The photobleaching of rhodopsin sensitized by flavin is also demonstrated.     

Chemical competition in target radical reactions: numerical simulation of the theory and comparison with measured oxygen effect on DNA damage in cells

An intracellular radiation-chemical reaction scheme is tested in which solute and solvent radicals R. react with non-target molecules Sa (scavengers) or with target molecules (presumed to be DNA) to produce target radicals T., which may also be produced by direct ionization of DNA. The rate of target radical decomposition to become 'uncommitted damage' that the cell may repair is affected by the concentration of oxygen (O2), thiols (S) and electronaffinic sensitizers (F), which compete with one another to form, respectively, target products TO2, TS and TF. This uncommitted damage is then subject to biochemical modification, including molecular repair, by the cell. The rate equations for this competing reaction scheme were written and programmed for computer simulations of changes in oxygen, thiol and electronaffinic sensitizer concentrations. A reaction scheme that also includes some non-radical target damage was also simulated. Simulations were made using available experimental data concerning intranuclear concentrations and reaction rate constants, respectively, ko, ks and k1 for the reactions T. + O2----TO2, T. + S----TS and T. + F----TF, which produce uncommitted chemical damage. Experimental data on strand-break induction in glutathione-proficient and glutathione-deficient cells, in cells treated with thiol active agents, and in cells treated with hypoxic sensitizers, along with the computer simulations, generally agree that thiol molecules can react with target radicals to reverse T. in competition with O2 and/or electronaffinic sensitizers. Forward reaction rate constants ko, ks (dithiothreitol), ks (glutathione) and k1 (misonidazole) in the approximate ratio 10:0.3:0.02:0.4 satisfied the above reaction scheme, and approximately 5 per cent non-radical target molecule damage could be included with satisfactory agreement with experimental data.     

陀螺旋转式立体定向放射治疗联合NP 方案治疗局部晚期非小细胞肺癌 的临床疗效观察

目的:观察陀螺旋转式立体定向放射治疗系统(陀螺刀)联合长春瑞滨、顺铂(NP)方案治疗局部晚期非小细胞肺癌(NSCLC)的临床疗效观察及毒副反应。方法:94例局部晚期NSCLC患者,先给予陀螺刀治疗,单次治疗剂量3.2-5.0 Gy,等剂量曲线50%-70%,计划靶体积(PTV)覆盖95%以上,总剂量35-50 Gy,治疗后进行NP方案化疗4-6个周期。与同期144例单纯陀螺刀治疗局部晚期NSCLC患者治疗结果相比较。结果:联合治疗的94例患者,近期有效率为86.17%(81/94),6、12和24个月生存率分别为86.17%(81/94)、60.64%(57/94)和36.17%(34/94),毒性反应较轻。同期单纯陀螺刀治疗患者,近期有效率为88.19%(127/144),6、12和24个月生存率分别为87.50%(126/144)、44.44%(64/144)和23.68%(33/144)。结论:陀螺刀联合NP方案是一种对局部晚期NSCLC比较有效的治疗方法,毒副反应较轻。     

On a systematic procedure for the predetermination of macroscopic reaction schemes

Macroscopic modeling of biological cell cultures involves two major steps: (a) the selection of a reaction scheme and (b) the determination of the reaction kinetics. The first step is usually accomplished based on prior knowledge, experimental investigation and trials and errors. This procedure can be time consuming, and more importantly, can lead to the selection of a reaction scheme omitting some important reaction pathways, or at the opposite, incorporating too many details (at least considering the data at hand and the modeling objectives). This paper addresses this modeling problem, and aims at the development of a method for systematically evaluating (i.e. setting up and comparing) all potential reaction schemes, based on a set of measured components, and satisfying structural identifiability properties. One of the main features of the method is that the yield (or pseudo-stoichiometric) coefficients can be estimated independently of the kinetics. The method is illustrated with simulation results and an experimental case study.     

