Carvalho,Nakédia M. F.; Pires, Bianca M.; Antunes,Octavio A. C.; Roberto B Faria; Osório,Renata E. H. M. B.; Clovis Piovezan; Ademir Neves
2010-01-01
The Michaelis-Menten equation is used in many biochemical and bioinorganic kinetic studies involving homogeneous catalysis. Otherwise, it is known that determination of Michaelis-Menten parameters K M, Vmax, and k cat by the well-known Lineweaver-Burk double reciprocal linear equation does not produce the best values for these parameters. In this paper we present a discussion on different linear equations which can be used to calculate these parameters and we compare their results with the va...
Nakédia M. F. Carvalho
2010-01-01
Full Text Available The Michaelis-Menten equation is used in many biochemical and bioinorganic kinetic studies involving homogeneous catalysis. Otherwise, it is known that determination of Michaelis-Menten parameters K M, Vmax, and k cat by the well-known Lineweaver-Burk double reciprocal linear equation does not produce the best values for these parameters. In this paper we present a discussion on different linear equations which can be used to calculate these parameters and we compare their results with the values obtained by the more reliable nonlinear least-square fit.
A comparison of the parameter estimating procedures for the Michaelis-Menten model.
Tseng, S J; Hsu, J P
1990-08-23
The performance of four parameter estimating procedures for the estimation of the adjustable parameters in the Michaelis-Menten model, the maximum initial rate Vmax, and the Michaelis-Menten constant Km, including Lineweaver & Burk transformation (L-B), Eadie & Hofstee transformation (E-H), Eisenthal & Cornish-Bowden transformation (ECB), and Hsu & Tseng random search (H-T) is compared. The analysis of the simulated data reveals the followings: (i) Vmax can be estimated more precisely than Km. (ii) The sum of square errors, from the smallest to the largest, follows the sequence H-T, E-H, ECB, L-B. (iii) Considering the sum of square errors, relative error, and computing time, the overall performance follows the sequence H-T, L-B, E-H, ECB, from the best to the worst. (iv) The performance of E-H and ECB are on the same level. (v) L-B and E-H are appropriate for pricesly measured data. H-T should be adopted for data whose error level are high. (vi) Increasing the number of data points has a positive effect on the performance of H-T, and a negative effect on the performance of L-B, E-H, and ECB.
Mechanistic interpretation of conventional Michaelis-Menten parameters in a transporter system.
Vivian, Diana; Polli, James E
2014-11-20
The aim was to elucidate how steps in drug translocation by a solute carrier transporter impact Michaelis-Menten parameters Km, Ki, and Vmax. The first objective was to derive a model for carrier-mediated substrate translocation and perform sensitivity analysis with regard to the impact of individual microrate constants on Km, Ki, and Vmax. The second objective was to compare underpinning microrate constants between compounds translocated by the same transporter. Equations for Km, Ki, and Vmax were derived from a six-state model involving unidirectional transporter flipping and reconfiguration. This unidirectional model is applicable to co-transporter type solute carriers, like the apical sodium-dependent bile acid transporter (ASBT) and the proton-coupled peptide cotransporter (PEPT1). Sensitivity analysis identified the microrate constants that impacted Km, Ki, and Vmax. Compound comparison using the six-state model employed regression to identify microrate constant values that can explain observed Km and Vmax values. Results yielded some expected findings, as well as some unanticipated effects of microrate constants on Km, Ki, and Vmax. Km and Ki were found to be equal for inhibitors that are also substrates. Additionally, microrate constant values for certain steps in transporter functioning influenced Km and Vmax to be low or high. Copyright © 2014 Elsevier B.V. All rights reserved.
Widmer, L A; Stelling, J; Doyle, F J
2013-10-28
Using the (slow-scale) linear noise approximation, we give parameter-independent bounds to the substrate and product intrinsic noise variance for the stochastic Michaelis-Menten approximation at steady state.
Optimal designs for Michaelis-Menten kinetic studies.
Matthews, J N S; Allcock, G C
2004-02-15
Many reactions in enzymology are governed by the Michaelis-Menten equation. Characterising these reactions requires the estimation of the parameters K(M) and V(max) which determine the Michaelis-Menten equation and this is done by observing rates of reactions at a set of substrate concentrations. The choice of substrate concentrations is investigated by determining Bayesian D-optimal designs for a model in which residuals have a normal distribution with constant variance. Designs which focus on alternative quantities, such as K(M) or the ratio V(max)/K(M) are also considered. The effect on the optimal designs of alternative error distributions is also considered.
Liao, Fei; Zhu, Xiao-Yun; Wang, Yong-Mei; Zuo, Yu-Ping
2005-01-31
The estimation of enzyme kinetic parameters by nonlinear fitting reaction curve to the integrated Michaelis-Menten rate equation ln(S(0)/S)+(S(0)-S)/K(m)=(V(m)/K(m))xt was investigated and compared to that by fitting to (S(0)-S)/t=V(m)-K(m)x[ln(S(0)/S)/t] (Atkins GL, Nimmo IA. The reliability of Michaelis-Menten constants and maximum velocities estimated by using the integrated Michaelis-Menten equation. Biochem J 1973;135:779-84) with uricase as the model. Uricase reaction curve was simulated with random absorbance error of 0.001 at 0.075 mmol/l uric acid. Experimental reaction curve was monitored by absorbance at 293 nm. For both CV and deviation kinetic parameters and applicable for the characterization of enzyme inhibitors.
Uso de equações lineares na determinação dos parâmetros de Michaelis-Menten
Carvalho,Nakédia M. F.; Pires, Bianca M.; Antunes,Octavio A. C.; Roberto B Faria; Osório,Renata E. H. M. B.; Piovezan, Clovis; Neves,Ademir
2010-01-01
The Michaelis-Menten equation is used in many biochemical and bioinorganic kinetic studies involving homogeneous catalysis. Otherwise, it is known that determination of Michaelis-Menten parameters K M, Vmax, and k cat by the well-known Lineweaver-Burk double reciprocal linear equation does not produce the best values for these parameters. In this paper we present a discussion on different linear equations which can be used to calculate these parameters and we compare their results with the va...
Sakoda, M; Hiromi, K
1976-09-01
The best-fit values of the Michaelis constant (Km) and the maximum velocity (V) in the Michaelis-Menten equation can be obtained by the method of least squares with the Taylor expansion for the sum of squares of the absolute residual, i.e., the difference between the observed velocity and the corresponding velocity by calculation. This method makes it possible to determine the values of Km and V not in a trial-and-error manner but in a deductive and unique manner after some iterative procedures starting from arbitrary approximate values of Km and V. These values can be said to be uniquely determined for a set of data as the finally converged values are no longer dependent upon the initial approximate values of Km and V. It is also very important to obtain initial approximate values of parameters for the application of the method described above. A simple method is proposed to estimate the approximate values of parameters involved in fractional functions. The method of rearrangement after canceling of denominator of a fractional function can be utilized to obtain approximate values, not only for cases of two unknown parameters such as the Michaelis-Menten equation, but also for cases with more than two unknowns.
Single-molecule Michaelis-Menten equations.
Kou, S C; Cherayil, Binny J; Min, Wei; English, Brian P; Xie, X Sunney
2005-10-20
This paper summarizes our present theoretical understanding of single-molecule kinetics associated with the Michaelis-Menten mechanism of enzymatic reactions. Single-molecule enzymatic turnover experiments typically measure the probability density f(t) of the stochastic waiting time t for individual turnovers. While f(t) can be reconciled with ensemble kinetics, it contains more information than the ensemble data; in particular, it provides crucial information on dynamic disorder, the apparent fluctuation of the catalytic rates due to the interconversion among the enzyme's conformers with different catalytic rate constants. In the presence of dynamic disorder, f(t) exhibits a highly stretched multiexponential decay at high substrate concentrations and a monoexponential decay at low substrate concentrations. We derive a single-molecule Michaelis-Menten equation for the reciprocal of the first moment of f(t), 1/, which shows a hyperbolic dependence on the substrate concentration [S], similar to the ensemble enzymatic velocity. We prove that this single-molecule Michaelis-Menten equation holds under many conditions, in particular when the intercoversion rates among different enzyme conformers are slower than the catalytic rate. However, unlike the conventional interpretation, the apparent catalytic rate constant and the apparent Michaelis constant in this single-molecule Michaelis-Menten equation are complicated functions of the catalytic rate constants of individual conformers. We also suggest that the randomness parameter r, defined as )2> / t2, can serve as an indicator for dynamic disorder in the catalytic step of the enzymatic reaction, as it becomes larger than unity at high substrate concentrations in the presence of dynamic disorder.
Optimal design for goodness-of-fit of the Michaelis-Menten enzyme kinetic function
Wong, Weng Kee; Melas, Viatcheslav B.; Dette, Holger
2004-01-01
We construct efficient designs for the Michaelis-Menten enzyme kinetic model capable of checking model assumption. An extended model, called EMAX model is also considered for this purpose. This model is widely used in pharmacokinetics and reduces to the Michaelis- Menten model for a specific choice of the parameter setting. Our strategy is to find efficient designs for estimating the parameters in the EMAX model and at the same time test the validity of the Michaelis-Menten model against the ...
Stochastic mapping of the Michaelis-Menten mechanism.
Dóka, Éva; Lente, Gábor
2012-02-07
The Michaelis-Menten mechanism is an extremely important tool for understanding enzyme-catalyzed transformation of substrates into final products. In this work, a computationally viable, full stochastic description of the Michaelis-Menten kinetic scheme is introduced based on a stochastic equivalent of the steady-state assumption. The full solution derived is free of restrictions on amounts of substance or parameter values and is used to create stochastic maps of the Michaelis-Menten mechanism, which show the regions in the parameter space of the scheme where the use of the stochastic kinetic approach is inevitable. The stochastic aspects of recently published examples of single-enzyme kinetic studies are analyzed using these maps.
Sheiner, L B; Beal, S L
1980-12-01
Individual pharmacokinetic par parameters quantify the pharmacokinetics of an individual, while population pharmacokinetic parameters quantify population mean kinetics, interindividual variability, and residual intraindividual variability plus measurement error. Individual pharmacokinetics are estimated by fitting individual data to a pharmacokinetic model. Population pharmacokinetic parameters are estimated either by fitting all individual's data together as though there was no individual kinetic differences (the naive pooled data approach), or by fitting each individual's data separately, and then combining the individual parameter estimates (the two-stage approach). A third approach, NONMEM, takes a middle course between these, and avoids shortcomings of each of them. A data set consisting of 124 steady-state phenytoin concentration-dosage pairs from 49 patients, obtained in the routine course of their therapy, was analyzed by each method. The resulting population parameter estimates differ considerably (population mean Km, for example, is estimated as 1.57, 5.36, and 4.44 micrograms/ml by the naive pooled data, two-stage, and NONMEN approaches, respectively). Simulations of the data were analyzed to investigate these differences. The simulations indicate that the pooled data approach fails to estimate variabilities and produces imprecise estimates of mean kinetics. The two-stage approach produces good estimates of mean kinetics, but biased and imprecise estimates of interindividual variability. NONMEN produces accurate and precise estimates of all parameters, and also reasonable confidence intervals for them. This performance is exactly what is expected from theoretical considerations and provides empirical support for the use of NONMEM when estimating population pharmacokinetics from routine type patient data.
Design issues for the Michaelis-Menten model.
López-Fidalgo, J; Wong, Weng Kee
2002-03-07
We discuss design issues for the Michaelis-Menten model and use geometrical arguments to find optimal designs for estimating a subset of the model parameters, or a linear combination of the parameters. We propose multiple-objective optimal designs when the parameters have different levels of interest to the researcher. In addition, we compare six commonly used sequence designs in the biological sciences for estimating parameters and, propose optimal choices for the parameters for geometric designs using closed-form efficiency formulas.
Thiopentone elimination in newborn infants: exploring Michaelis-Menten kinetics.
Larsson, P; Anderson, B J; Norman, E; Westrin, P; Fellman, V
2011-04-01
Thiopentone elimination has been described using Michaelis-Menten pharmacokinetics in adults after prolonged infusion or overdose, but there are few reports of elimination in neonates. Time-concentration profiles for neonates (n=37) given single-dose thiopentone were examined using both first-order (constant clearance) and mixed-order (Michaelis-Menten) elimination processes using nonlinear mixed effects models. These profiles included a 33-week post-menstrual age (PMA) neonate given an overdose. A two-compartment mamillary model was used to fit data. Parameter estimates were standardized to a 70 kg person using allometric models. There were 197 observations available for analysis from neonates with a mean post-menstrual age of 35 (SD 4.5) weeks and a mean weight of 2.5 (SD 0.9) kg. They were given a mean thiopentone dose of 3 (SD 0.4) mg/kg as a rapid bolus. Clearance at 26 weeks PMA was 0.015 l/min/70 kg and increased to 0.119 l/min/70 kg by 42 weeks PMA. The maximum rate of elimination (V(max)) at 26 weeks PMA was 0.22 mg/min/70 kg and increased to 4.13 mg/min/70 kg by 42 weeks PMA. These parameter estimates are approximately 40% adult values at term gestation. The Michaelis constant (K(m)) was 28.3 [between subject variability (BSV) 46.4%, 95% confidence interval (CI) 4.49-99.2] mg/l; intercompartment clearance was 0.44 (BSV 97.5%, 95% CI 0.27-0.63) l/min/70 kg; central volume of distribution was 46.4 (BSV 29.2%, 95% CI 41.7-59.8) l/70 kg; peripheral volume of distribution was 95.7 (BSV 70.3%, 95% CI 61.3-128) l/70 kg. Both first-order and mixed-order processes satisfactorily described elimination. First-order elimination adequately described the time-concentration profile in the premature neonate given an overdose. Clearance is immature in the pre-term neonate although there is rapid maturation around 40 weeks PMA, irrespective of post-natal age. © 2011 The Authors. Acta Anaesthesiologica Scandinavica © 2011 The Acta Anaesthesiologica Scandinavica Foundation.
Robust and efficient designs for the Michaelis-Menten model
Dette, Holger; Biedermann, Stefanie
2002-01-01
For the Michaelis-Menten model, we determine designs that maximize the minimum of the D-efficiencies over a certain interval for the nonlinear parameter. The best two point designs can be found explicitly, and a characterization is given when these designs are optimal within the class of all designs. In most cases of practical interest, the determined designs are highly efficient and robust with respect to misspecification of the nonlinear parameter. The results are illustrated and applied in...
Michaelis-Menten kinetics under non-isothermal conditions.
Lervik, Anders; Kjelstrup, Signe; Qian, Hong
2015-01-14
We extend the celebrated Michaelis-Menten kinetics description of an enzymatic reaction taking into consideration the presence of a thermal driving force. A coupling of chemical and thermal driving forces is expected from the principle of non-equilibrium thermodynamics, and specifically we obtain an additional term to the classical Michaelis-Menten kinetic equation, which describes the coupling in terms of a single parameter. A companion equation for the heat flux is also derived, which actually can exist even in the absence of a temperature difference. Being thermodynamic in nature, this result is general and independent of the detailed mechanism of the coupling. Conditions for the experimental verification of the new equation are discussed.
Determination of individual cell Michaelis-Menten constants.
Sunray, Merav; Zurgil, Naomi; Shafran, Yana; Deutsch, Mordechai
2002-01-01
A novel methodology for the measurement and analysis of apparent K(M) (Michaelis-Menten constant) and V(MAX) values of individual cells is suggested. It is based on a mathematical model that considers substrate influx into the cell, its intracellular enzymatic hydrolysis, and the product efflux. The mathematical formulation was approximated linearly in order to analyze intracellular substrate conversion characteristics via Michaelis-Menten theory. Utilizing static cytometry, the time dependence of the fluorescence intensity [FI(t)] emitted from prelocalized and defined FDA stained cells was recorded. This required frequent periodical measurements of the same cells, which are sequentially exposed to various fluorogenic substrate concentrations. Model simulations correlated with experimental results. Differences in distributions of individual K(M) and V(MAX) values of cells incubated with and without PHA were evident. Average K(M) and V(MAX) values of PHA-stimulated cells increased by 99% and 540%, respectively. This study may provide a tool for assessing intracellular enzymatic activity in individual intact cells under defined physiologic conditions. This may open new vistas in various areas, giving answers to critical questions arising in the field of cell and developmental biology, immunology, oncology, and pharmacology. Copyright 2001 Wiley-Liss, Inc.
Time-dependent corrections to effective rate and event statistics in Michaelis-Menten kinetics
Sinitsyn, N. A.; Nemenman, I.
2010-01-01
We generalize the concept of the geometric phase in stochastic kinetics to a noncyclic evolution. Its application is demonstrated on kinetics of the Michaelis-Menten reaction. It is shown that the nonperiodic geometric phase is responsible for the correction to the Michaelis-Menten law when parameters, such as a substrate concentration, are changing with time. We apply these ideas to a model of chemical reactions in a bacterial culture of a growing size, where the geometric correction qualita...
Extending the kinetic solution of the classic Michaelis-Menten model of enzyme action
BISPO, Jose Ailton Conceicao; Bonafe, Carlos Francisco Sampaio; SOUZA, Volnei Brito de; SILVA, Joao Batista de Almeida e; CARVALHO, Giovani Brandao Mafra de
2011-01-01
The principal aim of studies of enzyme-mediated reactions has been to provide comparative and quantitative information on enzyme-catalyzed reactions under distinct conditions. The classic Michaelis-Menten model (Biochem Zeit 49:333, 1913) for enzyme kinetic has been widely used to determine important parameters involved in enzyme catalysis, particularly the Michaelis-Menten constant (K (M) ) and the maximum velocity of reaction (V (max) ). Subsequently, a detailed treatment of the mechanisms ...
Michaelis-Menten dynamics in protein subnetworks
Rubin, Katy J
2016-01-01
To understand the behaviour of complex systems it is often necessary to use models that describe the dynamics of subnetworks. It has previously been established using projection methods that such subnetwork dynamics generically involves memory of the past, and that the memory functions can be calculated explicitly for biochemical reaction networks made up of unary and binary reactions. However, many established network models involve also Michaelis-Menten kinetics, to describe e.g. enzymatic reactions. We show that the projection approach to subnetwork dynamics can be extended to such networks, thus significantly broadening its range of applicability. To derive the extension we construct a larger network that represents enzymes and enzyme complexes explicitly, obtain the projected equations, and finally take the limit of fast enzyme reactions that gives back Michaelis-Menten kinetics. The crucial point is that this limit can be taken in closed form. The outcome is a simple procedure that allows one to obtain ...
Michaelis-Menten dynamics in protein subnetworks.
Rubin, Katy J; Sollich, Peter
2016-05-07
To understand the behaviour of complex systems, it is often necessary to use models that describe the dynamics of subnetworks. It has previously been established using projection methods that such subnetwork dynamics generically involves memory of the past and that the memory functions can be calculated explicitly for biochemical reaction networks made up of unary and binary reactions. However, many established network models involve also Michaelis-Menten kinetics, to describe, e.g., enzymatic reactions. We show that the projection approach to subnetwork dynamics can be extended to such networks, thus significantly broadening its range of applicability. To derive the extension, we construct a larger network that represents enzymes and enzyme complexes explicitly, obtain the projected equations, and finally take the limit of fast enzyme reactions that gives back Michaelis-Menten kinetics. The crucial point is that this limit can be taken in closed form. The outcome is a simple procedure that allows one to obtain a description of subnetwork dynamics, including memory functions, starting directly from any given network of unary, binary, and Michaelis-Menten reactions. Numerical tests show that this closed form enzyme elimination gives a much more accurate description of the subnetwork dynamics than the simpler method that represents enzymes explicitly and is also more efficient computationally.
