Predicting kinetic constants of protein-protein interactions based on structural properties

Elucidating kinetic processes of protein–protein interactions (PPI) helps to understand how basic building blocks affect overall behavior of living systems. In this study, we used structure‐based properties to build predictive models for kinetic constants of PPI. A highly diverse PPI dataset, protein–protein kinetic interaction data and structures (PPKIDS), was built. PPKIDS contains 62 PPI with complex structures and kinetic constants measured experimentally. The influence of structural properties on kinetics of PPI was studied using 35 structure‐based features, describing different aspects of complex structures. Linear models for the prediction of kinetic constants were built by fitting with selected subsets of structure‐based features. The models gave correlation coefficients of 0.801, 0.732, and 0.770 for k_off, k_on, and K_d, respectively, in leave‐one‐out cross validations. The predictive models reported here use only protein complex structures as input and can be generally applied in PPI studies as well as systems biology modeling. Our study confirmed that different properties play different roles in the kinetic process of PPI. For example, k_on was affected by overall structural features of complexes, such as the composition of secondary structures, the change of translational and rotational entropy, and the electrostatic interaction; while k_off was determined by interfacial properties, such as number of contacted atom pairs per 100 Ų. This information provides useful hints for PPI design. Proteins 2010;79:720–734. © 2010 Wiley‐Liss, Inc.     

Kinetic constants for the inhibition of camel retinal acetylcholinesterase by the carbamate insecticide lannate

We have designed this study to determine various kinetic parameters of camel retinal membrane‐bound acetylcholinesterase (AChE; EC 3.1.1.7) inhibition by carbamate insecticide lannate [methyl N‐{{(methylamino)carbonyl}oxy} ethanimidothioate]. All these kinetic constants were derived by simple graphical methods. The value of kinetic parameters was estimated as follows: 0.061 (μM)⁻¹, 1.14 (μM)⁻¹, 0.216 μM, 0.016 min⁻¹, 0.0741 (μM min)⁻¹, 0.746 μM, and 4.42 μM for velocity constant (K_v), new inhibition constant (K_nic), dissociation constant (K_d), carbamylation rate constant (k_2c), overall carbamylation rate constant (k′2 ), 50% inhibition constant (K_I50), and 99% inhibition constant (K_I99), respectively. These unique methods may be used to estimate such kinetic parameters for time‐dependent inhibition of enzymes by variety of chemicals, insecticides, herbicides, and drugs. © 1998 John Wiley & Sons, Inc. J Biochem Toxicol 13: 41–46, 1999     

13C NMR study of the stereospecificity of the thiohemiacetals formed on inhibition of papain by specific enantiomeric aldehydes

The inhibition of papain by N-acetyl-D- and N-acetyl-L-phenylalanyl[1-13C]glycinal was investigated by 13C nuclear magnetic resonance (NMR) spectroscopy. Both the L- and D-aldehyde enantiomers formed thiohemiacetals with papain. The 13C-enriched carbon of the thiohemiacetals formed with the L- and D-aldehydes has chemical shifts at 74.7 and 75.1 ppm, respectively. The difference in chemical shift for the two inhibitor complexes is attributed to each forming a different diastereomeric papain thiohemiacetal. Each enantiomeric inhibitor formed two diastereomeric thiohemiacetals with chiral thiols but produced a single diastereoisomer with papain. It is concluded that with papain thiohemiacetal formation is stereospecific. The D inhibitor is bound only 5-fold less tightly than the L inhibitor, which suggests that in both these inhibitor complexes the phenyl ring of the inhibitor phenylalanine is bound at the S2 hydrophobic pocket of papain. This is supported by computer modeling studies that show that both the N-acetyl-D- and N-acetyl-L-phenylalanine moieties can be separately fitted into the S2 subsite with the phenyl ring of phenylalanine in the S2 hydrophobic pocket. It is concluded that thiohemiacetal formation at S1 (S1 and S1' are the active center amino acid binding sites) is stereospecific with both D and L inhibitors. Computer modeling studies support this showing that, due to steric hindrance between the thiohemiacetal hydroxyl group and the backbone amide nitrogen of serine-24, only one of the two possible thiohemiacetal enantiomers can be formed at the S1 subsite. The thiohemiacetals formed from both the D- and L-aldehyde inhibitors therefore have only one permitted conformation at S1.(ABSTRACT TRUNCATED AT 250 WORDS)     