Kinetics and mechanism of peptide synthesis in solution

The kinetics of the reaction of Boc-Xaa fluorophenyl esters (where Xaa = Ala, Val, Phe, Ser, Leu, Gly, Met, Pro, or Ile) with leucinamide was studied measuring changes in the fluorescence emission at 375 nm of the fluorophenyl chromophore accompanying the reaction. It was found that the experimental kinetic data couldn't be described by a simple scheme of the second order reaction. The measurements of the kinetic parameters of the reaction at various initial concentrations of reagents indicated that the reaction rate can be expressed as: v = kCNaCAEb, where k is the reaction rate constant, CN is the concentration of leucinamide, and LeuNH2, CAE is the concentration of fluorophenyl ester. The a and b reaction orders were close to 1/2 and 3/2 for Xaa = Ala, Val, Phe, Ser, or Leu, 1/2 and 1 for Gly, Met, or Pro, and 1 and 2 for Ile. The experimental equations for the reaction rate can theoretically be derived from a single scheme of chain reactions with various deactivation ways for active intermediates. The English version of the paper.     

A new kinetic property characteristic of the actomyosin-nucleoside-triphosphatase.

The nucleoside triphosphatase [EC 3.6.1.15] activity of actomysin and that of myosin are measured by varying the concentration of nucleoside triphosphate and that of CaCl2 or MgGl2. The results thus obtained are examined by asking a question of which is responsbile for the activity, the true substrate and the active enzyme in terms of the reaction scheme shown in p. 719. The answers found for the above question are summarized in Table I (see p. 720). It is emphasized that the summmary (Table I) corresponds very well to the fact that myosin alone does not superprecipitate in the presence of either calcium or magnesium ions, whereas actomyosin does superprecipitate in the presence of magnesium ions and not in the presence of calcium ions. Obviously, the true substrate type of reaction scheme represents a kinetic property characteristic of the superprecipitation-coupled nucleoside-triphosphatase. It is also noted of the summary (Table I) that actin is capable of not only activating Mg-nucleoside-triphosphatase but also switiching the reaction scheme from the active enzyme type to the true substrate type. It is known that trinitrophenylation of myosin results in activation of the Mg-ATPase activity of myosin. However, it is now found that trinitrophenylation is not capable of switiching the reaction scheme, that is to say that the Mg-ATPase reaction of trinitrophenyl-myosin stays with the active enzyme type of reaction scheme and that of acto-trinitrophenyl-myosin with the true substrate type of reaction scheme. Effect of actin on the function of myosin seems, therefore, very unique.     

Kinetic amplification of enzyme discrimination.

The dependence of the accuracy of enzymatic systems on the mechanism of the catalyzed reaction is investigated, using a probabilistic approach. Certain mechanisms of reaction, involving a delay in one of the steps act as kinetic amplifiers of molecular discriminations. The relationship between our scheme for a delayed reaction [1] and Hopfield's scheme [i] is discussed.     

A stoichiometric reaction scheme for Saccharothrix algeriensis growth and thiolutin production

A new bacterial species, Saccharothrix algeriensis NRRL B-24137, was isolated in 1992 in the Sahara desert. This filamentous bacterium is able to produce dithiolopyrrolones, molecules presenting antibacterial, antifungal, and anticancer properties. In this study, a “reaction engineering” approach was adopted to gain more knowledge on the growth of Sa. algeriensis and its dithiolopyrrolone production on a semi-synthetic liquid medium. The objective is to establish a reaction scheme of the bacterium metabolism from extracellular experimental information, relatively easy to obtain. The approach enabled us to show that Sa. algeriensis could grow using several substrates that were sequentially consumed and that substrate limitation may induce a secondary metabolism in antibiotic production. From these qualitative data, a general reaction scheme was extracted consisting of four reactions: growth via amino acids, glucose consumption for maintenance, growth using glucose, and thiolutin production. The stoichiometric coefficients and the reaction extends were identified using a factorial analysis based on the bilinear structure of the component mass balances in a batch reactor. The analysis of the reaction stoichiometry enabled us to draw some conclusions concerning the substrate consumption pathway.     