Michaelis-Menten kinetics of stiripentol in normal humans.
Levy, R H; Loiseau, P; Guyot, M; Blehaut, H M; Tor, J; Moreland, T A
1984-08-01
Michaelis-Menten kinetic parameters for stiripentol, and anticonvulsant, were assessed in six normal volunteers. Stiripentol was administered orally three times a day in dosage increments of 600, 1,200, and 1,800 mg/day for consecutive periods of 3, 4, and 7 days, respectively. Stiripentol steady-state levels at the three dosing rates increased more than proportionally with dose. The mean +/- SD oral clearance of stiripentol at 600 mg/day (1,090 +/- 624 L/day) was significantly greater (p less than 0.01) than at 1,200 (506 +/- 219 L/day) or 1,800 (405 +/- 151 L/day) mg/day. Average steady-state concentrations predicted from individually determined Vm and Km parameters were in good agreement with experimentally observed levels, indicating that the kinetics of stiripentol are of the Michaelis-Menten type. The mean Vm, Km, and Vm/Km ratio were 2,299 +/- 490 mg/day, 2.20 +/- 1.28 mg/L, and 1,241 +/- 837 L/day, respectively. Neuropsychological tests carried out before and after 14 days of stiripentol treatment showed a significant decline in verbal learning ability (p = 0.038) and a significant improvement in a test of memory and attention (p less than 0.01).
Time-dependent corrections to effective rate and event statistics in Michaelis-Menten kinetics.
Sinitsyn, N A; Nemenman, I
2010-11-01
The authors generalise the concept of the geometric phase in stochastic kinetics to a non-cyclic evolution. Its application is demonstrated on kinetics of the Michaelis-Menten reaction. It is shown that the non-periodic geometric phase is responsible for the correction to the Michaelis-Menten law when parameters, such as a substrate concentration, are changing with time. The authors apply these ideas to a model of chemical reactions in a bacterial culture of a growing size, where the geometric correction qualitatively changes the outcome of the reaction kinetics.
The Michaelis-Menten-Stueckelberg Theorem
Alexander N. Gorban
2011-05-01
Full Text Available We study chemical reactions with complex mechanisms under two assumptions: (i intermediates are present in small amounts (this is the quasi-steady-state hypothesis or QSS and (ii they are in equilibrium relations with substrates (this is the quasiequilibrium hypothesis or QE. Under these assumptions, we prove the generalized mass action law together with the basic relations between kinetic factors, which are sufficient for the positivity of the entropy production but hold even without microreversibility, when the detailed balance is not applicable. Even though QE and QSS produce useful approximations by themselves, only the combination of these assumptions can render the possibility beyond the “rarefied gas” limit or the “molecular chaos” hypotheses. We do not use any a priori form of the kinetic law for the chemical reactions and describe their equilibria by thermodynamic relations. The transformations of the intermediate compounds can be described by the Markov kinetics because of their low density (low density of elementary events. This combination of assumptions was introduced by Michaelis and Menten in 1913. In 1952, Stueckelberg used the same assumptions for the gas kinetics and produced the remarkable semi-detailed balance relations between collision rates in the Boltzmann equation that are weaker than the detailed balance conditions but are still sufficient for the Boltzmann H-theorem to be valid. Our results are obtained within the Michaelis-Menten-Stueckelbeg conceptual framework.
Amyloid-like fibril elongation follows michaelis-menten kinetics
Milto, Katazyna; Botyriute, Akvile; Smirnovas, Vytautas
2013-01-01
... are. We obtained experimental data on insulin amyloid-like fibril elongation at the conditions where other processes which may impact kinetics of fibril formation are minor and fitted it using Michaelis-Menten equation...
Legitimacy of the stochastic Michaelis-Menten approximation.
Sanft, K R; Gillespie, D T; Petzold, L R
2011-01-01
Michaelis-Menten kinetics are commonly used to represent enzyme-catalysed reactions in biochemical models. The Michaelis-Menten approximation has been thoroughly studied in the context of traditional differential equation models. The presence of small concentrations in biochemical systems, however, encourages the conversion to a discrete stochastic representation. It is shown that the Michaelis-Menten approximation is applicable in discrete stochastic models and that the validity conditions are the same as in the deterministic regime. The authors then compare the Michaelis-Menten approximation to a procedure called the slow-scale stochastic simulation algorithm (ssSSA). The theory underlying the ssSSA implies a formula that seems in some cases to be different from the well-known Michaelis-Menten formula. Here those differences are examined, and some special cases of the stochastic formulas are confirmed using a first-passage time analysis. This exercise serves to place the conventional Michaelis-Menten formula in a broader rigorous theoretical framework.
Houston, J B; Kenworthy, K E
2000-03-01
Strategies for the prediction of in vivo drug clearance from in vitro drug metabolite kinetic data are well established for the rat. In this animal species, metabolism rate-substrate concentration relationships can commonly be described by the classic hyperbola consistent with the Michaelis-Menten model and simple scaling of the parameter intrinsic clearance (CL(int) - the ratio of V(max) to K(m)) is particularly valuable. The in vitro scaling of kinetic data from human tissue is more complex, particularly as many substrates for cytochrome P450 (CYP) 3A4, the dominant human CYP, show nonhyperbolic metabolism rate-substrate concentration curves. This review critically examines these types of data, which require the adoption of an enzyme model with multiple sites showing cooperative binding for the drug substrate, and considers the constraints this kinetic behavior places on the prediction of in vivo pharmacokinetic characteristics, such as metabolic stability and inhibitory drug interaction potential. The cases of autoactivation and autoinhibition are discussed; the former results in an initial lag in the rate-substrate concentration profile to generate a sigmoidal curve whereas the latter is characterized by a convex curve as V(max) is not maintained at high substrate concentrations. When positive cooperativity occurs, we suggest the use of CL(max), the maximal clearance resulting from autoactivation, as a substitute for CL(int). The impact of heteroactivation on this approach is also of importance. In the case of negative cooperativity, care in using the V(max)/K(m) approach to CL(int) determination must be taken. Examples of substrates displaying each type of kinetic behavior are discussed for various recombinant CYP enzymes, and possible artifactual sources of atypical rate-concentration curves are outlined. Finally, the consequences of ignoring atypical Michaelis-Menten kinetic relationships are examined, and the inconsistencies reported for both different
Tang, J. Y
2015-01-01
The Michaelis-Menten kinetics and the reverse Michaelis-Menten kinetics are two popular mathematical formulations used in many land biogeochemical models to describe how microbes and plants would...
Schnell, Santiago
2014-01-01
The Michaelis-Menten equation is generally used to estimate the kinetic parameters, V and K(M), when the steady-state assumption is valid. Following a brief overview of the derivation of the Michaelis-Menten equation for the single-enzyme, single-substrate reaction, a critical review of the criteria for validity of the steady-state assumption is presented. The application of the steady-state assumption makes the implicit assumption that there is an initial transient during which the substrate concentration remains approximately constant, equal to the initial substrate concentration, while the enzyme-substrate complex concentration builds up. This implicit assumption is known as the reactant stationary assumption. This review presents evidence showing that the reactant stationary assumption is distinct from and independent of the steady-state assumption. Contrary to the widely believed notion that the Michaelis-Menten equation can always be applied under the steady-state assumption, the reactant stationary assumption is truly the necessary condition for validity of the Michaelis-Menten equation to estimate kinetic parameters. Therefore, the application of the Michaelis-Menten equation only leads to accurate estimation of kinetic parameters when it is used under experimental conditions meeting the reactant stationary assumption. The criterion for validity of the reactant stationary assumption does not require the restrictive condition of choosing a substrate concentration that is much higher than the enzyme concentration in initial rate experiments. © 2013 FEBS.
Bentz, Joe; Tran, Thuy Thanh; Polli, Joseph W; Ayrton, Andrew; Ellens, Harma
2005-10-01
Typically, the kinetics of membrane transport is analyzed using the steady-state Michaelis-Menten (or Eadie-Hofstee or Hanes) equations. This approach has been successful when the substrate is picked up from the aqueous phase, like a water-soluble enzyme, for which the Michaelis-Menten steady-state analysis was developed. For membrane transporters whose substrate resides in the lipid bilayer of the plasma membrane, like P-glycoprotein (P-gp), there has been no validation of the accuracy of the steady-state analysis because the elementary rate constants for transport were not known. Recently, we fitted the mass action elementary kinetic rate constants of P-gp transport of three different drugs through a confluent monolayer of MDCKII-hMDR1 cells. With these elementary rate constants in hand, we use computer simulations to assess the accuracy of the steady-state Michaelis-Menten parameters. This limits the simulation to parameter ranges known to be physiologically relevant. Using over 2,300 different vectors of initial elementary parameters spanning the space bounded by the three drugs, which defines 2,300 "virtual substrates", the concentrations of substrate transported were calculated and fitted to Eadie-Hofstee plots. Acceptable plots were obtained for 1,338 cases. The fitted steady-state Vmax values from the analysis correlated to within a factor of 2-3 with the values predicted from the elementary parameters. However, the fitted Km value could be generated by a wide range of underlying "molecular" Km values. This is because of the convolution of the drug passive permeability kinetics into the fitted Km. This implies that Km values measured in simpler systems, e.g., microsomes or proteoliposomes, even if accurate, would not predict the Km values for the confluent monolayer system or, by logical extension, in vivo. Reliable in vitro-in vivo extrapolation seems to require using the elementary rate constants rather than the Michaelis-Menten steady-state parameters.
Single molecule Michaelis-Menten equation beyond quasistatic disorder.
Xue, Xiaochuan; Liu, Fei; Ou-Yang, Zhong-Can
2006-09-01
The classic Michaelis-Menten equation describes the catalytic activities for ensembles of enzyme molecules very well. But recent single-molecule experiments showed that the waiting time distribution and other properties of single enzyme molecules were not consistent with the prediction based on the ensemble viewpoint. They have contributed to the slow conformational changes of a single enzyme in the catalytic processes. In this work, we study the general dynamics of single enzymes in the presence of dynamic disorder. We find that, within the time separation regimes, i.e., the slow reaction and nondiffusion limits, the Michaelis-Menten equation holds exactly. In particular, by employing the decoupling approximation we demonstrate analytically that the classic Michaelis-Menten equation is still an excellent approximation in the presence of general dynamic disorder.
Michaelis-Menten equation and detailed balance in enzymatic networks.
Cao, Jianshu
2011-05-12
Many enzymatic reactions in biochemistry are far more complex than the celebrated Michaelis-Menten scheme, but the observed turnover rate often obeys the hyperbolic dependence on the substrate concentration, a relation established almost a century ago for the simple Michaelis-Menten mechanism. To resolve the longstanding puzzle, we apply the flux balance method to predict the functional form of the substrate dependence in the mean turnover time of complex enzymatic reactions and identify detailed balance (i.e., the lack of unbalanced conformational current) as a sufficient condition for the Michaelis-Menten equation to describe the substrate concentration dependence of the turnover rate in an enzymatic network. This prediction can be verified in single-molecule event-averaged measurements using the recently proposed signatures of detailed balance violations. The finding helps analyze recent single-molecule studies of enzymatic networks and can be applied to other external variables, such as force-dependence and voltage-dependence.
Tang, Sanyi; Xiao, Yanni
2007-12-01
The purpose of this article is to provide the analytical solutions of one-compartment models with Michaelis-Menten elimination kinetics for three different inputs (single intravenous dose, multiple-dose bolus injection and constant). All analytical solutions obtained in present paper can be described by the well defined Lambert W function which can be easily implemented in most mathematical softwares such as Matlab and Maple. These results will play an important role in fitting the Michaelis-Menten parameters and in designing a dosing regimen to maintain steady-state plasma concentrations. In particular, the analytical periodic solution for multi-dose inputs is also given, and we note that the maximum and minimum values of the periodic solution depends on the Michaelis-Menten parameters, dose and time interval of drug administration. In practice, it is important to maintain a concentration above the minimum therapeutic level at all times without exceeding the minimum toxic concentration. Therefore, the one-compartment model with therapeutic window is proposed, and further the existence of periodic solution, analytical expression and its period are analyzed. The analytical formula of period plays a key role in designing a dose regimen to maintain the plasma concentration within a specified range over long periods of therapy. Finally, the completely analytical solution for the constant input rate is derived and discussed which depends on the relations between constant input rate and maximum rate of change of concentration.
Differences in Michaelis-Menten kinetics for different cultivars of maize during cyanide removal.
Yu, Xiao-Zhang; Gu, Ji-Dong
2007-06-01
Knowledge of the kinetic parameters, the half-saturation constant (K(m)) and the maximum metabolic capacity (v(max)), is very useful for the characterization of enzymes and biochemical processes. Little is known about rates of which vegetation metabolizes environmental chemicals. It is known, however, that vascular plants possess an enzyme system that detoxifies cyanide by converting it into the amino acid asparagine. This study investigated the differences in Michaelis-Menten kinetics of cyanide removal by different cultivars of maize. Detached leaves (1.0 g fresh weight) of seven different cultivars of maize (Zea mays L.) were kept in glass vessels with 100mL of aqueous solution spiked with potassium cyanide at 25+/-0.5 degrees C for 28 h. Four treatment concentrations of cyanide were used, ranging from 0.43 to 7.67 mgCNL(-1). The disappearance of cyanide from the aqueous solution was analyzed spectrophotometrically. Realistic values of K(m) and v(max) were estimated by a computer program using non-linear regression treatment. Lineweaver-Burk plots were also used to estimate the kinetic parameters for comparison. Using non-linear regression treatments, values of v(max) and K(m) were found to be between 10.80 and 22.80 mgCNkg(-1)h(-1), and 2.57 and 7.09 mgCNL(-1), respectively. The highest v(max) was achieved by the cultivars HengFen 1, followed by NongDa 108. The lowest v(max) was demonstrated by JingKe 8. The highest K(m) was found in NongDa 108, followed by HengFen 1. The lowest K(m) was associated with JingKe 8. Results from this study indicated that significant removal of cyanide from an aqueous solution was observed in the presence of plant materials without apparent phytotoxicity, even at the high concentration of cyanide used in this study. All maize cultivars used in this study were able to metabolize cyanide efficiently, although with different metabolic capacities. Results also showed a small variation of metabolic rates between the different cultivars
Sinitsyn, Nikolai A [Los Alamos National Laboratory
2008-01-01
We generalize the concept of the geometric phase in stochastic kinetics to a noncyclic evolution. Its application is demonstrated on kinetics of the Michaelis-Menten reaction. It is shown that the noncyclic geometric phase is responsible for the correction to the Michaelis-Menten law when parameters, such as a substrate concentration, are changing with time. We also discuss a model, where this correction qualitatively changes the outcome of reaction kinetics.
Michaelis-Menten relations for complex enzymatic networks.
Kolomeisky, Anatoly B
2011-04-21
Most biological processes are controlled by complex systems of enzymatic chemical reactions. Although the majority of enzymatic networks have very elaborate structures, there are many experimental observations indicating that some turnover rates still follow a simple Michaelis-Menten relation with a hyperbolic dependence on a substrate concentration. The original Michaelis-Menten mechanism has been derived as a steady-state approximation for a single-pathway enzymatic chain. The validity of this mechanism for many complex enzymatic systems is surprising. To determine general conditions when this relation might be observed in experiments, enzymatic networks consisting of coupled parallel pathways are investigated theoretically. It is found that the Michaelis-Menten equation is satisfied for specific relations between chemical rates, and it also corresponds to a situation with no fluxes between parallel pathways. Our results are illustrated for a simple model. The importance of the Michaelis-Menten relationship and derived criteria for single-molecule experimental studies of enzymatic processes are discussed.
Alternative Analysis of the Michaelis-Menten Equations
Krogstad, Harald E.; Dawed, Mohammed Yiha; Tegegne, Tadele Tesfa
2011-01-01
Courses in mathematical modelling are always in need of simple, illustrative examples. The Michaelis-Menten reaction kinetics equations have been considered to be a basic example of scaling and singular perturbation. However, the leading order approximations do not easily show the expected behaviour, and this note proposes a different perturbation…
Reexamining Michaelis-Menten Enzyme Kinetics for Xanthine Oxidase
Bassingthwaighte, James B.; Chinn, Tamara M.
2013-01-01
Abbreviated expressions for enzyme kinetic expressions, such as the Michaelis-Menten (M-M) equations, are based on the premise that enzyme concentrations are low compared with those of the substrate and product. When one does progress experiments, where the solute is consumed during conversion to form a series of products, the idealized conditions…
Alternative Analysis of the Michaelis-Menten Equations
Krogstad, Harald E.; Dawed, Mohammed Yiha; Tegegne, Tadele Tesfa
2011-01-01
Courses in mathematical modelling are always in need of simple, illustrative examples. The Michaelis-Menten reaction kinetics equations have been considered to be a basic example of scaling and singular perturbation. However, the leading order approximations do not easily show the expected behaviour, and this note proposes a different perturbation…
Reexamining Michaelis-Menten Enzyme Kinetics for Xanthine Oxidase
Bassingthwaighte, James B.; Chinn, Tamara M.
2013-01-01
Abbreviated expressions for enzyme kinetic expressions, such as the Michaelis-Menten (M-M) equations, are based on the premise that enzyme concentrations are low compared with those of the substrate and product. When one does progress experiments, where the solute is consumed during conversion to form a series of products, the idealized conditions…
Oscillatory enzyme reactions and Michaelis-Menten kinetics.
Goldbeter, Albert
2013-09-02
Oscillations occur in a number of enzymatic systems as a result of feedback regulation. How Michaelis-Menten kinetics influences oscillatory behavior in enzyme systems is investigated in models for oscillations in the activity of phosphofructokinase (PFK) in glycolysis and of cyclin-dependent kinases in the cell cycle. The model for the PFK reaction is based on a product-activated allosteric enzyme reaction coupled to enzymatic degradation of the reaction product. The Michaelian nature of the product decay term markedly influences the period, amplitude and waveform of the oscillations. Likewise, a model for oscillations of Cdc2 kinase in embryonic cell cycles based on Michaelis-Menten phosphorylation-dephosphorylation kinetics shows that the occurrence and amplitude of the oscillations strongly depend on the ultrasensitivity of the enzymatic cascade that controls the activity of the cyclin-dependent kinase. Copyright © 2013 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.
Optimal designs for the Michaelis Menten model with correlated observations
Dette, Holger; Kunert, Joachim
2012-01-01
In this paper we investigate the problem of designing experiments for weighted least squares analysis in the Michaelis Menten model. We study the structure of exact D-optimal designs in a model with an autoregressive error structure. Explicit results for locally D-optimal are derived for the case where 2 observations can be taken per subject. Additionally standardized maximin D-optimal designs are obtained in this case. The results illustrate the enormous difficulties to find e...