Determination of the viscometric constants for chitosan

The viscometric constants a and K_m in the Mark-Houwink equation have been determined for chitosan in 0.1 m acetic acid 0.2 m sodium chloride solution, using the approach of Sharples and Major. The number-average molecular weights were determined by absorbance measurements on solutions of the phenylosazone derivatives. The values obtained a = 0.93, K_m = 1.81 × 10^?3 cm³ g¹ differ considerably from those reported previously by Lee but are in agreement with values found for other ionic polysaccharides having related β-(1 → 4)-linked structures.     

The formation constants of dimethylthallium(III)-glutathione complexes in aqueous solution

The complexes formed in the dimethylthallium(III) (Me₂Tl⁺), glutathionate (EGC³⁻) and hydrogen ion system in aqueous solution at 37 °C and I = 150 mmol dm⁻³ (NaCl) have been characterised by means of glass-electrode potentiometry. Glutathione protonation constants were found to be 9.123 ± 0.007, 17.42 ± 0.01, 20.78 ± 0.02, and 22.93 ± 0.02. Formation constants for the complexes [(Me₂Tl)EGCH]⁻ and [(·Me₂Tl) EGC]²⁻ were found to be 11.19 ± 0.03 and 2.39 ± 0.02, respectively. Particular attention has been paid to the evaluation of the effect of possible systematic errors on the constant values determined. Reliable standard deviation estimations have been made by applying a Monte Carlo calculation technique.     

Formation constants for interaction of citrate with calcium and magnesium ions

Formation constants for the interaction of citrate ion with calcium and magnesium ions in solution at 37°C and a constant ionic strength of 0.15 were determined by potentiometric titration. Values for the formation of CaL^? and CaHL⁰ complexes were 1.88 × 10³ and 67, respectively. Corresponding constants for MgL^? and MgHL⁰ were 2.19 × 10³ and 42, respectively. The existence of other complexes was not confirmed. Protonation constants were also determined under the same conditions.     

Conditional stability constants and binding capacities for copper (II) by ultrafilterable material isolated from six surface waters of Wyoming,USA

Ultrafilterable material < 0.15 µm was collected from six Wyoming surface waters, for which the chemical limnology had also been determined. The material was separated into four nominal size-fractions and the binding capacity of each for copper was determined by a hyperbolic, site-saturation model. The conditional, overall, thermodynamic stability constants (K) for binding of copper were determined by two discrete models: The one- and two-component Scatchard functions, and two continuous multiligand models; The one- and three-component Gaussian Scatchard functions. The accuracy of the stability constants to predict the speciation of Cu(II) in the titration of the isolated fractions and of whole waters was evaluated by comparing the predictions of the thermodynamic, geochemical simulation model, GEOCHEM to those measured by selective ion electrode. The Cu-binding capacity of material retained by ultrafilters was positively correlated with the hardness and alkalinity of the surface waters, from which they were isolated as well as the percent ash content of the ultrafilter-retained material. The magnitude of the conditional stability constant (K _infi ^sup ) decreased as the ratio of the total Cu concentration to total concentration of Cu-binding sites increased. The cumulative frequency distribution of K _infi ^sup was log-normally distributed. All four of the models used to estimate the conditional stability constants gave reasonable prediction of the speciation of Cu for both fractionated and whole waters but, depending on the situation, the one- or two-component Scatchard estimate generally gave the best predictions of the proportion of copper, which would be expected to be bound.     