WinBEST-KIT: Windows-based biochemical reaction simulator for metabolic pathways

We have implemented an efficient, user-friendly biochemical reaction simulator called Web-based BEST-KIT (Biochemical Engineering System analyzing Tool-KIT) for analyzing large-scale nonlinear networks such as metabolic pathways. Users can easily design and analyze an arbitrary reaction scheme through the Internet and an efficient graphical user interface without considering the mathematical equations. The reaction scheme can include several reaction types, which are represented by both the mass action law (mass balance) and approximated velocity functions of enzyme kinetics at steady state, such as Michaelis-Menten, Hill cooperative, Competitive inhibition. However, since all modules in Web-based BEST-KIT have been developed in Java applet style, users cannot optionally make use of original mathematical equations in addition to the prepared equations. In the present study, we have developed a new version of BEST-KIT (for Microsoft Windows called WinBEST-KIT) to allow users to define original mathematical equations and to customize these equations very easily as user-defined reaction symbols. The following powerful system-analytical methods are prepared for system analysis: time-course calculation, parameter scanning, estimation of the values of unknown kinetic parameters based on experimentally observed time-course data of reactants, dynamic response of reactants against virtual external perturbations, and real-time simulation (Virtual Dry Lab).     

Rapid automated synthesis on paper disks of oligodeoxyribonucleotides constituting the promoter fragment of the vaccinia virus genome

For automation of segmental solid-phase synthesis a simple approach leading to the optimal scheme of synthesis of a large numbers of oligonucleotides in one reaction vessel has been proposed. An advantage of the scheme as compared with synthesis in four reaction vessels is a lower number of condensation steps and increased economy of the process. Sixteen oligodeoxyribonucleotides constituting promoter fragment of the viral genome have been synthesised by the modified segmental method on "Victoriya-2" synthesizer according to the optimal scheme.     

Reaction of vanadate ion with chlorpromazine,formation of vanadyl ion and chlorpromazine free radical

The red colored product, which was identified as a chlorpromazine (CPZ) free radical, was observed in the reaction of CPZ with the vanadate ion (+5 oxidation state). The product and the mechanism for the reaction were characterized from optical and EPR spectrometries. Optimal conditions for generation of the free radical were determined as reaction time within one minute of pH 6 and free radical stabilizing time of 30 minutes by acidifying with HCl. Under these conditions, the stoichiometry for the reaction was found to be 1:1, indicating the involvement of one electron transfer from CPZ to the vanadate ion to form the free radical and vanadyl ion (+4 oxidation state). A possible reaction scheme was proposed:

The implications of this reaction were discussed with regard to the pharmacological action of the vanadate ion and CPZ.     

Chiral symmetry breaking: Experimental results and computer analysis of a liquid-phase autoxidation

The autoxidation of tetralin is treated as a model reaction system to define the applicability of stereospecific autocatalysis. This concept, predicting a spontaneous amplification of enantiomeric excess generated by an autocatalytic chemical reaction, is used in several theoretical models as an explanation for the origin of natural optical activity. The reaction system investigated obeys the basic criteria of these models: a chiral intermediate (tetralin hydroperoxide) is produced from an achiral substrate (tetralin) via an autocatalytic pathway where the feedback mechanism is expected to generate a state of broken chiral symmetry. In order to test the amplification capacity of this reaction a computer analysis of the kinetic scheme is performed. This simulation is derived from the known kinetic scheme of autoxidation and is validated by fitting the experimentally observed data of hydroperoxide evolution. Calculations show that this model allows powerful amplification of enantiomeric excess and a transient amplification of the optical rotation. It is also demonstrated that the model system exhibits pronounced sensitivity toward any loss of absolute configuration of the involved chiral species. Since an amplification effect results exclusively at a high degree of stereoselectivity, it is concluded that stereospecific autocatalysis is possible in systems which show template reactions, crystallization, or colloidal effects. © 1993 Wiley-Liss, Inc.     

Comparison of different biochemical and molecular methods for the identification of Vibrio parahaemolyticus

AIMS: Multicentre evaluation of biochemical and molecular methods for the identification of Vibrio parahaemolyticus. METHODS AND RESULTS: For the biochemical identification methods, API 20E and API 20NE and Alsina's scheme were evaluated in intra- and interlaboratory tests in order to determine the accuracy and concordance of each method. Both in intra- and interlaboratory tests, the Alsina's scheme showed the highest sensitivity (86% of correct identifications in the interlaboratory test). False-positive results were obtained by all methods (specificity was 95% for API 20E, 73% for API 20NE and 84% for Alsina's scheme) and concordance varied from 65% of API 20NE to 84% of API 20E. For the molecular identifications, polymerase chain reaction (PCR) for the detection of toxR gene, tl gene and pR72H fragment were tested on 30 strains by two laboratories. The PCR for toxR showed the highest inclusivity (96%), exclusivity (100%) and concordance (97%). CONCLUSIONS: Among the biochemical identification methods tested, the Alsina's scheme gave more reliable results; however, in order to avoid false-positive results, all the biochemical identifications should be confirmed by means of molecular methods. SIGNIFICANCE AND IMPACT OF THE STUDY: Availability of an efficient identification method of Vibrio parahaemolyticus to use in official control of fisheries products.     