Reith, David; Medlicott, Natalie J; Kumara De Silva, Rohana; Yang, Lin; Hickling, Jeremy; Zacharias, Mathew
2009-01-01
1. The aim of the present study was to perform an in vivo estimation of the Michaelis-Menten constants of the major metabolic pathways of paracetamol (APAP). 2. A two-occasion, single-dose cross-over trial was performed using 60 and 90 mg/kg doses of APAP in healthy patients undergoing third molar dental extraction. Plasma samples were collected over 24 h and urine was collected for 8 h after dosing. Twenty patients were enrolled in the study and complete data for plasma and urine were available for both doses for 13 volunteers who were included in the analysis; seven of the volunteers were men, the median age (range) was 22 years (19-31) and the median weight (range) was 68 kg (50-86). 3. The mean (95% CI) k(m) for APAP glucuronidation was 6.89 mmol/L (3.57-10.22) and the V(max) was 0.97 mmol/h per kg (0.65-1.28). The k(m) for APAP sulphation was 0.097 mmol/L (0.041-0.152) and the V(max) was 0.011 mmol/h per kg (0.009-0.013). For the combined excretion of APAP-cysteine and APAP-mercapturate, the k(m) was 0.303 mmol/L (0.131-0.475) and the V(max) was 0.004 mmol/h per kg (0.002-0.005). 4. The estimates for in vivo Michaelis-Menten constants for APAP glucuronidation and sulphation were in the order of those reported previously using in vitro methods.
Noise slows the rate of Michaelis-Menten reactions.
Van Dyken, J David
2017-10-07
Microscopic randomness and the small volumes of living cells combine to generate random fluctuations in molecule concentrations called "noise". Here I investigate the effect of noise on biochemical reactions obeying Michaelis-Menten kinetics, concluding that substrate noise causes these reactions to slow. I derive a general expression for the time evolution of the joint probability density of chemical species in arbitrarily connected networks of non-linear chemical reactions in small volumes. This equation is a generalization of the chemical master equation (CME), a common tool for investigating stochastic chemical kinetics, extended to reaction networks occurring in small volumes, such as living cells. I apply this equation to a generalized Michaelis-Menten reaction in an open system, deriving the following general result: 〈p〉≤p¯ and 〈s〉≥s¯, where s¯ and p¯ denote the deterministic steady-state concentration of reactant and product species, respectively, and 〈s〉 and 〈p〉 denote the steady-state ensemble average over independent realizations of a stochastic reaction. Under biologically realistic conditions, namely when substrate is degraded or diluted by cell division, 〈p〉≤p¯. Consequently, noise slows the rate of in vivo Michaelis-Menten reactions. These predictions are validated by extensive stochastic simulations using Gillespie's exact stochastic simulation algorithm. I specify the conditions under which these effects occur and when they vanish, therefore reconciling discrepancies among previous theoretical investigations of stochastic biochemical reactions. Stochastic slowdown of reaction flux caused by molecular noise in living cells may have functional consequences, which the present theory may be used to quantify. Copyright © 2017 Elsevier Ltd. All rights reserved.
Kumar, Ashutosh; Dua, Arti
2015-01-01
Recent fluorescence spectroscopy measurements of the turnover time distribution of single-enzyme turnover kinetics of $\\beta$-galactosidase provide evidence of Michaelis-Menten kinetics at low substrate concentration. However, at high substrate concentrations, the dimensionless variance of the turnover time distribution shows systematic deviations from the Michaelis-Menten prediction. This difference is attributed to conformational fluctuations in both the enzyme and the enzyme-substrate complex and to the possibility of both parallel and off-pathway kinetics. Here, we use the chemical master equation to model the kinetics of a single fluctuating enzyme that can yield a product through either parallel or off-pathway mechanisms. An exact expression is obtained for the turnover time distribution from which the mean turnover time and randomness parameters are calculated. The parallel and off-pathway mechanisms yield strikingly different dependences of the mean turnover time and the randomness parameter on the su...
Klinman, Judith P
2014-01-01
The final arbiter of enzyme mechanism is the ability to establish and test a kinetic mechanism. Isotope effects play a major role in expanding the scope and insight derived from the Michaelis-Menten equation. The integration of isotope effects into the formalism of the Michaelis-Menten equation began in the 1970s and has continued until the present. This review discusses a family of eukaryotic copper proteins, including dopamine β-monooxygenase, tyramine β-monooxygenase and peptidylglycine α-amidating enzyme, which are responsible for the synthesis of neuroactive compounds, norepinephrine, octopamine and C-terminally carboxamidated peptides, respectively. The review highlights the results of studies showing how combining kinetic isotope effects with initial rate parameters permits the evaluation of: (a) the order of substrate binding to multisubstrate enzymes; (b) the magnitude of individual rate constants in complex, multistep reactions; (c) the identification of chemical intermediates; and (d) the role of nonclassical (tunnelling) behaviour in C-H activation. © 2013 FEBS.
Park, Soohyung; Agmon, Noam
2008-05-15
We develop a uniform theory for the many-particle diffusion-control effects on the Michaelis-Menten scheme in solution, based on the Gopich-Szabo relaxation-time approximation (Gopich, I. V.; Szabo, A. J. Chem. Phys. 2002, 117, 507). We extend the many-particle simulation algorithm to the Michaelis-Menten case by utilizing the Green function previously derived for excited-state reversible geminate recombination with different lifetimes (Gopich, I. V.; Agmon, N. J. Chem. Phys. 2000, 110, 10433). Running the simulation for representative parameter sets in the time domain and under steady-state conditions, we find poor agreement with classical kinetics but excellent agreement with some of the modern theories for bimolecular diffusion-influenced reactions. Our simulation algorithm can be readily extended to the biologically interesting case of dense patches of membrane-bound enzymes.
Ever-fluctuating single enzyme molecules : Michaelis-Menten equation revisited
English, Brian P.; Min, Wei; Oijen, Antoine M. van; Lee, Kang Taek; Luo, Guobin; Sun, Hongye; Cherayil, Binny J.; Kou, S.C.; Xie, X. Sunney
2006-01-01
Enzymes are biological catalysts vital to life processes and have attracted century-long investigation. The classic Michaelis-Menten mechanism provides a highly satisfactory description of catalytic activities for large ensembles of enzyme molecules. Here we tested the Michaelis-Menten equation at
Eberwein, Jennifer; Shen, Weijun; Jenerette, G Darrel
2017-05-11
China experiences some of the highest rates of anthropogenic nitrogen deposition globally, with further increases projected. Understanding of soil feedbacks to the combined anthropogenic influences of climate change and nitrogen deposition in these systems is critical to improve predictive abilities for future climate scenarios. Here we used a Michaelis-Menten substrate-based kinetics framework to explore how soil CO2 production (Rsoil) responds to changes in temperature and available soil nitrogen (N) by combining field experiments with laboratory manipulations from sites experiencing elevated rates of anthropogenic N deposition but varying in soil N availabiltiy. The temperature sensitivity of Rsoil was strongly influenced by labile C additions. Furthermore, estimation of the temperature response of the Michaelis-Menten parameters supports the use of substrate-based kinetics in modeling efforts. Results from both field and laboratory experiments demonstrated a general decrease in Rsoil with increasing soil available N that was variably dependent on carbon (C) availability. Both the field and the laboratory measurements demonstrated a consistent decrease in the Michaelis-Menten parameter kM with increasing soil available N, indicating an increase in the efficiency of soil C decomposition with increasing N. Furthermore, these results provide evidence of interactions between N deposition and temperature sensitivity, which could influence C storage under combined anthropogenic global change drivers.
A note on the reverse Michaelis-Menten kinetics
Wang, Gangsheng [ORNL; Post, Wilfred M [ORNL
2013-01-01
We theoretically derive a general equation describing the enzyme kinetics that can be further simplified to the typical Michaelis-Menten (M-M) kinetics and the reverse M-M equation (RM-M) proposed by Schimel and Weintraub (2003). We discuss the conditions under which the RM-M is valid with this theoretical derivation. These conditions are contrary to the assumptions of Schimel and Weintraub (2003) and limit the applicability of the model in field soil environments. Nonetheless, Schimel and Weintraub s RM-M model is useful and has the ability to produce a non-linear response of SOM decomposition to enzyme concentration consistent with observations. Regardless of the theoretical basis, if we assume that the M-M and the RM-M could be equivalent, our sensitivity analysis indicates that enzyme plays a more sensitive role in the M-M kinetics compared with in the RM-M kinetics.
Amyloid-like fibril elongation follows michaelis-menten kinetics.
Milto, Katazyna; Botyriute, Akvile; Smirnovas, Vytautas
2013-01-01
A number of proteins can aggregate into amyloid-like fibrils. It was noted that fibril elongation has similarities to an enzymatic reaction, where monomers or oligomers would play a role of substrate and nuclei/fibrils would play a role of enzyme. The question is how similar these processes really are. We obtained experimental data on insulin amyloid-like fibril elongation at the conditions where other processes which may impact kinetics of fibril formation are minor and fitted it using Michaelis-Menten equation. The correlation of the fit is very good and repeatable. It speaks in favour of enzyme-like model of fibril elongation. In addition, obtained [Formula: see text] and [Formula: see text] values at different conditions may help in better understanding influence of environmental factors on the process of fibril elongation.
Enzymatic reactions in microfluidic devices: Michaelis-Menten kinetics.
Ristenpart, William D; Wan, Jiandi; Stone, Howard A
2008-05-01
Kinetic rate constants for enzymatic reactions are typically measured with a series of experiments at different substrate concentrations in a well-mixed container. Here we demonstrate a microfluidic technique for measuring Michaelis-Menten rate constants with only a single experiment. Enzyme and substrate are brought together in a coflow microfluidic device, and we establish analytically and numerically that the initial concentration of product scales with the distance x along the channel as x5/2. Measurements of the initial rate of product formation, combined with the quasi-steady rate of product formation further downstream, yield the rate constants. We corroborate the x5/2 scaling result experimentally using the bioluminescent reaction between ATP and luciferase/luciferin as a model system.
Stochastic Total Quasi-Steady-State Approximation for the Michaelis-Menten Scheme
Galstyan, Vahe
2015-01-01
In biochemical systems the Michaelis-Menten (MM) scheme is one of the best-known models of the enzyme- catalyzed kinetics. In the academic literature the MM approximation has been thoroughly studied in the context of differential equation models. At the level of the cell, however, molecular fluctuations have many important consequences, and thus, a stochastic investigation of the MM scheme is often necessary. In their work Barik et al. [Biophysical Journal, 95, 3563-3574, (2008)] presented a stochastic approximation of the MM scheme. They suggested a substitution of the propensity function in the reduced master equation with the total quasi-steady- state approximation (tQSSA) rate. The justification of the substitution, however, was provided for a special case only and did not cover the whole parameter domain of the tQSSA. In this manuscript we present a derivation of the stochastic tQSSA that is valid for the entire tQSSA parameter domain.
Golicnik, Marko
2011-01-01
The Michaelis-Menten rate equation can be found in most general biochemistry textbooks, where the time derivative of the substrate is a hyperbolic function of two kinetic parameters (the limiting rate "V", and the Michaelis constant "K"[subscript M]) and the amount of substrate. However, fundamental concepts of enzyme kinetics can be difficult to…
Golicnik, Marko
2011-01-01
The Michaelis-Menten rate equation can be found in most general biochemistry textbooks, where the time derivative of the substrate is a hyperbolic function of two kinetic parameters (the limiting rate "V", and the Michaelis constant "K"[subscript M]) and the amount of substrate. However, fundamental concepts of enzyme kinetics can be difficult to…
Michaelis-Menten kinetics, the operator-repressor system, and least squares approaches.
Hadeler, Karl Peter
2013-01-01
The Michaelis-Menten (MM) function is a fractional linear function depending on two positive parameters. These can be estimated by nonlinear or linear least squares methods. The non-linear methods, based directly on the defect of the MM function, can fail and not produce any minimizer. The linear methods always produce a unique minimizer which, however, may not be positive. Here we give sufficient conditions on the data such that the nonlinear problem has at least one positive minimizer and also conditions for the minimizer of the linear problem to be positive. We discuss in detail the models and equilibrium relations of a classical operator-repressor system, and we extend our approach to the MM problem with leakage and to reversible MM kinetics. The arrangement of the sufficient conditions exhibits the important role of data that have a concavity property (chemically feasible data).
Analysis of noise-induced bistability in Michaelis Menten single-step enzymatic cycle
Remondini, Daniel; Bazzani, Armando; Castellani, Gastone; Maritan, Amos
2011-01-01
In this paper we study noise-induced bistability in a specific circuit with many biological implications, namely a single-step enzymatic cycle described by Michaelis Menten equations with quasi-steady state assumption. We study the system both with a Master Equation formalism, and with the Fokker-Planck continuous approximation, characterizing the conditions in which the continuous approach is a good approximation of the exact discrete model. An analysis of the stationary distribution in both cases shows that bimodality can not occur in such a system. We discuss which additional requirements can generate stochastic bimodality, by coupling the system with a chemical reaction involving enzyme production and turnover. This extended system shows a bistable behaviour only in specific parameter windows depending on the number of molecules involved, providing hints about which should be a feasible system size in order that such a phenomenon could be exploited in real biological systems.
Non-Michaelis-Menten kinetics in cytochrome P450-catalyzed reactions.
Atkins, William M
2005-01-01
The cytochrome P450 monooxygenases (CYPs) are the dominant enzyme system responsible for xenobiotic detoxification and drug metabolism. Several CYP isoforms exhibit non-Michaelis-Menten, or "atypical," steady state kinetic patterns. The allosteric kinetics confound prediction of drug metabolism and drug-drug interactions, and they challenge the theoretical paradigms of allosterism. Both homotropic and heterotropic ligand effects are now widely documented. It is becoming apparent that multiple ligands can simultaneously bind within the active sites of individual CYPs, and the kinetic parameters change with ligand occupancy. In fact, the functional effect of any specific ligand as an activator or inhibitor can be substrate dependent. Divergent approaches, including kinetic modeling and X-ray crystallography, are providing new information about how multiple ligand binding yields complex CYP kinetics.
Youdim, K; Dodia, R
2010-04-01
Non-linear dose-exposure (supra-proportionality) occurs when plasma drug concentrations increase in a non-linear fashion with increasing dose. To predict the likelihood of this, an understanding is required of the K(M), which reflects a drug ability to saturate a specific enzyme involved in its metabolism. This study assessed the accuracy of K(M) and V(max) determinations for compounds using a substrate-depletion approach with those determined using the product-formation approach, using both recombinant human cytochrome P450 (CYP) enzymes and human liver microsomes. For the vast majority of the compounds studied, the K(M)'s using recombinant CYPs and human liver microsomes in the two approaches predicted within two-fold. Further comparisons between the K(M) and V(max)-values were made between those measured using the product-formation approach and those estimated following simultaneous fitting of the Michaelis-Menten equation to all substrate depletion plots. In each case values were comparable. In conclusion, the current study showed the substrate-depletion approach can be used to estimate K(M) and V(max) using both human liver microsomes and recombinant P450s. Estimation of these parameters during early discovery will aid in the understanding of dosages at which non-linearity may occur, but potentially aid predictions of likely clinical drug-drug interactions.
Conformational Nonequilibrium Enzyme Kinetics: Generalized Michaelis-Menten Equation.
Piephoff, D Evan; Wu, Jianlan; Cao, Jianshu
2017-08-03
In a conformational nonequilibrium steady state (cNESS), enzyme turnover is modulated by the underlying conformational dynamics. On the basis of a discrete kinetic network model, we use an integrated probability flux balance method to derive the cNESS turnover rate for a conformation-modulated enzymatic reaction. The traditional Michaelis-Menten (MM) rate equation is extended to a generalized form, which includes non-MM corrections induced by conformational population currents within combined cyclic kinetic loops. When conformational detailed balance is satisfied, the turnover rate reduces to the MM functional form, explaining its general validity. For the first time, a one-to-one correspondence is established between non-MM terms and combined cyclic loops with unbalanced conformational currents. Cooperativity resulting from nonequilibrium conformational dynamics can be achieved in enzymatic reactions, and we provide a novel, rigorous means of predicting and characterizing such behavior. Our generalized MM equation affords a systematic approach for exploring cNESS enzyme kinetics.
Role of substrate unbinding in Michaelis-Menten enzymatic reactions.
Reuveni, Shlomi; Urbakh, Michael; Klafter, Joseph
2014-03-25
The Michaelis-Menten equation provides a hundred-year-old prediction by which any increase in the rate of substrate unbinding will decrease the rate of enzymatic turnover. Surprisingly, this prediction was never tested experimentally nor was it scrutinized using modern theoretical tools. Here we show that unbinding may also speed up enzymatic turnover--turning a spotlight to the fact that its actual role in enzymatic catalysis remains to be determined experimentally. Analytically constructing the unbinding phase space, we identify four distinct categories of unbinding: inhibitory, excitatory, superexcitatory, and restorative. A transition in which the effect of unbinding changes from inhibitory to excitatory as substrate concentrations increase, and an overlooked tradeoff between the speed and efficiency of enzymatic reactions, are naturally unveiled as a result. The theory presented herein motivates, and allows the interpretation of, groundbreaking experiments in which existing single-molecule manipulation techniques will be adapted for the purpose of measuring enzymatic turnover under a controlled variation of unbinding rates. As we hereby show, these experiments will not only shed first light on the role of unbinding but will also allow one to determine the time distribution required for the completion of the catalytic step in isolation from the rest of the enzymatic turnover cycle.
Relation between pulmonary clearance and particle burden: a Michaelis-Menten-like kinetic model.
Yu, R. C.; Rappaport, S.M.
1996-01-01
OBJECTIVES: To test the validity of a Michaelis-Menten-like kinetic model of pulmonary clearance of insoluble dusts. METHODS: Data were investigated from studies of pulmonary clearance in F344 rats exposed to antimony trioxide (Sb2O3), photocopy test toner, polyvinyl chloride powder (PVC), and diesel exhaust particles. The Michaelis-Menten-like model was used to develop a relation in which the pulmonary clearance half time was a linear function of lung burden. After combining all data, linear...
Goličnik, Marko
2011-06-01
Many pharmacodynamic processes can be described by the nonlinear saturation kinetics that are most frequently based on the hyperbolic Michaelis-Menten equation. Thus, various time-dependent solutions for drugs obeying such kinetics can be expressed in terms of the Lambert W(x)-omega function. However, unfortunately, computer programs that can perform the calculations for W(x) are not widely available. To avoid this problem, the replacement of the integrated Michaelis-Menten equation with an empiric integrated 1--exp alternative model equation was proposed recently by Keller et al. (Ther Drug Monit. 2009;31:783-785), although, as shown here, it was not necessary. Simulated concentrations of model drugs obeying Michaelis-Menten elimination kinetics were generated by two approaches: 1) calculation of time-course data based on an approximation equation W2*(x) performed using Microsoft Excel; and 2) calculation of reference time-course data based on an exact W(x) function built in to the Wolfram Mathematica. I show here that the W2*(x) function approximates the actual W(x) accurately. W2*(x) is expressed in terms of elementary mathematical functions and, consequently, it can be easily implemented using any of the widely available software. Hence, with the example of a hypothetical drug, I demonstrate here that an equation based on this approximation is far better, because it is nearly equivalent to the original solution, whereas the same characteristics cannot be fully confirmed for the 1--exp model equation. The W2*(x) equation proposed here might have an important role as a useful shortcut in optional software to estimate kinetic parameters from experimental data for drugs, and it might represent an easy and universal analytical tool for simulating and designing dosing regimens.