Superoxide dismutase: a comparison of rate constants

O₂^?was introduced, at a constant rate, into buffered aqueous solutions, either by mechanical infusion of KO₂, dissolved in tetrahydrofuran, or by the in situ action of xanthine oxidase on xanthine plus oxygen. This O₂^? was allowed to react with ferricytochrome c or with tetranitromethane and the formation of the reaction products, ferrocytochrome c or nitroform, respectively, was monitored spectrophotometrically. That concentration of Superoxide dismutase, which competed equally with given levels of cytochrome c or tetranitromethane and which thus caused 50% inhibition of the rates of accumulation of ferrocytochrome c or of nitroform, was determined. The rate constant for the enzymatic dismutation of O₂^? by the copper and zinc containing enzyme from bovine erythrocytes was then calculated from the known rate constants for the reaction of O₂^? with ferricytochrome c and with tetranitromethane and was found to be 2 × 10⁹m^?1 sec^?1 at pH 7.8 and 8.5. This rate constant was obtained at steady-state concentrations of O₂^? in the 10^?8m → 10^?13m range and is in full agreement with the results of pulse radiolytic investigations which were performed at O₂^? concentrations in the 10^?5m range. The second order rate constant for the enzymatic dismutation of O₂^? is thus independent of the concentration of O₂^? in the range 10^?5 → 10^?13m.Several distinct types of Superoxide dismutase have been described. These include the mangano-enzymes from Escherichia coli and from chicken liver mitochondria and the iron-enzyme from E. coli. The rate constants for the dismutations catalyzed by these enzymes have also been investigated as a function of pH.     

Manganese Peroxidase-Dependent Oxidation of Glyoxylic and Oxalic Acids Synthesized by Ceriporiopsis subvermispora Produces Extracellular Hydrogen Peroxide

The ligninolytic system of the basidiomycete Ceriporiopsis subvermispora is composed of manganese peroxidase (MnP) and laccase. In this work, the source of extracellular hydrogen peroxide required for MnP activity was investigated. Our attention was focused on the possibility that hydrogen peroxide might be generated by MnP itself through the oxidation of organic acids secreted by the fungus. Both oxalate and glyoxylate were found in the extracellular fluid of C. subvermispora cultures grown in chemically defined media, where MnP is also secreted. The in vivo oxidation of oxalate was measured; ¹⁴CO₂ evolution was monitored after addition of exogenous [¹⁴C]oxalate to cultures at constant specific activity. In standard cultures, evolution of CO₂ from oxalate was maximal at day 6, although the MnP titers were highest at day 12, the oxalate concentration was maximal (2.5 mM) at day 10, and the glyoxylate concentration was maximal (0.24 mM) at day 5. However, in cultures containing low nitrogen levels, in which the pH is more stable, a better correlation between MnP titers and mineralization of oxalate was observed. Both MnP activity and oxidation of [¹⁴C]oxalate were negligible in cultures lacking Mn(II). In vitro assays confirmed that Mn(II)-dependent oxidation of [¹⁴C]oxalate by MnP occurs and that this reaction is stimulated by glyoxylate at the concentrations found in cultures. In addition, both organic acids supported phenol red oxidation by MnP without added hydrogen peroxide, and glyoxylate was more reactive than oxalate in this reaction. Based on these results, a model is proposed for the extracellular production of hydrogen peroxide by C. subvermispora.     

Malic enzyme of Chromatium vinosum

Malic enzyme of the phototrophic bacterium Chromatium vinosum strain D that lacks malate dehydrogenase was partially purified yielding a specific activity of 55 units/mg protein. The constitutive enzyme with a molecular weight of 110,000 and a pH optimum of 8.0 was absolutely dependent on the presence of a monovalent cation (NH ₄ ⁺ , K⁺, Cs⁺, or Rb⁺) as well as a divalent cation (Mn²⁺, or Mg²⁺). The enzyme was inhibited by oxaloacetate, glyoxylate, and NADPH. The K _0.5 value for L-malate and the inhibition constants for oxaloacetate and glyoxylate are dependent on the concentration of the monovalent cation, whereas the K _m value for NADP (18 M) and the K ₁ value for NADPH (42 M) are independent. Throughout all kinetic measurements hyperbolic saturation curves and linear double reciprocal plots were obtained.Abbreviations OAA oxaloacetate - OD optical density     

Activation parameters for directly determined first order rate constants for outer sphere electron transfer reactions,and crystal structure of a pertinent pentaammine of CoIII