Kinetics and mechanism of the cutinase-catalyzed transesterification of oils in AOT reversed micellar system

The kinetics of the enzymatic transesterification between a mixture of triglycerides (oils) and methanol for biodiesel production in a bis(2-ethylhexyl) sodium sulfosuccinate (AOT)/isooctane reversed micellar system, using recombinant cutinase from Fusarium solani pisi as a catalyst, was investigated. In order to describe the results that were obtained, a mechanistic scheme was proposed, based on the literature and on the experimental data. This scheme includes the following reaction steps: the formation of the active enzyme–substrate complex, the addition of an alcohol molecule to the complex followed by the separation of a molecule of the fatty acid alkyl ester and a glycerol moiety, and release of the active enzyme. Enzyme inhibition and deactivation effects due to methanol and glycerol were incorporated in the model. This kinetic model was fitted to the concentration profiles of the fatty acid methyl esters (the components of biodiesel), tri-, di- and monoglycerides, obtained for a 24 h transesterification reaction performed in a stirred batch reactor under different reaction conditions of enzyme and initial substrates concentration.     

The kinetic mechanism of ubiquinol: cytochrome c reductase at steady state.

The steady-state kinetics of ubiquinol: cytochrome c reductase (cytochrome bc1 complex) is analyzed in this work. The graphical pattern of the titrations is clearly indicative of a ping-pong mechanism, but the two products ubiquinone and reduced cytochrome c behave competitively with their substrate and noncompetitively with the other substrate. Hence, the mechanism of the reductase is of a ping-pong two-site type. A minimal reaction scheme for the enzymatic mechanism is proposed and approximate values of its rate constants are deduced on the assumption that each substrate is in rapid equilibrium at its catalytic site. This has been substantiated by presteady-state measurements of the reduction and oxidation of cytochrome b by a short-chain homolog of ubiquinol. Values of the rate constants of the reaction scheme have been deduced from the steady-state titrations for a series of 2,3-dimethoxy-5-methyl quinols having different hydrophobic substituents in position 6 of the ring. The results provide a quantitative estimation of the specificity of the quinol catalytic site in the transmembrane portion of the bc1 complex. In particular, a reasonable correlation is found between the rate of the second-order reaction of quinols with the enzyme and their solubility in lipids.     

The kinetics of oxidation of ferroperoxidase by molecular oxygen. A model of a terminal oxidase

1. The decay of oxyferroperoxidase to ferriperoxidase was studied by rapidly mixing solutions of ferroperoxidase with various amounts of oxygen and following the time-course of appearance of oxyferroperoxidase and its subsequent decay to ferriperoxidase by reaction with ferroperoxidase. 2. The scheme can be accommodated by and [Formula: see text] and occurs without detectable intermediates being observed in the millisecond time-range. 3. Analogue-computer simulation of the reaction is in agreement with the initial rate-limiting reaction being an intermolecular, not intramolecular, electron-donating process, and analysis of the data leads to quantitative values for the rate constants of the overall process. 4. The reaction of oxyferroperoxidase with ferroperoxidase is a model of a terminal oxidase, and the results are discussed in terms of the possible importance of this reaction in peroxidase function, and also in the light it throws on autoxidation of haem compounds.     