Kumar, Ashutosh; Maity, Hiranmay; Dua, Arti
2015-07-09
Recent fluorescence spectroscopy measurements of the turnover time distribution of single-enzyme turnover kinetics of β-galactosidase provide evidence of Michaelis-Menten kinetics at low substrate concentration. However, at high substrate concentrations, the dimensionless variance of the turnover time distribution shows systematic deviations from the Michaelis-Menten prediction. This difference is attributed to conformational fluctuations in both the enzyme and the enzyme-substrate complex and to the possibility of both parallel- and off-pathway kinetics. Here, we use the chemical master equation to model the kinetics of a single fluctuating enzyme that can yield a product through either parallel- or off-pathway mechanisms. An exact expression is obtained for the turnover time distribution from which the mean turnover time and randomness parameters are calculated. The parallel- and off-pathway mechanisms yield strikingly different dependences of the mean turnover time and the randomness parameter on the substrate concentration. In the parallel mechanism, the distinct contributions of enzyme and enzyme-substrate fluctuations are clearly discerned from the variation of the randomness parameter with substrate concentration. From these general results, we conclude that an off-pathway mechanism, with substantial enzyme-substrate fluctuations, is needed to rationalize the experimental findings of single-enzyme turnover kinetics of β-galactosidase.
Costa, Rafael S; Machado, Daniel; Rocha, Isabel; Ferreira, Eugénio C
2010-05-01
The construction of dynamic metabolic models at reaction network level requires the use of mechanistic enzymatic rate equations that comprise a large number of parameters. The lack of knowledge on these equations and the difficulty in the experimental identification of their associated parameters, represent nowadays the limiting factor in the construction of such models. In this study, we compare four alternative modeling approaches based on Michaelis-Menten kinetics for the bi-molecular reactions and different types of simplified rate equations for the remaining reactions (generalized mass action, convenience kinetics, lin-log and power-law). Using the mechanistic model for Escherichia coli central carbon metabolism as a benchmark, we investigate the alternative modeling approaches through comparative simulations analyses. The good dynamic behavior and the powerful predictive capabilities obtained using the hybrid model composed of Michaelis-Menten and the approximate lin-log kinetics indicate that this is a possible suitable approach to model complex large-scale networks where the exact rate laws are unknown. 2010 Elsevier Ireland Ltd. All rights reserved.
Moffitt, Jeffrey R; Bustamante, Carlos
2014-01-01
Enzyme-catalyzed reactions are naturally stochastic, and precision measurements of these fluctuations, made possible by single-molecule methods, promise to provide fundamentally new constraints on the possible mechanisms underlying these reactions. We review some aspects of statistical kinetics: a new field with the goal of extracting mechanistic information from statistical measures of fluctuations in chemical reactions. We focus on a widespread and important statistical measure known as the randomness parameter. This parameter is remarkably simple in that it is the squared coefficient of variation of the cycle completion times, although it places significant limits on the minimal complexity of possible enzymatic mechanisms. Recently, a general expression has been introduced for the substrate dependence of the randomness parameter that is for rate fluctuations what the Michaelis-Menten expression is for the mean rate of product generation. We discuss the information provided by the new kinetic parameters introduced by this expression and demonstrate that this expression can simplify the vast majority of published models. © 2013 FEBS.
Ever-fluctuating single enzyme molecules: Michaelis-Menten equation revisited.
English, Brian P; Min, Wei; van Oijen, Antoine M; Lee, Kang Taek; Luo, Guobin; Sun, Hongye; Cherayil, Binny J; Kou, S C; Xie, X Sunney
2006-02-01
Enzymes are biological catalysts vital to life processes and have attracted century-long investigation. The classic Michaelis-Menten mechanism provides a highly satisfactory description of catalytic activities for large ensembles of enzyme molecules. Here we tested the Michaelis-Menten equation at the single-molecule level. We monitored long time traces of enzymatic turnovers for individual beta-galactosidase molecules by detecting one fluorescent product at a time. A molecular memory phenomenon arises at high substrate concentrations, characterized by clusters of turnover events separated by periods of low activity. Such memory lasts for decades of timescales ranging from milliseconds to seconds owing to the presence of interconverting conformers with broadly distributed lifetimes. We proved that the Michaelis-Menten equation still holds even for a fluctuating single enzyme, but bears a different microscopic interpretation.
Goličnik, Marko
2011-04-15
Various explicit reformulations of time-dependent solutions for the classical two-step irreversible Michaelis-Menten enzyme reaction model have been described recently. In the current study, I present further improvements in terms of a generalized integrated form of the Michaelis-Menten equation for computation of substrate or product concentrations as functions of time for more real-world, enzyme-catalyzed reactions affected by the product. The explicit equations presented here can be considered as a simpler and useful alternative to the exact solution for the generalized integrated Michaelis-Menten equation when fitted to time course data using standard curve-fitting software. Copyright © 2011 Elsevier Inc. All rights reserved.
Stroberg, Wylie; Schnell, Santiago
2016-12-01
The conditions under which the Michaelis-Menten equation accurately captures the steady-state kinetics of a simple enzyme-catalyzed reaction is contrasted with the conditions under which the same equation can be used to estimate parameters, KM and V, from progress curve data. Validity of the underlying assumptions leading to the Michaelis-Menten equation are shown to be necessary, but not sufficient to guarantee accurate estimation of KM and V. Detailed error analysis and numerical "experiments" show the required experimental conditions for the independent estimation of both KM and V from progress curves. A timescale, tQ, measuring the portion of the time course over which the progress curve exhibits substantial curvature provides a novel criterion for accurate estimation of KM and V from a progress curve experiment. It is found that, if the initial substrate concentration is of the same order of magnitude as KM, the estimated values of the KM and V will correspond to their true values calculated from the microscopic rate constants of the corresponding mass-action system, only so long as the initial enzyme concentration is less than KM. Copyright © 2016 Elsevier B.V. All rights reserved.
Chaudhury, Srabanti; Cherayil, Binny J
2007-09-14
Single-molecule equations for the Michaelis-Menten [Biochem. Z. 49, 333 (1913)] mechanism of enzyme action are analyzed within the Wilemski-Fixman [J. Chem. Phys. 58, 4009 (1973); 60, 866 (1974)] approximation after the effects of dynamic disorder--modeled by the anomalous diffusion of a particle in a harmonic well--are incorporated into the catalytic step of the reaction. The solution of the Michaelis-Menten equations is used to calculate the distribution of waiting times between successive catalytic turnovers in the enzyme beta-galactosidase. The calculated distribution is found to agree qualitatively with experimental results on this enzyme obtained at four different substrate concentrations. The calculations are also consistent with measurements of correlations in the fluctuations of the fluorescent light emitted during the course of catalysis, and with measurements of the concentration dependence of the randomness parameter.
Accuracy of the Michaelis-Menten approximation when analysing effects of molecular noise.
Lawson, Michael J; Petzold, Linda; Hellander, Andreas
2015-05-06
Quantitative biology relies on the construction of accurate mathematical models, yet the effectiveness of these models is often predicated on making simplifying approximations that allow for direct comparisons with available experimental data. The Michaelis-Menten (MM) approximation is widely used in both deterministic and discrete stochastic models of intracellular reaction networks, owing to the ubiquity of enzymatic activity in cellular processes and the clear biochemical interpretation of its parameters. However, it is not well understood how the approximation applies to the discrete stochastic case or how it extends to spatially inhomogeneous systems. We study the behaviour of the discrete stochastic MM approximation as a function of system size and show that significant errors can occur for small volumes, in comparison with a corresponding mass-action system. We then explore some consequences of these results for quantitative modelling. One consequence is that fluctuation-induced sensitivity, or stochastic focusing, can become highly exaggerated in models that make use of MM kinetics even if the approximations are excellent in a deterministic model. Another consequence is that spatial stochastic simulations based on the reaction-diffusion master equation can become highly inaccurate if the model contains MM terms. © 2015 The Author(s) Published by the Royal Society. All rights reserved.
Kosmidis, Kosmas; Karalis, Vangelis; Argyrakis, Panos; Macheras, Panos
2004-09-01
Two different approaches were used to study the kinetics of the enzymatic reaction under heterogeneous conditions to interpret the unusual nonlinear pharmacokinetics of mibefradil. Firstly, a detailed model based on the kinetic differential equations is proposed to study the enzymatic reaction under spatial constraints and in vivo conditions. Secondly, Monte Carlo simulations of the enzyme reaction in a two-dimensional square lattice, placing special emphasis on the input and output of the substrate were applied to mimic in vivo conditions. Both the mathematical model and the Monte Carlo simulations for the enzymatic reaction reproduced the classical Michaelis-Menten (MM) kinetics in homogeneous media and unusual kinetics in fractal media. Based on these findings, a time-dependent version of the classic MM equation was developed for the rate of change of the substrate concentration in disordered media and was successfully used to describe the experimental plasma concentration-time data of mibefradil and derive estimates for the model parameters. The unusual nonlinear pharmacokinetics of mibefradil originates from the heterogeneous conditions in the reaction space of the enzymatic reaction. The modified MM equation can describe the pharmacokinetics of mibefradil as it is able to capture the heterogeneity of the enzymatic reaction in disordered media.
Reduction for Michaelis-Menten-Henri kinetics in the presence of diffusion.
Kalachev, L.V.; Kaper, H.G.; Kaper, T.J.; Popovic, N.; Zagaris, A.
2007-01-01
Abstract: The Michaelis-Menten-Henri (MMH) mechanism is one of the paradigm reaction mechanisms in biology and chemistry. In its simplest form, it involves a substrate that reacts (reversibly) with an enzyme, forming a complex which is transformed (irreversibly) into a product and the enzyme. Given
Bozlee, Brian J.
2007-01-01
The impact of raising Gibbs energy of the enzyme-substrate complex (G[subscript 3]) and the reformulation of the Michaelis-Menten equation are discussed. The maximum velocity of the reaction (v[subscript m]) and characteristic constant for the enzyme (K[subscript M]) will increase with increase in Gibbs energy, indicating that the rate of reaction…
A generalized Michaelis-Menten type equation for the analysis of growth
Lopez, S.; France, J.; Gerrits, W.J.J.; Dhanoa, M.S.; Humphries, D.J.; Dijkstra, J.
2000-01-01
The functional form W = (W0Kc Wf t(c)) /(Kc t(c)), where W is body size at age t, W0 and Wf are the zero- and infinite-time values of W, respectively, and K and c are constants, is derived. This new generalized Michaelis-Menten-type equation provides a flexible model for animal growth capable of
Reduction for Michaelis-Menten-Henri kinetics in the presence of diffusion
A. Zagaris (Antonios); L.V. Kalachev; H.G. Kaper; T.J. Kaper (Tasso Joost); N. Popovic
2007-01-01
textabstractThe Michaelis-Menten-Henri (MMH) mechanism is one of the paradigm reaction mechanisms in biology and chemistry. In its simplest form, it involves a substrate that reacts (reversibly) with an enzyme, forming a complex which is transformed (irreversibly) into a product and the enzyme.
A Simple Classroom Teaching Technique to Help Students Understand Michaelis-Menten Kinetics
Runge, Steven W.; Hill, Brent J. F.; Moran, William M.
2006-01-01
A new, simple classroom technique helps cell biology students understand principles of Michaelis-Menten enzyme kinetics. A student mimics the enzyme and the student's hand represents the enzyme's active site. The catalytic event is the transfer of marbles (substrate molecules) by hand from one plastic container to another. As predicted, increases…
Filobello-Nino, Uriel; Vazquez-Leal, Hector; Benhammouda, Brahim; Hernandez-Martinez, Luis; Khan, Yasir; Jimenez-Fernandez, Victor Manuel; Herrera-May, Agustin Leobardo; Castaneda-Sheissa, Roberto; Pereyra-Diaz, Domitilo; Cervantes-Perez, Juan; Agustin Perez-Sesma, Jose Antonio; Hernandez-Machuca, Sergio Francisco; Cuellar-Hernandez, Leticia
2014-01-01
In this article, Perturbation Method (PM) is employed to obtain a handy approximate solution to the steady state nonlinear reaction diffusion equation containing a nonlinear term related to Michaelis-Menten of the enzymatic reaction. Comparing graphics between the approximate and exact solutions, it will be shown that the PM method is quite efficient.
A two-substrate Michaelis-Menten model for the growth of self-replicating polymers.
Ferreira, R
1987-10-07
A two-substrate Michaelis-Menten model is proposed for the growth of autocatalytic self-replicating polymers. Selective growth depends on the existence of two complementary pairs of monomers. Discrimination among sequences results from different products of binding constants, KCGnKAUm. The results support an earlier renormalization group treatment (Ferreira & Tsallis, 1985).
Filobello-Nino, Uriel; Vazquez-Leal, Hector; Benhammouda, Brahim; Hernandez-Martinez, Luis; Khan, Yasir; Jimenez-Fernandez, Victor Manuel; Herrera-May, Agustin Leobardo; Castaneda-Sheissa, Roberto; Pereyra-Diaz, Domitilo; Cervantes-Perez, Juan; Agustin Perez-Sesma, Jose Antonio; Hernandez-Machuca, Sergio Francisco; Cuellar-Hernandez, Leticia
2014-01-01
In this article, Perturbation Method (PM) is employed to obtain a handy approximate solution to the steady state nonlinear reaction diffusion equation containing a nonlinear term related to Michaelis-Menten of the enzymatic reaction. Comparing graphics between the approximate and exact solutions, it will be shown that the PM method is quite efficient.
A Simple Classroom Teaching Technique to Help Students Understand Michaelis-Menten Kinetics
Runge, Steven W.; Hill, Brent J. F.; Moran, William M.
2006-01-01
A new, simple classroom technique helps cell biology students understand principles of Michaelis-Menten enzyme kinetics. A student mimics the enzyme and the student's hand represents the enzyme's active site. The catalytic event is the transfer of marbles (substrate molecules) by hand from one plastic container to another. As predicted, increases…
Yan, Xiaoyu; Krzyzanski, Wojciech
2012-04-01
The Michaelis-Menten (M-M) approximation of the target-mediated drug disposition (TMDD) pharmacokinetic (PK) model was derived based on the rapid binding (RB) or quasi steady-state (QSS) assumptions that implied that the target and drug binding and dissociation were in equilibrium. However, the initial dose for an IV bolus injection for the M-M model did not account for a fraction bound to the target. We postulated a correction to an initial condition that was consistent with the assumptions underlying the M-M approximation. We determined that the difference between the injected dose and one that should be used for the initial condition is equal to the amount of drug bound to the target upon reaching the equilibrium. We also observed that the corrected initial condition made the internalization rate constant an identifiable parameter that was not for the original M-M model. Finally, we performed a simulation exercise to check if the correction will impact the model performance and the bias of the M-M parameter estimates. We used literature data to simulate plasma drug concentrations described by the RB/QSS TMDD model. The simulated data were refitted by both models. All the parameters estimated from the original M-M model were substantially biased. On the other hand, the corrected M-M is able to accurately estimate these parameters except for equilibrium constant K(m). Weighted sum of square residual and Akaike information criterion suggested a better performance of the corrected M-M model compared with the original M-M model. Further studies are necessary to determine the importance of this correction for the M-M model applications to analysis of TMDD driven PK data.
Reeve, Russell; Turner, J Rick
2013-05-01
The Hill equation is often used in dose-response or exposure-response modeling. Aliases for the Hill model include the Emax model, and the Michaelis-Menten model. There is confusion about the appropriate parameterization, how to interpret the parameters, what the meaning is of the various parameterizations found in the literature, and which parameterization best approximates the statistical inferences produced when fitting the Hill equation to data. In this paper, we present several equivalent versions of the Hill model; show that they are equivalent in terms of yielding the same prediction for a given dose, and are equivalent to the four-parameter logistic model in this same sense; and deduce which parameterization is optimal in the sense of having the least statistical curvature and preferable multicollinearity.
Wu, Xiaotian; Li, Jun; Nekka, Fahima
2015-04-01
The current study aims to provide the closed form solutions of one-compartment open models exhibiting simultaneous linear and nonlinear Michaelis-Menten elimination kinetics for single- and multiple-dose intravenous bolus administrations. It can be shown that the elimination half-time ([Formula: see text]) has a dose-dependent property and is upper-bounded by [Formula: see text] of the first-order elimination model. We further analytically distinguish the dominant role of different elimination pathways in terms of model parameters. Moreover, for the case of multiple-dose intravenous bolus administration, the existence and local stability of the periodic solution at steady state are established. The closed form solutions of the models are obtained through a newly introduced function motivated by the Lambert W function.
Yan, Shaomin; Wu, Guang
2011-10-01
In this study, we attempted to use the neural network to model a quantitative structure-K(m) (Michaelis-Menten constant) relationship for beta-glucosidase, which is an important enzyme to cut the beta-bond linkage in glucose while K(m) is a very important parameter in enzymatic reactions. Eight feedforward backpropagation neural networks with different layers and neurons were applied for the development of predictive model, and twenty-five different features of amino acids were chosen as predictors one by one. The results show that the 20-1 feedforward backpropagation neural network can serve as a predictive model while the normalized polarizability index as well as the amino-acid distribution probability can serve as the predictors. This study threw lights on the possibility of predicting the K(m) in beta-glucosidases based on their amino-acid features.
Statistical reconstruction of transcription factor activity using Michaelis-Menten kinetics.
Khanin, R; Vinciotti, V; Mersinias, V; Smith, C P; Wit, E
2007-09-01
The basic building block of a gene regulatory network consists of a gene encoding a transcription factor (TF) and the gene(s) it regulates. Considerable efforts have been directed recently at devising experiments and algorithms to determine TFs and their corresponding target genes using gene expression and other types of data. The underlying problem is that the expression of a gene coding for the TF provides only limited information about the activity of the TF, which can also be controlled posttranscriptionally. In the absence of a reliable technology to routinely measure the activity of regulators, it is of great importance to understand whether this activity can be inferred from gene expression data. We here develop a statistical framework to reconstruct the activity of a TF from gene expression data of the target genes in its regulatory module. The novelty of our approach is that we embed the deterministic Michaelis-Menten model of gene regulation in this statistical framework. The kinetic parameters of the gene regulation model are inferred together with the profile of the TF regulator. We also obtain a goodness-of-fit test to verify the fit of the model. The model is applied to a time series involving the Streptomyces coelicolor bacterium. We focus on the transcriptional activator cdaR, which is partly responsible for the production of a particular type of antibiotic. The aim is to reconstruct the activity profile of this regulator. Our approach can be extended to include more complex regulatory relationships, such as multiple regulatory factors, competition, and cooperativity.
Michel, Denis
2013-01-01
The Michaelis-Menten enzymatic reaction is sufficient to perceive many subtleties of network modeling, including the concentration and time scales separations, the formal equivalence between bulk phase and single-molecule approaches, or the relationships between single-cycle transient probabilities and steady state rates. Seven methods proposed by different authors and yielding the same famous Michaelis-Menten equation, are selected here to illustrate the kinetic and probabilistic use of rate constants and to review basic techniques for handling them. Finally, the general rate of an ordered multistep reaction, of which the Michaelis-Menten reaction is a particular case, is deduced from a Markovian approach.