The outer sphere reductions of Co(NH₃)₅B³⁺ by Fe(CN)₅A³⁻ have been studied. The observed pseudo first order rate constants (Co complex in excess) obey the dependence k_obs=K_osk_et[Co]/(1 +K_os[Co]), as expected for outer sphere electron transfer reactions. Values of the fundamental electron transfer rate constants k_et have been determined, along with the equilibrium constant K_os for a range of reactions in which A and B are pyridyl ligands of different sizes. The first order electron transfer rate constants vary in a manner that is consistcnt with adiabatic electron transfer. The outer sphere ion pairing equilibrium constants K_os have been calculated: K_os=8.6 ± 0.1 × 10² M⁻¹ when A and B=pyridine; K_os=1.07 ± 0.09 × 10³ M⁻¹ where A=pyridine, B=1-phenyl-3-(4-pyridyl)propane; K_os=1.86 ± 0.11 × 10³ M⁻¹ when A=4,4′-bipyridine, B=pyridine; K_os=1.27 ± 0.08 × 10³ M⁻¹ when A=4,4′-bipyridine, B=4-phenylpyridine. Distances of closest approach between the metal centers in the reactive ion pairs are compared, and it is concluded that there is a common mechanism, in which the ammonia side of the cobalt complex approaches the cyano side of the iron complex in each reactive ion pair.The distance of closest approach between the two metal centers (a) was calculated from the experimental values for the ion pairing equilibrium constant K_os at 25 °C: 5.2 Å when A=4,4′-bipyridine, B=pyridine; 5.4 Å when A=4,4′-bipyridine, B=4-phenylpyridine; 5.5 Å when A=pyridine, B=1-phenyl-3-(4-pyridyl)propane; 5.7 Å when A=B=pyridine. These relatively short metal-metal distances, when compared to the X-ray structure of the compound [Co(NH₃)₅(4-phenylpyridine)]₂[S₂O₆]₃· 4H₂O, do not support an ion pair orientation in which the two substituted pyridine ligands A and B are oriented toward each other. [P2₁/c,a=7.399(3), b=22.355(10), c=13.776(4) Å, β=92.02(3)°, R=0.070.] The crystallographic results show that if the two pseudo-octahedral coordination spheres are oriented in the reactive ion pair so that an ammonia face of the cobalt complex is at hydrogen bonding distance from a cyano face on the iron complex, the metal-metal distance is 5.3 Å, a distance which is in agreement with the kinetic results.     

Equilibrium constants under physiological conditions for the reactions of the nonphosphorylated pathway of L-serine biosynthesis

The observed equilibrium constants (K_obs) for the reactions of d-2-phosphoglycerate phosphatase, d-2-Phosphoglycerate^3? + H₂O → d-glycerate^? + HPO₄^2?; d-glycerate dehydrogenase (EC 1.1.1.29), d-Glycerate^? + NAD⁺ → NADH + hydroxypyruvate^? + H⁺; and l-serine:pyruvate aminotransferase (EC 2.6.1.51), Hydroxypyruvate^? + l-H · alanine^± → pyruvate^? + l-H · serine^±; have been determined, directly and indirectly, at 38 °C and under conditions of physiological ionic strength (0.25 m) and physiological ranges of pH and magnesium concentrations. From these observed constants and the acid dissociation and metal-binding constants of the substrates, an ionic equilibrium constant (K) also has been calculated for each reaction. The value of K for the d-2-phosphoglycerate phosphatase reaction is 4.00 × 10³m [ΔG⁰ = ?21.4 kJ/mol (?5.12 kcal/mol)]([H₂0] = 1). Values of K_obs for this reaction at 38 °C, [K⁺] = 0.2 m, I = 0.25 M, and pH 7.0 include 3.39 × 10³m (free [Mg²⁺] = 0), 3.23 × 10³m (free [Mg²⁺] = 10^?3m), and 2.32 × 10³m (free [Mg²⁺] = 10^?2m). The value of K for the d-glycerate dehydrogenase reaction has been determined to be 4.36 ± 0.13 × 10^?13m (38 °C, I = 0.25 M) [ΔG⁰ = 73.6 kJ/mol (17.6 kcal/mol)]. This constant is relatively insensitive to free magnesium concentrations but is affected by changes in temperature [ΔH⁰ = 46.9 kJ/mol (11.2 kcal/mol)]. The value of K for the serine:pyruvate aminotransferase reaction is 5.41 ± 0.11 [ΔG⁰ = ?4.37 kJ/mol (?1.04 kcal/mol)] at 38 °C (I = 0.25 M) and shows a small temperature effect [ΔH⁰ = 16.3 kJ/ mol (3.9 kcal/mol)]. The constant showed no significant effect of ionic strength (0.06–1.0 m) and a response to the hydrogen ion concentration only above pH 8.5. The value of K_obs is 5.50 ± 0.11 at pH 7.0 (38 °C, [K⁺] = 0.2 m, [Mg²⁺] = 0, I = 0.25 M). The results have also allowed the value of K for the d-glycerate kinase reaction (EC 2.7.1.31), d-Glycerate^? + ATP^4? → d-2-phosphoglycerate^3? + ADP^3? + H⁺, to be calculated to be 32.5 m (38 °C, I = 0.25 M). Values for K_obs for this reaction under these conditions and at pH 7.0 include 236 (free [Mg²⁺] = 0) and 50.8 (free [Mg²⁺] = 10^?3m).     