DFT study on gas-phase hydrodeoxygenation of guaiacol by various reaction schemes

Guaiacol is an important phenolic component present in pyrolytic bio-oils; and in this work its hydrodeoxygenation (HDO) by various reaction schemes has been considered within the framework of density functional theory. In this computational study, primarily three reaction schemes for the HDO of guaiacol are considered. In the first reaction scheme (RS 1), guaiacol undergoes hydrogenolysis at O–CH₃ bond site of methoxy group to produce catechol and methane followed by HDO of catechol forming phenol and water, followed by HDO of phenol producing benzene and water and finally benzene leading to cyclohexane formation. In the second reaction scheme (RS 2), guaiacol undergoes hydrogenolysis at C_aromatic–O bond of methoxy group producing phenol and methanol followed by hydrotreatment of phenol to form cyclohexane along with same intermediates as in the first reaction scheme. In the third reaction scheme (RS 3), HDO of guaiacol compound at C_aromatic–OH sigma bond produces anisole and water; and then anisole follows two secondary pathways to produce cyclohexane. In this computational study, the transition state optimisations, vibrational frequency and IRC calculations are carried out by B3LYP functional with 6-311+g(d,p) basis set using Gaussian 09 and Gauss View 5 software package.     

Photocatalytic Water Splitting for Solar Hydrogen Production Using the Carbonate Effect and the Z‐Scheme Reaction

The development of innovative technologies for solar energy conversion and storage is important for solving the global warming problem and for establishing a sustainable society. The photocatalytic water‐splitting reaction using semiconductor powders has been intensively studied as a promising technology for direct and simple solar energy conversion. However, the evolution of H₂ and O₂ gases in a stoichiometric ratio (H₂/O₂ = 2) is very difficult owing to various issues, such as an unfavorable backward reaction and mismatched band potentials. Two important findings have widened the variety of photocatalysts available for stoichiometric water‐splitting, viz. the carbonate anion effect and the Z‐scheme photocatalytic reaction using a redox mediator. The bicarbonate anion has been found to act as a redox catalyst via preferential peroxide formation and subsequent decomposition to O₂. As the Z‐scheme reaction using a redox mediator mitigates band potential mismatches, it is widely applicable for various visible‐light‐active photocatalysts. This review describes the development of photocatalytic water‐splitting for solar hydrogen production using the carbonate anion effect and the Z‐scheme reaction. Moreover, recent developments in photocatalysis–electrolysis hybrid systems, an advanced Z‐scheme reaction concept, are also reviewed for practical and economical hydrogen production.     

The carboxybiotin complex of pyruvate carboxylase. A kinetic analysis of the effects of Mg2+ ions on its stability and on its reaction with pyruvate.

The enzyme-[14C] carboxybiotin complex of sheep liver pyruvate carboxylase was isolated and the reaction between this and pyruvate was studied by using the quenched-flow rapid-reaction technique. At 0.5 degrees C the reaction was 80% complete within 180 ms. The reaction was monophasic and obeyed pseudo-first-order kinetics. Increasing concentrations of Mg2+ caused a decrease in the magnitude of the observed pseudo-first-order rate constant. Throughout the carboxylation of pyruvate, the rate-limiting step of the reaction occurred after the dissociation of carboxybiotin from the first sub-site, whereas in the slow phase of the reaction with 2-oxobutyrate this dissociation is the rate-limiting step. It is possible, from the reaction scheme proposed, that the inhibition of overall enzymic activity by high concentrations of Mg2+ could be caused by the transfer of the carboxy group from biotin to pyruvate becoming rate-limiting. The efficacy of a substrate as a signal for the movement of carboxybiotin from the first sub-site is reflected by the amount that the effective affinity of the enzyme- carboxybiotin complex for Mg2+ is lowered. In the presence of the substrates tested, the affinities of the carboxybiotin complex can be arranged in order of increasing magnitude, i.e.: (formula; see text). The kinetics of the decay of the enzyme-[14C] carboxybiotin complex at 0 degree C in the absence of substrates are similar to the reaction with pyruvate except that the carboxybiotin is also unstable in the first sub-site, to some degree. This similarity allows for the proposal of a general scheme for the decarboxylation of the enzyme- carboxybiotin complex in the presence or in the absence of substrates.     

ENZO: a web tool for derivation and evaluation of kinetic models of enzyme catalyzed reactions

We describe a web tool ENZO (Enzyme Kinetics), a graphical interface for building kinetic models of enzyme catalyzed reactions. ENZO automatically generates the corresponding differential equations from a stipulated enzyme reaction scheme. These differential equations are processed by a numerical solver and a regression algorithm which fits the coefficients of differential equations to experimentally observed time course curves. ENZO allows rapid evaluation of rival reaction schemes and can be used for routine tests in enzyme kinetics. It is freely available as a web tool, at http://enzo.cmm.ki.si.