A Squared Michaelis-Menten Function of Substrate Concentration for Plant Mitochondrial Respiration 1
James, Alan T.; Wiskich, Joseph T.; Dry, Ian B.
1990-01-01
Dry and Wiskich ([1987] Arch Biochem Biophys 257: 92-99) have published data showing the response of plant mitochondrial respiration to increasing additions of oxaloacetate or malate when these substrates have been depleted by inhibition of succinate dehydrogenase by malonate, and coenzyme A (CoA) has been sequestered as acetyl-CoA by pyruvate dehydrogenase. In the presence of 2-oxoglutarate, it is shown that the response is given by a Michaelis-Menten curve, but in its absence, when malate has to supply substrate for dehydrogenation as well as to liberate CoA via malate dehydrogenase and citrate synthase, the response is presumably the product of two Michaelis-Menten functions, which can be approximated by the square of a single function. PMID:16667257
Wenzhen Gan
2013-01-01
Full Text Available This paper is concerned with the asymptotical behavior of solutions to the reaction-diffusion system under homogeneous Neumann boundary condition. By taking food ingestion and species' moving into account, the model is further coupled with Michaelis-Menten type functional response and nonlocal delay. Sufficient conditions are derived for the global stability of the positive steady state and the semitrivial steady state of the proposed problem by using the Lyapunov functional. Our results show that intraspecific competition benefits the coexistence of prey and predator. Furthermore, the introduction of Michaelis-Menten type functional response positively affects the coexistence of prey and predator, and the nonlocal delay is harmless for stabilities of all nonnegative steady states of the system. Numerical simulations are carried out to illustrate the main results.
Global stability of enzymatic chains of full reversible Michaelis-Menten reactions.
Belgacem, Ismail; Gouzé, Jean-Luc
2013-09-01
We consider a chain of metabolic reactions catalyzed by enzymes, of reversible Michaelis-Menten type with full dynamics, i.e. not reduced with any quasi-steady state approximations. We study the corresponding dynamical system and show its global stability if the equilibrium exists. If the system is open, the equilibrium may not exist. The main tool is monotone systems theory. Finally we study the implications of these results for the study of coupled genetic-metabolic systems.
Robustness of optimal designs for the Michaelis-Menten model under a variation of criteria
Dette, Holger; Kiss, Christine; Wong, Weng Kee
2009-01-01
The Michaelis-Menten model has and continues to be one of the most widely used models in many diverse fields. In the biomedical sciences, the model continues to be ubiquitous in biochemistry, enzyme kinetics studies, nutrition science and in the pharmaceutical sciences. Despite its wide ranging applications across disciplines, design issues for this model are given short shrift. This paper focuses on design issues and provides a variety of optimal designs of this model. In addition, we ...
Wenzhen Gan; Canrong Tian; Qunying Zhang; Zhigui Lin
2013-01-01
This paper is concerned with the asymptotical behavior of solutions to the reaction-diffusion system under homogeneous Neumann boundary condition. By taking food ingestion and species' moving into account, the model is further coupled with Michaelis-Menten type functional response and nonlocal delay. Sufficient conditions are derived for the global stability of the positive steady state and the semitrivial steady state of the proposed problem by using the Lyapunov functional. Our results show...
Optimal Designs for Discriminating Between some Extensions of the Michaelis-Menten Model
Jesus Lopez Fidalgo; Chiara Tommasi; Camelia Trandafir
2005-01-01
In this paper some results on the problem of computing optimal designs for discriminating between rival models are provided. Using T-optimality for two rival models a compound criterion is developed to discriminate between more than two models. Surprising results arise when T-optimal designs are compared with classical c-optimal designs for nonlinear models. In particular, some practical deviations of the Michaelis-Menten model are considered in order to measure and compare efficiencies of di...
Solution of the Michaelis-Menten equation using the decomposition method.
Sonnad, Jagadeesh R; Goudar, Chetan T
2009-01-01
We present a low-order recursive solution to the Michaelis-Menten equation using the decomposition method. This solution is algebraic in nature and provides a simpler alternative to numerical approaches such as differential equation evaluation and root-solving techniques that are currently used to compute substrate concentration in the Michaelis-Menten equation. A detailed characterization of the errors in substrate concentrations computed from decomposition, Runge-Kutta, and bisection methods over a wide range of s(0) : K(m) values was made by comparing them with highly accurate solutions obtained using the Lambert W function. Our results indicated that solutions obtained from the decomposition method were usually more accurate than those from the corresponding classical Runge-Kutta methods. Moreover, these solutions required significantly fewer computations than the root-solving method. Specifically, when the stepsize was 0.1% of the total time interval, the computed substrate concentrations using the decomposition method were characterized by accuracies on the order of 10(-8) or better. The algebraic nature of the decomposition solution and its relatively high accuracy make this approach an attractive candidate for computing substrate concentration in the Michaelis-Menten equation.
无
2012-01-01
In this paper,the existence of eight periodic solutions to a Michaelis-Menten-type predator-prey system with delay and harvesting in patch environment is established using the analytical techniques and Mawhin's coincidence degree theory.
Michel, Denis; Ruelle, Philippe
2013-01-01
International audience; The Michaelis-Menten enzymatic reaction is sufficient to perceive many subtleties of network modeling, including the concentration and time scales separations, the formal equivalence between bulk phase and single-molecule approaches, or the relationships between single-cycle transient probabilities and steady state rates. Seven methods proposed by different authors and yielding the same famous Michaelis-Menten equation, are selected here to illustrate the kinetic and p...
Selection between Michaelis-Menten and target-mediated drug disposition pharmacokinetic models.
Yan, Xiaoyu; Mager, Donald E; Krzyzanski, Wojciech
2010-02-01
Target-mediated drug disposition (TMDD) models have been applied to describe the pharmacokinetics of drugs whose distribution and/or clearance are affected by its target due to high binding affinity and limited capacity. The Michaelis-Menten (M-M) model has also been frequently used to describe the pharmacokinetics of such drugs. The purpose of this study is to investigate conditions for equivalence between M-M and TMDD pharmacokinetic models and provide guidelines for selection between these two approaches. Theoretical derivations were used to determine conditions under which M-M and TMDD pharmacokinetic models are equivalent. Computer simulations and model fitting were conducted to demonstrate these conditions. Typical M-M and TMDD profiles were simulated based on literature data for an anti-CD4 monoclonal antibody (TRX1) and phenytoin administered intravenously. Both models were fitted to data and goodness of fit criteria were evaluated for model selection. A case study of recombinant human erythropoietin was conducted to qualify results. A rapid binding TMDD model is equivalent to the M-M model if total target density R ( tot ) is constant, and R ( tot ) K ( D ) /(K ( D ) + C) ( 2 ) < 1 where K ( D ) represents the dissociation constant and C is the free drug concentration. Under these conditions, M-M parameters are defined as: V ( max ) = k ( int ) R ( tot ) V ( c ) and K ( m ) = K ( D ) where k ( int ) represents an internalization rate constant, and V ( c ) is the volume of the central compartment. R ( tot ) is constant if and only if k ( int ) = k ( deg,) where k ( deg ) is a degradation rate constant. If the TMDD model predictions are not sensitive to k ( int ) or k ( deg ) parameters, the condition of R ( tot ) K ( D ) /(K ( D ) + C) ( 2 ) < 1 alone can preserve the equivalence between rapid binding TMDD and M-M models. The model selection process for drugs that exhibit TMDD should involve a full mechanistic model as well as reduced models. The best model
Meyer, Markus R; Orschiedt, Tina; Maurer, Hans H
2013-02-27
The pharmacokinetics of various important drugs are known to be significantly influenced by the human ABC transporter P-glycoprotein (P-gp), which may lead to clinically relevant drug-drug interactions. In contrast to therapeutic drugs, emerging drugs of abuse (DOA) are sold and consumed without any safety pharmacology testing. Only some studies on their metabolism were published, but none about their affinity to the transporter systems. Therefore, 47 DOAs from various classes were tested for their P-gp affinity using human P-gp (hP-gp) to predict possible drug-drug interactions. DOAs were initially screened for general hP-gp affinity and further characterized by modeling classic Michaelis-Menten kinetics and assessing their K(m) and V(max) values. Among the tested drugs, 12 showed a stimulation of ATPase activity. The most intensive stimulating DOAs were further investigated and compared with the known P-gp model substrates sertraline and verapamil. ATPase stimulation kinetics could be modeled for the entactogen 3,4-methylenedioxy-α-ethylphenethylamine (3,4-BDB), the hallucinogen 2,5-dimethoxy-4-iodoamphetamine (DOI), the abused alkaloid glaucine, the opioid-like drugs N-iso-propyl-1,2-diphenylethylamine (NPDPA), and N-(1-phenylcyclohexyl)-3-ethoxypropanamine (PCEPA), with K(m) and V(max) values within the same range as for verapamil or sertraline. As a consequence interactions with other drugs being P-gp substrates might be considered to be very likely and further studies should be encouraged. Copyright © 2013 Elsevier Ireland Ltd. All rights reserved.
Ochab-Marcinek, Anna
2010-04-21
The study of biochemical pathways usually focuses on a small section of a protein interactions network. Two distinct sources contribute to the noise in such a system: intrinsic noise, inherent in the studied reactions, and extrinsic noise generated in other parts of the network or in the environment. We study the effect of extrinsic noise entering the system through a nonlinear uptake reaction which acts as a nonlinear filter. Varying input noise intensity varies the mean of the noise after the passage through the filter, which changes the stability properties of the system. The steady-state displacement due to small noise is independent on the kinetics of the system but it only depends on the nonlinearity of the input function. For monotonically increasing and concave input functions such as the Michaelis-Menten uptake rate, we give a simple argument based on the small-noise expansion, which enables qualitative predictions of the steady-state displacement only by inspection of experimental data: when weak and rapid noise enters the system through a Michaelis-Menten reaction, then the graph of the system's steady states vs. the mean of the input signal always shifts to the right as noise intensity increases. We test the predictions on two models of lac operon, where TMG/lactose uptake is driven by a Michaelis-Menten enzymatic process. We show that as a consequence of the steady state displacement due to fluctuations in extracellular TMG/lactose concentration the lac switch responds in an asymmetric manner: as noise intensity increases, switching off lactose metabolism becomes easier and switching it on becomes more difficult. (c) 2009 Elsevier Ltd. All rights reserved.
Perturbation theory in the catalytic rate constant of the Henri-Michaelis-Menten enzymatic reaction.
Bakalis, Evangelos; Kosmas, Marios; Papamichael, Emmanouel M
2012-11-01
The Henry-Michaelis-Menten (HMM) mechanism of enzymatic reaction is studied by means of perturbation theory in the reaction rate constant k (2) of product formation. We present analytical solutions that provide the concentrations of the enzyme (E), the substrate (S), as well as those of the enzyme-substrate complex (C), and the product (P) as functions of time. For k (2) small compared to k (-1), we properly describe the entire enzymatic activity from the beginning of the reaction up to longer times without imposing extra conditions on the initial concentrations E ( o ) and S ( o ), which can be comparable or much different.
Michaelis-Menten speeds up tau-leaping under a wide range of conditions.
Wu, Sheng; Fu, Jin; Cao, Yang; Petzold, Linda
2011-04-07
This paper examines the benefits of Michaelis-Menten model reduction techniques in stochastic tau-leaping simulations. Results show that although the conditions for the validity of the reductions for tau-leaping remain the same as those for the stochastic simulation algorithm (SSA), the reductions result in a substantial speed-up for tau-leaping under a different range of conditions than they do for SSA. The reason of this discrepancy is that the time steps for SSA and for tau-leaping are determined by different properties of system dynamics.
Michaelis-Menten speeds up tau-leaping under a wide range of conditions
Wu, Sheng; Fu, Jin; Cao, Yang; Petzold, Linda
2011-04-01
This paper examines the benefits of Michaelis-Menten model reduction techniques in stochastic tau-leaping simulations. Results show that although the conditions for the validity of the reductions for tau-leaping remain the same as those for the stochastic simulation algorithm (SSA), the reductions result in a substantial speed-up for tau-leaping under a different range of conditions than they do for SSA. The reason of this discrepancy is that the time steps for SSA and for tau-leaping are determined by different properties of system dynamics.
Standardization of α-L-iduronidase enzyme assay with Michaelis-Menten kinetics.
Ou, Li; Herzog, Tyler L; Wilmot, Carrie M; Whitley, Chester B
2014-02-01
The lack of methodological uniformity in enzyme assays has been a long-standing difficulty, a problem for bench researchers, for the interpretation of clinical diagnostic tests, and an issue for investigational drug review. Illustrative of the problem, α-L-iduronidase enzyme catalytic activity is frequently measured with the substrate 4-methylumbelliferyl-α-L-iduronide (4MU-iduronide); however, final substrate concentrations used in different assays vary greatly, ranging from 25 μM to 1425 μM (Km ≈ 180 μM) making it difficult to compare results between laboratories. In this study, α-L-iduronidase was assayed with 15 different substrate concentrations. The resulting activity levels from the same specimens varied greatly with different substrate concentrations but, as a group, obeyed the expectations of Michaelis-Menten kinetics. Therefore, for the sake of improved comparability, it is proposed that α-L-iduronidase enzyme assays should be conducted either (1) under substrate saturating conditions; or (2) when concentrations are significantly below substrate saturation, with results standardized by arithmetic adjustment that considers Michaelis-Menten kinetics. The approach can be generalized to many other enzyme assays. Copyright © 2013 Elsevier Inc. All rights reserved.
Bueno, Paulo R; Watanabe, Ailton M; Faria, Ronaldo C; Santos, Márcio L; Riccardi, Carla S
2010-12-16
A piezoelectric detection of enzyme-modified surface was performed under Michaelis-Menten presumptions of steady-state condition. The approach herein presented showed promise in the study of enzymatic kinetics by measuring the frequency changes associated with mass changes at the piezoelectric crystal surface. Likewise, real-time frequency shifts, that is, dΔf/dt, indicated the rate of products formation from enzymatic reaction. In this paper, acetylcholinesterase was used as the enzymatic model and acetylcholine as substrate. The enzymatic rate has its maximum value for a short time during the kinetic reaction, for instance, during the first ten minutes of the reaction time scale. The values found for the kinetic constant rate and Michaelis-Menten constant were (1.4 ± 0.8) 10(5) s(-1) and (5.2 ± 3) 10(-4) M, respectively, in agreement with the values found in classical Michaelis-Menten kinetic experiments.
Extended Parker-Sochacki method for Michaelis-Menten enzymatic reaction model.
Abdelrazik, Ismail M; Elkaranshawy, Hesham A
2016-03-01
In this article, a new approach--namely, the extended Parker-Sochacki method (EPSM)--is presented for solving the Michaelis-Menten nonlinear enzymatic reaction model. The Parker-Sochacki method (PSM) is combined with a new resummation method called the Sumudu-Padé resummation method to obtain approximate analytical solutions for the model. The obtained solutions by the proposed approach are compared with the solutions of PSM and the Runge-Kutta numerical method (RKM). The comparison proves the practicality, efficiency, and correctness of the presented approach. It serves as a basis for solving other nonlinear biochemical reaction models in the future. Copyright © 2015 Elsevier Inc. All rights reserved.
Explicit reformulations of time-dependent solution for a Michaelis-Menten enzyme reaction model.
Golicnik, Marko
2010-11-01
The exact closed-form solution to the Michaelis-Menten equation is expressed in terms of the Lambert W(x) function. However, the utility of this solution is limited because the W(x) function is not widely available in curve-fitting software. Based on various approximations to the W(x) function, different explicit equations expressed in terms of the elementary functions are proposed here as useful shortcuts to fit time depletion of substrate concentration directly to progress curves using commonly available nonlinear regression computer programs. The results are compared with those obtained by fitting other algebraic equations that have been proposed previously in the literature. 2010 Elsevier Inc. All rights reserved.
Liao, Fei; Tian, Kao-Cong; Yang, Xiao; Zhou, Qi-Xin; Zeng, Zhao-Chun; Zuo, Yu-Ping
2003-03-01
The reliability of kinetic substrate quantification by nonlinear fitting of the enzyme reaction curve to the integrated Michaelis-Menten equation was investigated by both simulation and preliminary experimentation. For simulation, product absorptivity epsilon was 3.00 mmol(-1) L cm(-1) and K(m) was 0.10 mmol L(-1), and uniform absorbance error sigma was randomly inserted into the error-free reaction curve of product absorbance A(i) versus reaction time t(i) calculated according to the integrated Michaelis-Menten equation. The experimental reaction curve of arylesterase acting on phenyl acetate was monitored by phenol absorbance at 270 nm. Maximal product absorbance A(m) was predicted by nonlinear fitting of the reaction curve to Eq. (1) with K(m) as constant. There were unique A(m) for best fitting of both the simulated and experimental reaction curves. Neither the error in reaction origin nor the variation of enzyme activity changed the background-corrected value of A(m). But the range of data under analysis, the background absorbance, and absorbance error sigma had an effect. By simulation, A(m) from 0.150 to 3.600 was predicted with reliability and linear response to substrate concentration when there was 80% consumption of substrate at sigma of 0.001. Restriction of absorbance to 0.700 enabled A(m) up to 1.800 to be predicted at sigma of 0.001. Detection limit reached A(m) of 0.090 at sigma of 0.001. By experimentation, the reproducibility was 4.6% at substrate concentration twice the K(m), and A(m) linearly responded to phenyl acetate with consistent absorptivity for phenol, and upper limit about twice the maximum of experimental absorbance. These results supported the reliability of this new kinetic method for enzymatic analysis with enhanced upper limit and precision.
Li, Albert P; Schlicht, Kari E
2014-01-01
A higher throughput platform was developed for the determination of K(M) values for isoformselective P450 substrates in human hepatocytes via incubation of the hepatocytes with substrates in 384- well plates and metabolite quantification by RapidFire™ mass spectrometry. Isoform-selective P450 substrates were incubated at 8 concentrations in triplicate with cryopreserved human hepatocytes from 16 donors. The metabolic pathways examined were the CYP1A2-catalyzed tacrine 1-hydroxylation, CYP2B6-catalyzed bupropion hydroxylation, CYP2C8-catalyzed amodiaquine N-deethylation, CYP2C9- catalyzed diclofenac 4'-hydroxylation, CYP2D6-catalyzed dextromethorphan O-demethylation, and CYP3A4-catalyzed midazolam 1'-hydroxylation. Typical saturation enzyme kinetics was observed for all the pathways evaluated. Individual differences in the apparent V(max) and K(M) values were observed among the human hepatocytes from each of the 16 individual donors, with no statistically significant gender- or age-associated differences. A "composite" K(M) value was calculated for each of the pathways via normalizing the individual activities to their respective V(max) values to develop "relative activities" followed by Michaelis-Menten analysis of the mean relative activities of the 16 donors at each of the 8 substrate concentrations. The resulting "composite" K(M) values for the P450 substrates may be used to guide in vitro P450 inhibition and induction studies and kinetic modeling of in vivo drug-drug interaction.