Kinetic characteristics and modelling of growth and substrate removal by <Emphasis Type="Italic">Alcaligenes faecalis</Emphasis> strain NR

Alcaligenes faecalis strain NR has the capability of simultaneous ammonium and organic carbon removal under sole aerobic conditions. The growth and substrate removal characteristics of A. faecalis strain NR were studied and appropriate kinetic models were developed. The maximum substrate removal rate of NH₄ ⁺-N and TOC were determined as 2.27 mg NH₄ ⁺-N/L/h and 30.00 mg TOC/L/h, respectively with initial NH₄ ⁺-N = 80 mg/L and TOC = 800 mg/L. Single-substrate models and double-substrate models based on Monod, Contois, Moser and Teissier were employed to describe the bioprocess kinetic coefficients. As a result, two double-substrate models, Teissier-Contois and Contois-Contois, were considered to be appropriate to model growth kinetics with both NH₄ ⁺-N and TOC as limiting substrates. The kinetic constants of maximum growth rate (μ _max) and half-saturation constant (K _S and B _S) were obtained by solving multiple equations with regression. This work can be used to further understand and predict the performance of heterotrophic nitrifiers, and thus provides specific guidance of these functional strains in practical wastewater treatment process.     

Sensitive and Accurate Methodology for Measuring the Kinetics of Concentration-Dependent Hydrocarbon Metabolism Rates in Seawater by Microbial Communities

A method having sufficient sensitivity to resolve the kinetic constants for dissolved nonpolar substrate metabolism, together with the related rate constants in natural waters, is presented. The method is based on the rate of ¹⁴CO₂ recovery from radioactive dissolved substrate. Sensitivity is enhanced by using large seawater volumes, high-specific-activity isotopes, and by reducing background radioactivity. Before use, commercial isotopes are purified by mild alkaline hydrolysis followed by sublimation from base to remove ¹⁴CO₂ as well as interfering polar ¹⁴C-substrates. During sample analysis, chilled Tenax resin is used to remove volatile ¹⁴C-substrate from the nitrogen stream containing ¹⁴CO₂ recovered from substrate oxidation. Chromatographic evidence of purity, shown to be insufficient, is augmented by kinetic data from toluene utilization by mixed cultures and by rates in induced versus noninduced pure cultures. Accuracy is enhanced by using short (<10 h) incubation times and small hydrocarbon concentrations so that the metabolism rates in unamended natural water systems can be evaluated. Toluene metabolism rates in seawater as low as 1 pg/liter per h and at concentrations as low as 20 ng/liter have been determined.     

Yield and kinetic constants estimation in the production of hydroxy fatty acids from oleic acid in a bioreactor by Pseudomonas aeruginosa 42A2

We modelled the production of hydroxy fatty acids from oleic acid by Pseudomonas aeruginosa 42A2 in a bioreactor with a non-dispersive aeration system. First, we designed an adapted wetted-wall gas-absorption column, offering a k _La value of 39.9 h^?1, to enhance oxygen absorption in the culture media and prevent foam formation. Then, we analysed different kinetic models to simulate the yield coefficients and the kinetic constants in this bacterial transformation. Monod model fitting (μ _max1?=?0.51 h^?1, K _S1?=?1.60 C-mol l^?1, μ _max2?=?0.12 h^?1, K _S2?=?0.035 C-mol l^?1, and k ₂?=?0.033 h^?1) showed a good accuracy with the experimental data sets and was chosen for its simplicity. Lastly, mass balances were carried out to establish the stoichiometry of this biotransformation with the following yield coefficients, Υ _X/OA, Υ _{X/(10S)-HPOME} and Υ _{(10S)-HPOME/(7S10S)-HPOME} of 0.172, 0.347 and 2.388 C-mol C-mol^?1, respectively.     

Structural and kinetic evidence that catalytic reaction of human UDP-glucose 6-dehydrogenase involves covalent thiohemiacetal and thioester enzyme intermediates

Biosynthesis of UDP-glucuronic acid by UDP-glucose 6-dehydrogenase (UGDH) occurs through the four-electron oxidation of the UDP-glucose C6 primary alcohol in two NAD⁺-dependent steps. The catalytic reaction of UGDH is thought to involve a Cys nucleophile that promotes formation of a thiohemiacetal enzyme intermediate in the course of the first oxidation step. The thiohemiacetal undergoes further oxidation into a thioester, and hydrolysis of the thioester completes the catalytic cycle. Herein we present crystallographic and kinetic evidence for the human form of UGDH that clarifies participation of covalent catalysis in the enzymatic mechanism. Substitution of the putative catalytic base for water attack on the thioester (Glu¹⁶¹) by an incompetent analog (Gln¹⁶¹) gave a UGDH variant (E161Q) in which the hydrolysis step had become completely rate-limiting so that a thioester enzyme intermediate accumulated at steady state. By crystallizing E161Q in the presence of 5 mm UDP-glucose and 2 mm NAD⁺, we succeeded in trapping a thiohemiacetal enzyme intermediate and determined its structure at 2.3 Å resolution. Cys²⁷⁶ was covalently modified in the structure, establishing its role as catalytic nucleophile of the reaction. The thiohemiacetal reactive C6 was in a position suitable to become further oxidized by hydride transfer to NAD⁺. The proposed catalytic mechanism of human UGDH involves Lys²²⁰ as general base for UDP-glucose alcohol oxidation and for oxyanion stabilization during formation and breakdown of the thiohemiacetal and thioester enzyme intermediates. Water coordinated to Asp²⁸⁰ deprotonates Cys²⁷⁶ to function as an aldehyde trap and also provides oxyanion stabilization. Glu¹⁶¹ is the Brønsted base catalytically promoting the thioester hydrolysis.     

Degradation of phenol and phenolic compounds by a defined denitrifying bacterial culture

Phenol, a major pollutant in several industrial waste waters is often used as a model compound for studies on biodegradation. This study investigated the anoxic degradation of phenol and other phenolic compounds by a defined mixed culture of Alcaligenes faecalis and Enterobacter species. The culture was capable of degrading high concentrations of phenol (up to 600 mg/l) under anoxic conditions in a simple minimal mineral medium at an initial cell mass of 8 mg/l. However, the lag phase in growth and phenol removal increased with increase in phenol concentration. Dissolved CO₂ was an absolute requirement for phenol degradation. In addition to nitrate, nitrite and oxygen could be used as electron acceptors. The kinetic constants, maximum specific growth rate _max; inhibition constant, K _i and saturation constant, K _s were determined to be 0.206 h^–1, 113 and 15 mg phenol/l respectively. p-Hydroxybenzoic acid was identified as an intermediate during phenol degradation. Apart from phenol, the culture utilized few other monocyclic aromatic compounds as growth substrates. The defined culture has remained stable with consistent phenol-degrading ability for more than 3 years and thus shows promise for its application in anoxic treatment of industrial waste waters containing phenolic compounds.     