Bezerra, Rui M F; Fraga, Irene; Dias, Albino A
2013-01-01
Enzyme kinetic parameters are usually determined from initial rates nevertheless, laboratory instruments only measure substrate or product concentration versus reaction time (progress curves). To overcome this problem we present a methodology which uses integrated models based on Michaelis-Menten equation. The most severe practical limitation of progress curve analysis occurs when the enzyme shows a loss of activity under the chosen assay conditions. To avoid this problem it is possible to work with the same experimental points utilized for initial rates determination. This methodology is illustrated by the use of integrated kinetic equations with the well-known reaction catalyzed by alkaline phosphatase enzyme. In this work nonlinear regression was performed with the Solver supplement (Microsoft Office Excel). It is easy to work with and track graphically the convergence of SSE (sum of square errors). The diagnosis of enzyme inhibition was performed according to Akaike information criterion. Copyright © 2012 Elsevier Ireland Ltd. All rights reserved.
Gattu, Srikanth; Crihfield, Cassandra L; Holland, Lisa A
2017-01-03
Phospholipid nanogels enhance the stability and performance of the exoglycosidase enzyme neuraminidase and are used to create a fixed zone of enzyme within a capillary. With nanogels, there is no need to covalently immobilize the enzyme, as it is physically constrained. This enables rapid quantification of Michaelis-Menten constants (KM) for different substrates and ultimately provides a means to quantify the linkage (i.e., 2-3 versus 2-6) of sialic acids. The fixed zone of enzyme is inexpensive and easily positioned in the capillary to support electrophoresis mediated microanalysis using neuraminidase to analyze sialic acid linkages. To circumvent the limitations of diffusion during static incubation, the incubation period is reproducibly achieved by varying the number of forward and reverse passes the substrate makes through the stationary fixed zone using in-capillary electrophoretic mixing. A KM value of 3.3 ± 0.8 mM (Vmax, 2100 ± 200 μM/min) was obtained for 3'-sialyllactose labeled with 2-aminobenzoic acid using neuraminidase from Clostridium perfringens that cleaves sialic acid monomers with an α2-3,6,8,9 linkage, which is similar to values reported in the literature that required benchtop analyses. The enzyme cleaves the 2-3 linkage faster than the 2-6, and a KM of 2 ± 1 mM (Vmax, 400 ± 100 μM/min) was obtained for the 6'-sialyllactose substrate. An alternative neuraminidase selective for 2-3 sialic acid linkages generated a KM value of 3 ± 2 mM (Vmax, 900 ± 300 μM/min) for 3'-sialyllactose. With a knowledge of Vmax, the method was applied to a mixture of 2-3 and 2-6 sialyllactose as well as 2-3 and 2-6 sialylated triantennary glycan. Nanogel electrophoresis is an inexpensive, rapid, and simple alternative to current technologies used to distinguish the composition of 3' and 6' sialic acid linkages.
The original Michaelis constant: translation of the 1913 Michaelis-Menten paper.
Michaelis, Leonor; Menten, Maud Leonora; Johnson, Kenneth A; Goody, Roger S
2011-10-04
Nearly 100 years ago Michaelis and Menten published their now classic paper [Michaelis, L., and Menten, M. L. (1913) Die Kinetik der Invertinwirkung. Biochem. Z. 49, 333-369] in which they showed that the rate of an enzyme-catalyzed reaction is proportional to the concentration of the enzyme-substrate complex predicted by the Michaelis-Menten equation. Because the original text was written in German yet is often quoted by English-speaking authors, we undertook a complete translation of the 1913 publication, which we provide as Supporting Information . Here we introduce the translation, describe the historical context of the work, and show a new analysis of the original data. In doing so, we uncovered several surprises that reveal an interesting glimpse into the early history of enzymology. In particular, our reanalysis of Michaelis and Menten's data using modern computational methods revealed an unanticipated rigor and precision in the original publication and uncovered a sophisticated, comprehensive analysis that has been overlooked in the century since their work was published. Michaelis and Menten not only analyzed initial velocity measurements but also fit their full time course data to the integrated form of the rate equations, including product inhibition, and derived a single global constant to represent all of their data. That constant was not the Michaelis constant, but rather V(max)/K(m), the specificity constant times the enzyme concentration (k(cat)/K(m) × E(0)).
Michaelis-Menten kinetics in shear flow: Similarity solutions for multi-step reactions.
Ristenpart, W D; Stone, H A
2012-03-01
Models for chemical reaction kinetics typically assume well-mixed conditions, in which chemical compositions change in time but are uniform in space. In contrast, many biological and microfluidic systems of interest involve non-uniform flows where gradients in flow velocity dynamically alter the effective reaction volume. Here, we present a theoretical framework for characterizing multi-step reactions that occur when an enzyme or enzymatic substrate is released from a flat solid surface into a linear shear flow. Similarity solutions are developed for situations where the reactions are sufficiently slow compared to a convective time scale, allowing a regular perturbation approach to be employed. For the specific case of Michaelis-Menten reactions, we establish that the transversally averaged concentration of product scales with the distance x downstream as x(5/3). We generalize the analysis to n-step reactions, and we discuss the implications for designing new microfluidic kinetic assays to probe the effect of flow on biochemical processes.
Müller, R; Babel, W
1980-01-01
Investigations of the 3-hexulosephosphate synthase (HPS) from different methylotrophic bacteria have revealed apparent discrepancies in kinetic behaviour. In all methanol-utilizing species investigated by us the kinetic characteristics showed intermediary plateau regions. Therefore, this behaviour is assumed to be a general feature of the HPS from all non-methane-utilizing methylotrophic bacteria. However, this assumption is in contrast to the results of other authors. Both for Methylomonas M15 (SAHM et al. 1976) and Methylomonas aminofaciens 77a (KATO et al. 1977, 1978) MICHAELIS-MENTEN kinetics of the HPS were stated. To check the validity of our assumption we have analyzed the kinetic data given by others. Indications of the existence of intermediary plateau regions could be found with the enzyme from Arthrobacter globiformis (BYKOVSKAYA and VORONKOV 1977) and Methylomonas aminofaciens 77a (KATO et al. 1978). Furthermore, biphasic ARRHENIUS plots indicate a multiple character of the HPS from these species as could already be demonstrated with the enzyme from Bacterium MB 58 and Pseudomonas oleovorans. In addition, causes which may obscure the detection of intermediary plateau regions are demonstrated.
eduction for Michaelis-Menten-Henri kinetics in the presence of diffusion
Leonid V. Kalachev
2007-05-01
Full Text Available The Michaelis-Menten-Henri (MMH mechanism is one of the paradigm reaction mechanisms in biology and chemistry. In its simplest form, it involves a substrate that reacts (reversibly with an enzyme, forming a complex which is transformed (irreversibly into a product and the enzyme. Given these basic kinetics, a dimension reduction has traditionally been achieved in two steps, by using conservation relations to reduce the number of species and by exploiting the inherent fast-slow structure of the resulting equations. In the present article, we investigate how the dynamics change if the species are additionally allowed to diffuse. We study the two extreme regimes of large diffusivities and of small diffusivities, as well as an intermediate regime in which the time scale of diffusion is comparable to that of the fast reaction kinetics. We show that reduction is possible in each of these regimes, with the nature of the reduction being regime dependent. Our analysis relies on the classical method of matched asymptotic expansions to derive approximations for the solutions that are uniformly valid in space and time.
Burchardt, Malte; Träuble, Markus; Wittstock, Gunther
2009-06-15
The formalism for simulating scanning electrochemical microscopy (SECM) experiments by boundary element methods in three space coordinates has been extended to allow consideration of nonlinear boundary conditions. This is achieved by iteratively refining the boundary conditions that are encoded in a boundary condition matrix. As an example, the simulations are compared to experimental approach curves in the SECM feedback mode toward samples modified with glucose oxidase (GOx). The GOx layer was prepared by the layer-by-layer assembly of polyelectrolytes using glucose oxidase as one of the polyelectrolytes. The comparison of the simulated and experimental curves showed that under a wide range of experimentally accessible conditions approximations of the kinetics at the sample by first order models yield misleading results. The approach curves differ also qualitatively from curves calculated with first order models. As a consequence, this may lead to severe deviations when such curves are fitted to first order kinetic models. The use of linear approximations to describe the enzymatic reaction in SECM feedback experiments is justified only if the ratio of the mediator and Michaelis-Menten constant is equal to or smaller than 0.1 (deviation less than 10%).
Lee, Hye Jin; Wark, Alastair W; Goodrich, Terry T; Fang, Shiping; Corn, Robert M
2005-04-26
Real-time surface plasmon resonance (SPR) imaging measurements of surface enzymatic reactions on DNA microarrays are analyzed using a kinetics model that couples the contributions of both enzyme adsorption and surface enzyme reaction kinetics. For the case of a 1:1 binding of an enzyme molecule (E) to a surface-immobilized substrate (S), the overall enzymatic reaction can be described in terms of classical Langmuir adsorption and Michaelis-Menten concepts and three rate constants: enzyme adsorption (k(a)), enzyme desorption (k(d)) and enzyme catalysis (k(cat)). In contrast to solution enzyme kinetics, the amount of enzyme in solution is in excess as compared to the amount of substrate on the surface. Moreover, the surface concentration of the intermediary enzyme-substrate complex (ES) is not constant with time, but goes to zero as the reaction is completed. However, kinetic simulations show that the fractional surface coverage of ES on the remaining unreacted sites does reach a steady-state value throughout the course of the surface reaction. This steady-state value approaches the Langmuir equilibrium value for cases where k(a)[E] > k(cat). Experiments using the 3' --> 5' exodeoxyribonuclease activity of Exonuclease III on double-stranded DNA microarrays as a function of temperature and enzyme concentration are used to demonstrate how this model can be applied to quantitatively analyze the SPR imaging data.
Simon Brown
2010-06-01
Full Text Available The behavior of enzyme-catalyzed reactions is not made clear to many students by the standard mathematical description of enzyme kinetics. An enzyme-machine analogy is described that has made the details of the Michaelis-Menten mechanism and the associated kinetics more accessible with minimal use of mathematics. Students taught using the analogy appear to have fewer of the misconceptions than those taught using a more mathematical approach.
Putz, Mihai V
2011-04-13
The conceptual and practical issues regarding the reduction of the Haldane-Radić enzymic mechanism, specific for cholinesterase kinetics, to the consecrated or logistically modified Michaelis-Menten kinetics, specific for some mutant enzymes, are here clarified as due to the limited initial substrate concentration, through detailed initial rate and progress curve analysis, even when other classical conditions for such equivalence are not entirely fulfilled.
Simon Brown
2010-01-01
The behavior of enzyme-catalyzed reactions is not made clear to many students by the standard mathematical description of enzyme kinetics. An enzyme-machine analogy is described that has made the details of the Michaelis-Menten mechanism and the associated kinetics more accessible with minimal use of mathematics. Students taught using the analogy appear to have fewer of the misconceptions than those taught using a more mathematical approach.
2009-01-01
A different view of Henri-Michaelis-Menten (HMM) enzyme kinetics is presented. In the first part of the paper, a simplified but useful description that stresses the cyclic nature of the catalytic process is introduced. The time-dependence of the substrate concentration after the initial transient phase is derived in a simple way that dispenses the mathematical technique known as quasi-steady-state approximation. In the second part of the paper an exact one-dimensional formulation of HMM kinet...
Mihai V. Putz
2011-04-01
Full Text Available The conceptual and practical issues regarding the reduction of the Haldane-Radić enzymic mechanism, specific for cholinesterase kinetics, to the consecrated or logistically modified Michaelis-Menten kinetics, specific for some mutant enzymes, are here clarified as due to the limited initial substrate concentration, through detailed initial rate and progress curve analysis, even when other classical conditions for such equivalence are not entirely fulfilled.
廖飞; 杨晓; 周岐新; 曾昭淳; 左渝萍
2003-01-01
Objective: To investigate the reliability for fast estimation of Michaelis-Menten constant (Km) with calibrated specific activity at only two medium concentrations of substrate by both simulation and experimentation with arylesterase (ArE)as model. Methods: Initial rates were simulated by randomly inserting uniform absolute error, and the experimental initial rates of ArE were determined by measuring the increaser of product absorbance. Calibrated specific activities at two substrate concentrations were obtained by regression analysis, and Km was calculated according to Michaelis-Menten equation. Results: By simulation with calibrated specific activities at two medium substrate concentrations, Km could be calculated according to Michaelis-Menten equation with reasonable precision and accuracy. By experimentation with substrates of 2-naphthyl acetate, phenyl acetate, and p-nitrophenyl acetate, there were no differences between the mean and SD of Km of ArE for either substrate by this linear kinetic method and the Lineweaver-Burk plot. Conclusion: This linear kinetic method was reliable for fast estimation of the Km of some specified enzyme on its substrate of lower solubility or lower sensitivity for quantification by common methods.
About and beyond the Henri-Michaelis-Menten rate equation for single-substrate enzyme kinetics.
Bajzer, Zeljko; Strehler, Emanuel E
2012-01-20
For more than a century the simple single-substrate enzyme kinetics model and related Henri-Michaelis-Menten (HMM) rate equation have been thoroughly explored in various directions. In the present paper we are concerned with a possible generalization of this rate equation recently proposed by F. Kargi (BBRC 382 (2009) 157-159), which is assumed to be valid both in the case that the total substrate or enzyme is in excess and the quasi-steady-state is achieved. We demonstrate that this generalization is grossly inadequate and propose another generalization based on application of the quasi-steady-state condition and conservation equations for both enzyme and substrate. The standard HMM equation is derived by (a) assuming the quasi-steady-state condition, (b) applying the conservation equation only for the enzyme, and (c) assuming that the substrate concentration at quasi-steady-state can be approximated by the total substrate concentration [S](0). In our formula the rate is already expressed through [S](0), and we only assume that when quasi-steady-state is achieved the amount of product formed is negligible compared to [S](0). Numerical simulations show that our formula is generally more accurate than the HMM formula and also can provide a good approximation when the enzyme is in excess, which is not the case for the HMM formula. We show that the HMM formula can be derived from our expression by further assuming that the total enzyme concentration is negligible compared to [S](0). Copyright © 2011 Elsevier Inc. All rights reserved.
Biphasic character of ribosomal translocation and non-Michaelis-Menten kinetics of translation.
Xie, Ping
2014-12-01
We study theoretically the kinetics of mRNA translocation in the wild-type (WT) Escherichia coli ribosome, which is composed of a small 30S and large 50S subunit, and the ribosomes with mutations to some intersubunit bridges such as B1a, B4, B7a, and B8. The theoretical results reproduce well the available in vitro experimental data on the biphasic kinetics of the forward mRNA translocation catalyzed by elongation factor G (EF-G) hydrolyzing GTP, which can be best fit by the sum of two exponentials, and the monophasic kinetics of the spontaneous reverse mRNA translocation in the absence of the elongation factor, which can be best fit by a single-exponential function, in both the WT and mutant ribosomes. We show that both the mutation-induced increase in the maximal rate of the slow phase for the forward mRNA translocation and that in the rate of the spontaneous reverse mRNA translocation result from a reduction in the intrinsic energy barrier to resist the rotational movements between the two subunits, giving the same degree of increase in the two rates. The mutation-induced increase in the maximal rate of the fast phase for the forward mRNA translocation results mainly from the increase in the rate of the ribosomal unlocking, a conformational change in the ribosome that widens the mRNA channel for the mRNA translocation to take place, which could be partly due to the effect of the mutation on the intrasubunit 30S head rotation. Moreover, we study the translation rate of the WT and mutant ribosomes. It is shown that the translation rate versus the concentration of EF-G-GTP does not follow the Michaelis-Menten (MM) kinetics, which is in sharp contrast to the general property of other enzymes that the rate of the enzymatic reaction versus the concentration of a substrate follows the MM kinetics. The physical origin of this non-MM kinetics for the ribosome is revealed.
Hum, Ryan J; Jha, Prabhat; McGahan, Anita M; Cheng, Yu-Ling
2012-12-13
Life expectancy has risen sharply in the last 50 years. We applied the classic Michaelis-Menten enzyme kinetics to demonstrate a novel mathematical relationship of income to childhood (aged 0-5 years) and adult (aged 15-60 years) survival. We treat income as a substrate that is catalyzed to increase survival (from technologies that income buys) for 180 countries from 1970 and 2007. Michaelis-Menten kinetics permit estimates of maximal survival and, uniquely, the critical income needed to achieve half of the period-specific maximum. Maximum child and adult survival rose by about 1% per year. Critical incomes fell by half for children, but doubled for men. HIV infection and smoking account for some, but not all, of the rising critical incomes for adult survival. Altering the future cost curve for adult survival will require more widespread use of current interventions, most notably tobacco control, but also research to identify practicable low-cost drugs, diagnostics, and strategies.DOI:http://dx.doi.org/10.7554/eLife.00051.001.
André Rosa Martins
2014-11-01
Full Text Available The enzymatic processes according Michaelis-Menten kinetics have been studied from various approaches to describe the inhibition state. Proposals for inhibition were compared from a generic process, where kinetic constants have received unitary values, and the numeric value of the concentration of substrate was ten (10 times higher than the numerical value of the concentration of enzyme. For each inhibition model proposed, numerical solutions were obtained from nonlinear system of ordinary differential equations, generating results presents by graphs showing the variation of the enzyme and enzyme complexes, also the variation of substrate and product of the reaction. Also, was designed a model with performance, indicating similar behavior to that seen in the Michaelis-Menten kinetics, where complex of reaction is rapidly formed and throughout the process, tends to decay to zero. Thus, in this new proposed model, the effect of inhibition starts at zero and, throughout the process, tends to the nominal value of the initial enzyme concentration. Such responses have proved to be valid for different values of enzyme concentration and process time, showing robustness. The proposed model was applied to the hydrolysis of disaccharides, providing a setting with conservation of mass of the model at the end of the process regarding the responses of the carbohydrate concentration.
Pulkkinen, O
2016-01-01
Many chemical reactions in biological cells occur at very low concentrations of constituent molecules. Thus, transcriptional gene-regulation is often controlled by poorly expressed transcription-factors, such as E.coli lac repressor with few tens of copies. Here we study the effects of inherent concentration fluctuations of substrate-molecules on the seminal Michaelis-Menten scheme of biochemical reactions. We present a universal correction to the Michaelis-Menten equation for the reaction-rates. The relevance and validity of this correction for enzymatic reactions and intracellular gene-regulation is demonstrated. Our analytical theory and simulation results confirm that the proposed variance-corrected Michaelis-Menten equation predicts the rate of reactions with remarkable accuracy even in the presence of large non-equilibrium concentration fluctuations. The major advantage of our approach is that it involves only the mean and variance of the substrate-molecule concentration. Our theory is therefore accessi...
Padayachee, Letrisha; Pillay, Ché S
2016-07-01
The thioredoxin system, consisting of thioredoxin reductase, thioredoxin and NADPH, is present in most living organisms and reduces a large array of target protein disulfides. The insulin reduction assay is commonly used to characterise thioredoxin activity in vitro, but it is not clear whether substrate saturation datasets from this assay should be fitted and modeled with the Michaelis-Menten equation (thioredoxin enzyme model), or fitted to the thioredoxin system with insulin reduction described by mass-action kinetics (redox couple model). We utilized computational modeling and in vitro assays to determine which of these approaches yield consistent and accurate kinetic parameter sets for insulin reduction. Using computational modeling, we found that fitting to the redox couple model, rather than to the thioredoxin enzyme model, resulted in consistent parameter sets over a range of thioredoxin reductase concentrations. Furthermore, we established that substrate saturation in this assay was due to the progressive redistribution of the thioredoxin moiety into its oxidised form. We then confirmed these results in vitro using the yeast thioredoxin system. This study shows how consistent parameter sets for thioredoxin activity can be obtained regardless of the thioredoxin reductase concentration used in the insulin reduction assay, and validates computational systems biology modeling studies that have described the thioredoxin system with the redox couple modeling approach.
Bezerra, Rui M F; Dias, Albino A
2004-03-01
The kinetics of exoglucanase (Cel7A) from Trichoderma reesei was investigated in the presence of cellobiose and 24 different enzyme/Avicel ratios for 47 h, in order to establish which of the eight available kinetic models best explained the factors involved. The heterogeneous catalysis was studied and the kinetic parameters were estimated employing integrated forms of Michaelis-Menten equations through the use of nonlinear least squares. It was found that cellulose hydrolysis follows a model that takes into account competitive inhibition by cellobiose (final product) with the following parameters: Km = 3.8 mM, Kic = 0.041 mM, kcat = 2 h-1 (5.6 x 10-4 s-1). Other models, such as mixed type inhibition and those incorporating improvements concerning inhibition by substrate and parabolic inhibition, increased the modulation performance very slightly. The results support the hypothesis that nonproductive enzyme substrate complexes, parabolic inhibition, and enzyme inactivation (Selwyn test) are not the principal constraints in enzymatic cellulose hydrolysis. Under our conditions, the increment in hydrolysis was not significant for substrate/enzyme ratios <6.5.
Longatte, Guillaume; Guille-Collignon, Manon; Lemaître, Frédéric
2017-06-15
In the past years, many strategies have been implemented to benefit from oxygenic photosynthesis to harvest photosynthetic electrons and produce a significant photocurrent. Therefore, electrochemical tools were considered and have globally relied on the electron transfer(s) between the photosynthetic chain and a collecting electrode. In this context, we recently reported the implementation of an electrochemical set-up at the preparative scale to produce photocurrents from a Chlamydomonas reinhardtii algae suspension with an appropriate mediator (2,6-DCBQ) and a carbon gauze as the working electrode. In the present work, we wish to describe a mathematical modeling of the recorded photocurrents to better understand the effects of the experimental conditions on the photosynthetic extraction of electrons. In that way, we established a general model of an electrocatalytic mechanism at the preparative scale (that is, assuming a homogenous bulk solution at any time and a constant diffusion layer, both assumptions being valid under forced convection) in which the chemical step involves a Michaelis-Menten-like behaviour. Dependences of transient and steady-state corresponding currents were analysed as a function of different parameters by means of zone diagrams. This model was tested to our experimental data related to photosynthesis. The corresponding results suggest that competitive pathways beyond photosynthetic harvesting alone should be taken into account. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.
Lu, Jian; Dong, Yuxia; Ng, Emily C; Siehl, Daniel L
2017-05-01
One of applications of directed evolution is to desensitize an enzyme to an inhibitor. kcat,1/KM and KI are three dimensions that when multiplied measure an enzyme's intrinsic capacity for catalysis in the presence of an inhibitor. The ideal values for the individual dimensions depend on substrate and inhibitor concentrations under the conditions of the application. When attempting to optimize those values by directed evolution, (kcat/KM)*KI can be an informative parameter for evaluating libraries of variants, but throughput is limited. We describe a manipulation of the Michaelis-Menten equation for competitive inhibition that isolates (kcat/KM)*KI on one side of the equation. If velocity is measured at constant enzyme and substrate concentrations with two different inhibitor concentrations (one of which can be 0), the data are sufficient to calculate (kcat/KM)*KI with just two rate measurements. The procedure is validated by correlating values obtained by the rapid method with those obtained by substrate saturation kinetics. © The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.
Garneau-Tsodikova, Sylvie; Shkel, Irina A; Tsodikov, Oleg V
2009-04-15
Most enzyme kinetic experiments are carried out under pseudo-first-order conditions, that is, when one of the reactant species (the enzyme or the substrate) is in a large excess of the other species. More accurate kinetic information about the system can be gained without the restrictions of the pseudo-first-order conditions. We present a practical and general method of analysis of the common two-step rapid equilibrium Michaelis-Menten mechanism. The formalism is exact in that it does not involve any other approximations such as the steady-state, limitations on the reactant concentrations or on reaction times. We apply this method to the global analysis of kinetic progress curves for bovine alkaline phosphatase assays carried out under both pseudo-first-order and pseudo-second-order conditions.
Sudhamalla, Babu; Kumar, Mahesh; Roy, Karnati R; Kumar, R Sunil; Bhuyan, Abani K
2013-11-01
It is known that tandem domains of enzymes can carry out catalysis independently or by collaboration. In the case of cysteine proteases, domain sequestration abolishes catalysis because the active site residues are distributed in both domains. The validity of this argument is tested here by using isolated human ribosomal protein S4, which has been recently identified as an unorthodox cysteine protease. Cleavage of the peptide substrate Z-FR↓-AMC catalyzed by recombinant C-terminal domain of human S4 (CHS4) is studied by fluorescence-monitored steady-state and stopped-flow kinetic methods. Proteolysis and autoproteolysis were analyzed by electrophoresis. The CHS4 domain comprised of sequence residues 116-263 has been cloned and ovreexpressed in Escherichia coli. The purified domain is enzymatically active. Barring minor differences, steady-state kinetic parameters for catalysis by CHS4 are very similar to those for full-length human S4. Further, stopped-flow transient kinetics of pre-steady-state substrate binding shows that the catalytic mechanism for both full-length S4 and CHS4 obeys the Michaelis-Menten model adequately. Consideration of the evolutionary domain organization of the S4e family of ribosomal proteins indicates that the central domain (residues 94-170) within CHS4 is indispensable. The C-terminal domain can carry out catalysis independently and as efficiently as the full-length human S4 does. Localization of the enzyme function in the C-terminal domain of human S4 provides the only example of a cysteine endoprotease where substrate-mediated intramolecular domain interaction is irrelevant for catalytic activity. Copyright © 2013 Elsevier B.V. All rights reserved.
The integrated Michaelis-Menten rate equation: déjà vu or vu jàdé?
Goličnik, Marko
2013-08-01
A recent article of Johnson and Goody (Biochemistry, 2011;50:8264-8269) described the almost-100-years-old paper of Michaelis and Menten. Johnson and Goody translated this classic article and presented the historical perspective to one of incipient enzyme-reaction data analysis, including a pioneering global fit of the integrated rate equation in its implicit form to the experimental time-course data. They reanalyzed these data, although only numerical techniques were used to solve the model equations. However, there is also the still little known algebraic rate-integration equation in a closed form that enables direct fitting of the data. Therefore, in this commentary, I briefly present the integral solution of the Michaelis-Menten rate equation, which has been largely overlooked for three decades. This solution is expressed in terms of the Lambert W function, and I demonstrate here its use for global nonlinear regression curve fitting, as carried out with the original time-course dataset of Michaelis and Menten.
Verlindo de Araujo, Bibiana; Farias da Silva, Cristófer; Costa, Teresa Dalla
2010-01-01
the determination of oral bioavailability of drugs which follow nonlinear pharmacokinetics is difficult and few methods are available. In this work, an alternative approach to determine oral bioavailability of voriconazole (VRC), used as a model drug, is presented. VRC pharmacokinetics was investigated in Wistar rats after p.o. (40 mg/kg) and i.v. administration (2.5, 5 and 10 mg/kg). VRC elimination showed saturation in all doses investigated, except the lower i.v. dose in which case a 3-compartment model with linear elimination adequately fitted the data. Data for the 2 higher i.v. doses were best described by a 3-compartment model with Michaelis-Menten elimination. A 1-compartment disposition with a saturable metabolic elimination model described the oral profile. VRC absolute oral bioavailability was determined by simultaneous fitting of the i.v. and oral profiles. the Michaelis constant and the maximum velocity estimated after 5 and 10 mg/kg i.v. dosing were 0.54 +/- 0.25 microg/ml and 2.53 +/- 0.54 microg/h, and 0.62 +/- 0.12 microg/ml and 2.74 +/- 0.84 microg/h, respectively. VRC oral bioavailability was determined to be 82.8%. the approach presented is an alternative for determining the bioavailability of drugs with similar nonlinear behavior. 2010 S. Karger AG, Basel.
Lee, Byung-Yo; Kwon, Kwang-Il; Kim, Min-Soo; Baek, In-Hwan
2016-08-01
Etanercept was approved by the Food and Drug Administration (FDA) in 2010 as a biologic agent for the treatment of rheumatoid arthritis (RA). The aim of the study was to investigate the pharmacokinetic properties of etanercept after intravenous and subcutaneous injection in rats. The plasma concentration of etanercept was determined using an enzyme-linked immunosorbent assay (ELISA). Intravenous and subcutaneous administration of 2 mg/kg of etanercept to rats showed that etanercept was slowly absorbed (time to reach the peak drug concentration [T max] = 1.60 days, bioavailability [F] = 47.18 %) and slowly eliminated (half-life [t 1/2], 2.33 days after intravenous administration and 3.31 days after subcutaneous administration). The area under the curve values on day 13 (AUC13day) were 121.25 ± 14.37 and 48.56 ± 6.78 μg day/mL after intravenous and subcutaneous administration, respectively. A two-compartment model with Michaelis-Menten elimination kinetics (V max = 94.28 µg/day; K m = 10.88 µg/mL) was used to describe the pharmacokinetic profile of etanercept. Our results describe the pharmacokinetic profile of etanercept, and these results could be used for the development of etanercept biosimilars.
Liu, Ai-Lin; Zhou, Ting; He, Feng-Yun; Xu, Jing-Juan; Lu, Yu; Chen, Hong-Yuan; Xia, Xing-Hua
2006-06-01
We firstly transformed the traditional Michaelis-Menten equation into an off-line form which can be used for evaluating the Michaelis-Menten constant after the enzymatic reaction. For experimental estimation of the kinetics of enzymatic reactions, we have developed a facile and effective method by integrating an enzyme microreactor into direct-printing polymer microchips. Strong nonspecific adsorption of proteins was utilized to effectively immobilize enzymes onto the microchannel wall, forming the integrated on-column enzyme microreactor in a microchip. The properties of the integrated enzyme microreactor were evaluated by using the enzymatic reaction of glucose oxidase (GOx) with its substrate glucose as a model system. The reaction product, hydrogen peroxide, was electrochemically (EC) analyzed using a Pt microelectrode. The data for enzyme kinetics using our off-line form of the Michaelis-Menten equation was obtained (K(m) = 2.64 mM), which is much smaller than that reported in solution (K(m) = 6.0 mM). Due to the hydrophobic property and the native mesoscopic structure of the poly(ethylene terephthalate) film, the immobilized enzyme in the microreactor shows good stability and bioactivity under the flowing conditions.
Pereira, Félix Monteiro; Oliveira, Samuel Conceição
2016-11-01
In this article, the occurrence of dead core in catalytic particles containing immobilized enzymes is analyzed for the Michaelis-Menten kinetics. An assessment of numerical methods is performed to solve the boundary value problem generated by the mathematical modeling of diffusion and reaction processes under steady state and isothermal conditions. Two classes of numerical methods were employed: shooting and collocation. The shooting method used the ode function from Scilab software. The collocation methods included: that implemented by the bvode function of Scilab, the orthogonal collocation, and the orthogonal collocation on finite elements. The methods were validated for simplified forms of the Michaelis-Menten equation (zero-order and first-order kinetics), for which analytical solutions are available. Among the methods covered in this article, the orthogonal collocation on finite elements proved to be the most robust and efficient method to solve the boundary value problem concerning Michaelis-Menten kinetics. For this enzyme kinetics, it was found that the dead core can occur when verified certain conditions of diffusion-reaction within the catalytic particle. The application of the concepts and methods presented in this study will allow for a more generalized analysis and more accurate designs of heterogeneous enzymatic reactors.
Pulkkinen, Otto; Metzler, Ralf
2015-12-04
Many chemical reactions in biological cells occur at very low concentrations of constituent molecules. Thus, transcriptional gene-regulation is often controlled by poorly expressed transcription-factors, such as E.coli lac repressor with few tens of copies. Here we study the effects of inherent concentration fluctuations of substrate-molecules on the seminal Michaelis-Menten scheme of biochemical reactions. We present a universal correction to the Michaelis-Menten equation for the reaction-rates. The relevance and validity of this correction for enzymatic reactions and intracellular gene-regulation is demonstrated. Our analytical theory and simulation results confirm that the proposed variance-corrected Michaelis-Menten equation predicts the rate of reactions with remarkable accuracy even in the presence of large non-equilibrium concentration fluctuations. The major advantage of our approach is that it involves only the mean and variance of the substrate-molecule concentration. Our theory is therefore accessible to experiments and not specific to the exact source of the concentration fluctuations.
Choi, I Y; Lee, S P; Kim, S G; Gruetter, R
2001-06-01
Glucose is the major substrate that sustains normal brain function. When the brain glucose concentration approaches zero, glucose transport across the blood-brain barrier becomes rate limiting for metabolism during, for example, increased metabolic activity and hypoglycemia. Steady-state brain glucose concentrations in alpha-chloralose anesthetized rats were measured noninvasively as a function of plasma glucose. The relation between brain and plasma glucose was linear at 4.5 to 30 mmol/L plasma glucose, which is consistent with the reversible Michaelis-Menten model. When the model was fitted to the brain glucose measurements, the apparent Michaelis-Menten constant, Kt, was 3.3 +/- 1.0 mmol/L, and the ratio of the maximal transport rate relative to CMRglc, Tmax/CMRglc, was 2.7 +/- 0.1. This Kt is comparable to the authors' previous human data, suggesting that glucose transport kinetics in humans and rats are similar. Cerebral blood flow (CBF) was simultaneously assessed and constant above 2 mmol/L plasma glucose at 73 +/- 6 mL 100 g(-1) min(-1). Extrapolation of the reversible Michaelis-Menten model to hypoglycemia correctly predicted the plasma glucose concentration (2.1 +/- 0.6 mmol/L) at which brain glucose concentrations approached zero. At this point, CBF increased sharply by 57% +/- 22%, suggesting that brain glucose concentration is the signal that triggers defense mechanisms aimed at improving glucose delivery to the brain during hypoglycemia.
Utilization of Integrated Michaelis-Menten Equation to Determine Kinetic Constants
Bezerra, Rui M. F.; Dias, Albino A.
2007-01-01
Students of biochemistry and related biosciences are urged to solve problems where kinetic parameters are calculated from initial rates obtained at different substrate concentrations. Troubles begin when they go to the laboratory to perform kinetic experiments and realize that usual laboratory instruments do not measure initial rates but only…
Utilization of Integrated Michaelis-Menten Equation to Determine Kinetic Constants
Bezerra, Rui M. F.; Dias, Albino A.
2007-01-01
Students of biochemistry and related biosciences are urged to solve problems where kinetic parameters are calculated from initial rates obtained at different substrate concentrations. Troubles begin when they go to the laboratory to perform kinetic experiments and realize that usual laboratory instruments do not measure initial rates but only…
Leonard, Erin M; Marentette, Julie R; Balshine, Sigal; Wood, Chris M
2014-03-01
Traditionally, water quality guidelines/criteria are based on lethality tests where results are expressed as a function of waterborne concentrations (e.g. LC50). However, there is growing interest in the use of uptake and binding relationships, such as biotic ligand models (BLM), and in bioaccumulation parameters, such as critical body residue values (e.g. CBR50), to predict metal toxicity in aquatic organisms. Nevertheless, all these approaches only protect species against physiological death (e.g. mortality, failed recruitment), and do not consider ecological death which can occur at much lower concentrations when the animal cannot perform normal behaviours essential for survival. Therefore, we investigated acute (96 h) Ni toxicity in two freshwater fish species, the round goby (Neogobius melanostomus) and rainbow trout (Oncorhynchus mykiss) and compared LC, BLM, and CBR parameters for various organs, as well as behavioural responses (spontaneous activity). In general, round goby were more sensitive. Ni bioaccumulation displayed Michaelis-Menten kinetics in most tissues, and round goby gills had lower Kd (higher binding affinity) but similar Bmax (binding site density) values relative to rainbow trout gills. Round goby also accumulated more Ni than did trout in most tissues at a given exposure concentration. Organ-specific 96 h acute CBR values tended to be higher in round goby but 96 h acute CBR50 and CBR10 values in the gills were very similar in the two species. In contrast, LC50 and LC10 values were significantly higher in rainbow trout. With respect to BLM parameters, gill log KNiBL values for bioaccumulation were higher by 0.4-0.8 log units than the log KNiBL values for toxicity in both species, and both values were higher in goby (more sensitive). Round goby were also more sensitive with respect to the behavioural response, exhibiting a significant decline of 63-75 % in movements per minute at Ni concentrations at and above only 8 % of the LC50 value
The Impact of Deviation from Michaelis-Menten Saturation on Mathematical Model Stability Properties
Blackwell, Charles; Kliss, Mark (Technical Monitor)
1998-01-01
Based on purely abstract ecological theory, it has been argued that a system composed of two or more consumers competing for the same resource cannot persist. By analysis on a Monod format mathematical model, Hubble and others demonstrated that this assertion is true for all but very special cases of such competing organisms which are determined by an index formed by a grouping of. the parameters which characterize the biological processes of the competing organisms. In the laboratory, using a bioreactor, Hansen and Hubble obtained confirmatory results for several cases of two competing species, and they characterized it as "qualitative confirmation" of the assertion. This result is amazing, since the analysis required the exact equality of the hey index, and it seems certain that no pair of organism species could have exactly equal values. It is quite plausible, however, that pairs of organism species could have approximately equal indices, and the question of how different they could be and still have coexistence of the two (or more) presents itself. In this paper, the pursuit of this question and a compatible resolution is presented.
Mafrica, Stefano; Godiot, Stéphanie; Menouni, Mohsine; Boyron, Marc; Expert, Fabien; Juston, Raphaël; Marchand, Nicolas; Ruffier, Franck; Viollet, Stéphane
2015-03-09
In this paper, we present: (i) a novel analog silicon retina featuring auto-adaptive pixels that obey the Michaelis-Menten law, i.e. V=V(m) I(n)/I(n)+σ(n); (ii) a method of characterizing silicon retinas, which makes it possible to accurately assess the pixels' response to transient luminous changes in a ±3-decade range, as well as changes in the initial steady-state intensity in a 7-decade range. The novel pixel, called M(2)APix, which stands for Michaelis-Menten Auto-Adaptive Pixel, can auto-adapt in a 7-decade range and responds appropriately to step changes up to ±3 decades in size without causing any saturation of the Very Large Scale Integration (VLSI) transistors. Thanks to the intrinsic properties of the Michaelis-Menten equation, the pixel output always remains within a constant limited voltage range. The range of the Analog to Digital Converter (ADC) was therefore adjusted so as to obtain a Least Significant Bit (LSB) voltage of 2.35mV and an effective resolution of about 9 bits. The results presented here show that the M(2)APix produced a quasi-linear contrast response once it had adapted to the average luminosity. Differently to what occurs in its biological counterparts, neither the sensitivity to changes in light nor the contrast response of the M(2)APix depend on the mean luminosity (i.e. the ambient lighting conditions). Lastly, a full comparison between the M(2)APix and the Delbrück auto-adaptive pixel is provided.