Nutrient Uptake by Microorganisms according to Kinetic Parameters from Theory as Related to Cytoarchitecture

The abilities of organisms to sequester substrate are described by the two kinetic constants specific affinity, a°, and maximal velocity V_max. Specific affinity is derived from the frequency of substrate-molecule collisions with permease sites on the cell surface at subsaturating concentrations of substrates. V_max is derived from the number of permeases and the effective residence time, τ, of the transported molecule on the permease. The results may be analyzed with affinity plots (v/S versus v, where v is the rate of substrate uptake), which extrapolate to the specific affinity and are usually concave up. A third derived parameter, the affinity constant K_A, is similar to K_M but is compared to the specific affinity rather than V_max and is defined as the concentration of substrate necessary to reduce the specific affinity by half. It can be determined in the absence of a maximal velocity measurement and is equal to the Michaelis constant for a system with hyperbolic kinetics. Both are taken as a measure of τ, with departure of K_M from K_A being affected by permease/enzyme ratios. Compilation of kinetic data indicates a 10⁸-fold range in specific affinities and a smaller (10³-fold) range in V_max values. Data suggest that both specific affinities and maximal velocities can be underestimated by protocols which interrupt nutrient flow prior to kinetic analysis. A previously reported inverse relationship between specific affinity and saturation constants was confirmed. Comparisons of affinities with ambient concentrations of substrates indicated that only the largest a°_S values are compatible with growth in natural systems.     

31P-NMR saturation transfer study of the in vivo kinetics of arginine kinase in Carcinus crab leg muscle

The kinetics of the reaction catalyzed by arginine kinase have been determined at 9.5 and 23°C for in vivo leg muscle of Carcinus maenas (the common shore crab) using the noninvasive technique of ³¹P-NMR spectroscopy. Concentrations of mobile phosphorus metabolites were the same at both temperatures: 78.7 mM for arginine phosphate, 9.0 mM for adenosine triphosphate (ATP), and 2.6 mM for inorganic phosphate (P_i), as estimated from NMR resonance intensities and literature values for ATP concentration as assayed by traditional biochemical methods. Apparent unidirectional rate constants for formation of ATP from arginine phosphate and ADP were 0.09 s^?1 at 9.5°C and 0.27 s^?1 at 23°C. Pseudo-first-order rate constants for arginine phosphate generation from Arg and ATP were 0.38 and 1.10 s^?1 at 9.5 and 23°C, respectively. In vivo Q₁₀ for the arginine kinase reaction between 9.5 and 23°C was thus 2.2 for both directions. When the kinetic data are analyzed using the Arrhenius equation, activation energies of 126 kJ/mol for ATP formation and 105 kJ/mol for arginine phosphate formation are found. The measured chemical fluxes through arginine kinase in the forward reaction (arginine phosphate hydrolysis) were twice those in the reverse reaction, consistent with either compartmentation of substrates or participation of substrates in alternative metabolic pathways.     

Kinetic Modeling and Mechanisms of Acid-Catalyzed Delignification of Sugarcane Bagasse by Aqueous Acetic Acid

Organosolv pretreatment of lignocellulose pertains to a biomass fractionation process to obtain cellulosic pulp, high-purity lignin, and hemicellulosic syrup. In the present work, sugarcane bagasse was delignified by aqueous acetic acid (AcH) under atmospheric pressure with addition of sulfuric acid (SA) as a catalyst. Based on the multilayered structure of plant cell wall and the inhibitive effect of dissolved lignin on delignification rate, a novel pseudo-homogeneous kinetic model was proposed by introducing the concept of “potential degree of delignification (d _D)” into the model. It was found that delignification rate was a first-order reaction with respect to SA concentration, while AcH concentration showed a high reaction order to delignification rate. The activation energy for delignification was determined to be 64.41 kJ/mol. The relationships of kinetic constants and d _D with reaction temperature, AcH, and SA concentrations were determined according to experimental data. Mechanism analysis indicated that cleavage of α-aryl ethers bonds were mainly responsible for the formation of lignin fragments. AcH concentration affected the solubility parameter (δ value) of AcH solution and the ability to form hydrogen bonds with lignin fragments. Therefore, the driving force for solubilizing lignin fragments increased with AcH concentration, and thus AcH concentration had a very significant influence on delignification rate.