Goličnik, Marko
2011-09-01
The exact closed-form solutions to the integrated rate equations for one-compartment pharmacokinetic models that obey Michaelis-Menten elimination kinetics were derived recently (Tang and Xiao in J Pharmacokin Pharmacodyn 34:807-827, 2007). These solutions are expressed in terms of the Lambert W(x)-omega function; however, unfortunately, most of the available computer programs are not set up to handle equations that involve the W(x) function. Therefore, in this article, I provide alternative explicit analytical equations expressed in terms of elementary mathematical functions that accurately approximate exact solutions and can be simply calculated using any optional standard software.
Yunxian Dai; Yiping Lin; Huitao Zhao
2014-01-01
We consider a predator-prey system with Michaelis-Menten type functional response and two delays. We focus on the case with two unequal and non-zero delays present in the model, study the local stability of the equilibria and the existence of Hopf bifurcation, and then obtain explicit formulas to determine the properties of Hopf bifurcation by using the normal form method and center manifold theorem. Special attention is paid to the global continuation of local Hopf bifurcation when the delay...
Bezerra, Rui M F; Pinto, Paula A; Fraga, Irene; Dias, Albino A
2016-03-01
To determine initial velocities of enzyme catalyzed reactions without theoretical errors it is necessary to consider the use of the integrated Michaelis-Menten equation. When the reaction product is an inhibitor, this approach is particularly important. Nevertheless, kinetic studies usually involved the evaluation of other inhibitors beyond the reaction product. The occurrence of these situations emphasizes the importance of extending the integrated Michaelis-Menten equation, assuming the simultaneous presence of more than one inhibitor because reaction product is always present. This methodology is illustrated with the reaction catalyzed by alkaline phosphatase inhibited by phosphate (reaction product, inhibitor 1) and urea (inhibitor 2). The approach is explained in a step by step manner using an Excel spreadsheet (available as a template in Appendix). Curve fitting by nonlinear regression was performed with the Solver add-in (Microsoft Office Excel). Discrimination of the kinetic models was carried out based on Akaike information criterion. This work presents a methodology that can be used to develop an automated process, to discriminate in real time the inhibition type and kinetic constants as data (product vs. time) are achieved by the spectrophotometer. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.
Dutta, Annwesha; Chowdhury, Debashish
2017-05-01
The sequence of amino acid monomers in the primary structure of a protein is decided by the corresponding sequence of codons (triplets of nucleic acid monomers) on the template messenger RNA (mRNA). The polymerization of a protein, by incorporation of the successive amino acid monomers, is carried out by a molecular machine called ribosome. We develop a stochastic kinetic model that captures the possibilities of mis-reading of mRNA codon and prior mis-charging of a tRNA. By a combination of analytical and numerical methods, we obtain the distribution of the times taken for incorporation of the successive amino acids in the growing protein in this mathematical model. The corresponding exact analytical expression for the average rate of elongation of a nascent protein is a 'biologically motivated' generalization of the Michaelis-Menten formula for the average rate of enzymatic reactions. This generalized Michaelis-Menten-like formula (and the exact analytical expressions for a few other quantities) that we report here display the interplay of four different branched pathways corresponding to selection of four different types of tRNA.
Bosquet, Laurent; Duchene, Antoine; Lecot, François; Dupont, Grégory; Leger, Luc
2006-05-01
The purpose of this study was to evaluate the validity of maximal velocity (Vmax) estimated from three-parameter systems models, and to compare the predictive value of two- and three-parameter models for the 800 m. Seventeen trained male subjects (VO2max=66.54+/-7.29 ml min(-1) kg(-1)) performed five randomly ordered constant velocity tests (CVT), a maximal velocity test (mean velocity over the last 10 m portion of a 40 m sprint) and a 800 m time trial (V 800 m). Five systems models (two three-parameter and three two-parameter) were used to compute V max (three-parameter models), critical velocity (CV), anaerobic running capacity (ARC) and V800m from times to exhaustion during CVT. Vmax estimates were significantly lower than (0.19Critical velocity (CV) alone explained 40-62% of the variance in V800m. Combining CV with other parameters of each model to produce a calculated V800m resulted in a clear improvement of this relationship (0.83
Machado, Eustáquio José
2014-01-01
A equação hiperbólica, conhecida no contexto bioquímico como o modelo de Michaelis-Menten, é utilizada para descrever a velocidade de reações químicas envolvendo enzimas (cinética enzimática). Este estudo teve como objetivo comparar os ajustes do modelo de Michaelis-Menten (1913) que fez uso de dois modelos não-lineares e quatro modelos linearizados. Os dois modelos não-lineares (um utilizou o método clássico assintotico usual e o outro fez uso da abordagem "bootstrap"). Os modelos linearizad...
Moaty Sayed, A A; Hussein, M A; Becker, T
2010-04-01
Lattice Boltzmann models (LBM) are rapidly showing their ability to simulate a lot of fluid dynamics problems that previously required very complex approaches. This study presents a LBM for simulating diffusion-advection transport of substrate in a 2-D laminar flow. The model considers the substrate influx into a set of active cells placed inside the flow field. A new innovative method was used to simulate the cells activity using the LBM by means of Michaelis-Menten kinetics. The model is validated with some numerical benchmark problems and proved highly accurate results. After validation the model was used to simulate the transport of oxygen substrates that diffuse in water to feed a set of active cartilage cells inside a new designed bioreactor.
Coluzzi, Barbara; Bersani, Enrico
2016-01-01
We recall the perturbation expansion for Michaelis-Menten kinetics, beyond the standard quasi-steady-state approximation (sQSSA). Against this background, we are able to appropriately apply the alternative approach to the study of singularly perturbed differential equations that is based on the renormalization group (SPDERG), by clarifying similarities and differences. In the present demanding situation, we directly renormalize the bare initial condition value for the substrate. Our main results are: i) the 2nd order SPDERG uniform approximations to the correct solutions contain, up to 1st order, the same outer components as the known perturbation expansion ones; ii) the differential equation to be solved for the derivation of the 1st order outer substrate component is simpler within the SPDERG approach; iii) the approximations better reproduce the numerical solutions of the original problem in a region encompassing the matching one, because of the 2nd order terms in the inner components, calculated here for ...
Fowler, Stephen; Guerini, Elena; Qiu, NaHong; Cleary, Yumi; Parrott, Neil; Greig, Gerard; Mallalieu, Navita L
2017-01-01
Basimglurant, a novel mGlu5-negative allosteric modulator under development for the treatment of major depressive disorder, is cleared via cytochrome P450 (P450)-mediated oxidative metabolism. Initial enzyme phenotyping studies indicated that CYP3A4/5 dominates basimglurant metabolism and highlights a risk for drug-drug interactions when it is comedicated with strong CYP3A4/5 inhibitors or inactivators; however, a clinical drug-drug interaction (DDI) study using the potent and selective CYP3A4/5 inhibitor ketoconazole resulted in an area under the curve (AUC) AUCi/AUC ratio of only 1.24. A further study using the CYP3A4 inducer carbamazepine resulted in an AUCi/AUC ratio of 0.69. More detailed in vitro enzyme phenotyping and kinetics studies showed that, at the low concentrations attained clinically, basimglurant metabolic clearance is catalyzed mainly by CYP1A2. The relative contributions of the enzymes were estimated as 70:30 CYP1A2:CYP3A4/5. Using this information, a clinical study using the CYP1A2 inhibitor fluvoxamine was performed, resulting in an AUCi/AUC ratio of 1.60, confirming the role of CYP1A2 and indicating a balanced DDI risk profile. Basimglurant metabolism kinetics show enzyme dependency: CYP1A2-mediated metabolism follows Michaelis-Menten kinetics, whereas CYP3A4 and CYP3A5 follow sigmoidal kinetics [with similar constant (KM) and S50 values]. The interplay of the different enzyme kinetics leads to changing fractional enzyme contributions to metabolism with substrate concentration, even though none of the metabolic enzymes is saturated. This example demonstrates the relevance of non-Michaelis-Menten P450 enzyme kinetics and highlights the need for a thorough understanding of metabolism enzymology to make accurate predictions for human metabolism in vivo. Copyright © 2016 by The American Society for Pharmacology and Experimental Therapeutics.
Yusof, Siti R; Abbott, N Joan; Avdeef, Alex
2017-08-30
Most studies of blood-brain barrier (BBB) permeability and transport are conducted at a single pH, but more detailed information can be revealed by using multiple pH values. A pH-dependent biophysical model was applied to the mechanistic analysis of published pH-dependent BBB luminal uptake data from three opioid derivatives in rat: pentazocine (Suzuki et al., 2002a, 2002b), naloxone (Suzuki et al., 2010a), and oxycodone (Okura et al., 2008). Two types of data were processed: in situ brain perfusion (ISBP) and brain uptake index (BUI). The published perfusion data were converted to apparent luminal permeability values, Papp, and analyzed by the pCEL-X program (Yusof et al., 2014), using the pH-dependent Crone-Renkin equation (pH-CRE) to determine the impact of cerebrovascular flow on the Michaelis-Menten transport parameters (Avdeef and Sun, 2011). For oxycodone, the ISBP data had been measured at pH7.4 and 8.4. The present analysis indicates a 7-fold lower value of the cerebrovascular flow velocity, Fpf, than that expected in the original study. From the pyrilamine-inhibited data, the flow-corrected passive intrinsic permeability value was determined to be P0=398×10(-6)cm·s(-1). The uptake data indicate that the neutral form of oxycodone is affected by a transporter at pH8.4. The extent of the cation uptake was less certain from the available data. For pentazocine, the brain uptake by the BUI method had been measured at pH5.5, 6.5, and 7.4, in a concentration range 0.1-40mM. Under similar conditions, ISBP data were also available. The pH-CRE determined values of Fpf from both methods were nearly the same, and were smaller than the expected value in the original publication. The transport of the cationic pentazocine was not fully saturated at pH5.5 at 40mM. The transport of the neutral species at pH7.4 appeared to reach saturation at 40mM pentazocine concentration, but not at 12mM. In the case of naloxone, a pH-dependent Michaelis-Menten equation (p
磁流变阻尼器的米氏模型及试验验证%MICHAELIS-MENTEN MODEL OF MAGNETORHEOLOGICAL DAMPER AND TEST VERIFICATION
张香成; 徐赵东; 王绍安; 沙凌峰
2013-01-01
为研究磁流变阻尼器(MRD)非线性滞回性能的影响因素,建立精确的MRD力学模型,对MRD进行力学性能试验,并基于米氏方程提出一个综合考虑电流、位移和频率影响的力学模型——米氏模型.对所提模型和传统经典力学模型进行数值模拟,并与试验结果进行对比分析,结果表明:该模型可以模拟MRD的非线性滞回性能、体现位移和频率对阻尼力及非线性滞回性能的影响.%To find the effect factors of the nonlinear hysteresis capability of a magnetorheological damper (MRD) and establish a precise mathematical model, a Michaelis-Menten (MM) Model was presented based on the MM equation which considers the effects of current, amplitude and frequency. Numerical simulations of the MM Model and traditional classical mathematic model were carried out to compare with the test results. Comparison results indicate that the MM Model could simulate the hysteresis capability of MRD and reflect the effects of current, amplitude and frequency on damping force and nonlinear hysteresis capability.
André Rosa Martins
2015-01-01
.... One model was obtained, among the evaluated proposals, with performance indicating behavior similar to the classical Michaelis-Menten model, where the reaction complex is rapidly formed and, along...
Gejl, Michael; Rungby, Jørgen; Brock, Birgitte; Gjedde, Albert
2014-08-01
Glucagon-like peptide-1 (GLP-1) is a potent insulinotropic incretin hormone with both pancreatic and extrapancreatic effects. Studies of GLP-1 reveal significant effects in regions of brain tissue that regulate appetite and satiety. GLP-1 mimetics are used for the treatment of type 2 diabetes mellitus. GLP-1 interacts with peripheral functions in which the autonomic nervous system plays an important role, and emerging pre-clinical findings indicate a potential neuroprotective role of the peptide, for example in models of stroke and in neurodegenerative disorders. A century ago, Leonor Michaelis and Maud Menten described the steady-state enzyme kinetics that still apply to the multiple receptors, transporters and enzymes that define the biochemical reactions of the brain, including the glucose-dependent impact of GLP-1 on blood-brain glucose transfer and metabolism. This MiniReview examines the potential of GLP-1 as a molecule of interest for the understanding of brain energy metabolism and with reference to the impact on brain metabolism related to appetite and satiety regulation, stroke and neurodegenerative disorders. These effects can be understood only by reference to the original formulation of the Michaelis-Menten equation as applied to a chain of kinetically controlled steps. Indeed, the effects of GLP-1 receptor activation on blood-brain glucose transfer and brain metabolism of glucose depend on the glucose concentration and relative affinities of the steps both in vitro and in vivo, as in the pancreas. © 2014 Nordic Association for the Publication of BCPT (former Nordic Pharmacological Society).
Igamberdiev, Abir U; Roussel, Marc R
2012-03-01
Rubisco, the most abundant protein serving as the primary engine generating organic biomass on Earth, is characterized by a low catalytic constant (in higher plants approx. 3s(-1)) and low specificity for CO(2) leading to photorespiration. We analyze here why this enzyme evolved as the main carbon fixation engine. The high concentration of Rubisco exceeding the concentration of its substrate CO(2) by 2-3 orders of magnitude makes application of Michaelis-Menten kinetics invalid and requires alternative kinetic approaches to describe photosynthetic CO(2) assimilation. Efficient operation of Rubisco is supported by a strong flux of CO(2) to the chloroplast stroma provided by fast equilibration of bicarbonate and CO(2) and forwarding the latter to Rubisco reaction centers. The main part of this feedforward mechanism is a thylakoidal carbonic anhydrase associated with photosystem II and pumping CO(2) from the thylakoid lumen in coordination with the rate of electron transport, water splitting and proton gradient across the thylakoid membrane. This steady flux of CO(2) limits photosynthesis at saturating CO(2) concentrations. At low ambient CO(2) and correspondingly limited capacity of the bicarbonate pool in the stroma, its depletion at the sites of Rubisco is relieved by utilizing O(2) instead of CO(2), i.e. by photorespiration, a process which supplies CO(2) back to Rubisco and buffers the redox state and energy level in the chloroplast. Thus, the regulation of Rubisco function aims to keep steady non-equilibrium levels of CO(2), NADPH/NADP and ATP/ADP in the chloroplast stroma and to optimize the condition of homeostatic photosynthetic flux of matter and energy. Copyright © 2011 Elsevier Ireland Ltd. All rights reserved.
Yu, Xiao-Zhang; Zhang, Xue-Hong
2016-07-01
Hydroponic experiments were conducted with different species of plants (rice, maize, soybean and willow) exposed to ferri-cyanide to investigate the half-saturation constant (K M ) and the maximal metabolic capacity (v max ) involved in phyto-assimilation. Three varieties for each testing species were collected from different origins. Measured concentrations show that the uptake rates responded biphasically to ferri-cyanide treatments by showing increases linearly at low and almost constant at high concentrations from all treatments, indicating that phyto-assimilation of ferri-cyanide followed the Michaelis-Menten kinetics. Using non-linear regression, the highest v max was by rice, followed by willows. The lowest v max was found for soybean. All plants, except maize (DY26) and rice (XJ12), had a similar K M value, suggesting the same enzyme was active in phyto-assimilation of ferri-cyanide. Transcript level, by real-time quantitative PCR, of enzymes involved in degradation of cyanides showed that the analyzed genes were differently expressed during different cyanides exposure. The expression of CAS and ST genes responded positively to KCN exposure, suggesting that β-CAS and ST pathways were two possible pathways for cyanide detoxification in rice. The transcript level of NIT and ASPNASE genes also showed a remarkable up-regulation to KCN, implying the contribution to the pool of amino acid aspartate, which is an end product of CN metabolism. Up-regulation of GS genes suggests that acquisition of ammonium released from cyanide degradation may be an additional nitrogen source for plant nutrition. Results also revealed that the expressions of these genes, except for GS, were relatively constant during iron cyanide exposure, suggesting that they are likely metabolized by plants through a non-defined pathway rather than the β-CAS pathway.
Blum, Philipp; Hunkeler, Daniel; Weede, Matthias; Beyer, Christof; Grathwohl, Peter; Morasch, Barbara
2009-04-01
At a former wood preservation plant severely contaminated with coal tar oil, in situ bulk attenuation and biodegradation rate constants for several monoaromatic (BTEX) and polyaromatic hydrocarbons (PAH) were determined using (1) classical first order decay models, (2) Michaelis-Menten degradation kinetics (MM), and (3) stable carbon isotopes, for o-xylene and naphthalene. The first order bulk attenuation rate constant for o-xylene was calculated to be 0.0025 d - 1 and a novel stable isotope-based first order model, which also accounted for the respective redox conditions, resulted in a slightly smaller biodegradation rate constant of 0.0019 d - 1 . Based on MM-kinetics, the o-xylene concentration decreased with a maximum rate of kmax = 0.1 µg/L/d. The bulk attenuation rate constant of naphthalene retrieved from the classical first order decay model was 0.0038 d - 1 . The stable isotope-based biodegradation rate constant of 0.0027 d - 1 was smaller in the reduced zone, while residual naphthalene in the oxic part of the plume further downgradient was degraded at a higher rate of 0.0038 d - 1 . With MM-kinetics a maximum degradation rate of kmax = 12 µg/L/d was determined. Although best fits were obtained by MM-kinetics, we consider the carbon stable isotope-based approach more appropriate as it is specific for biodegradation (not overall attenuation) and at the same time accounts for the dominant electron-accepting process. For o-xylene a field based isotope enrichment factor ɛfield of - 1.4 could be determined using the Rayleigh model, which closely matched values from laboratory studies of o-xylene degradation under sulfate-reducing conditions.
Blum, Philipp; Hunkeler, Daniel; Weede, Matthias; Beyer, Christof; Grathwohl, Peter; Morasch, Barbara
2009-04-01
At a former wood preservation plant severely contaminated with coal tar oil, in situ bulk attenuation and biodegradation rate constants for several monoaromatic (BTEX) and polyaromatic hydrocarbons (PAH) were determined using (1) classical first order decay models, (2) Michaelis-Menten degradation kinetics (MM), and (3) stable carbon isotopes, for o-xylene and naphthalene. The first order bulk attenuation rate constant for o-xylene was calculated to be 0.0025 d(-1) and a novel stable isotope-based first order model, which also accounted for the respective redox conditions, resulted in a slightly smaller biodegradation rate constant of 0.0019 d(-1). Based on MM-kinetics, the o-xylene concentration decreased with a maximum rate of k(max)=0.1 microg/L/d. The bulk attenuation rate constant of naphthalene retrieved from the classical first order decay model was 0.0038 d(-1). The stable isotope-based biodegradation rate constant of 0.0027 d(-1) was smaller in the reduced zone, while residual naphthalene in the oxic part of the plume further downgradient was degraded at a higher rate of 0.0038 d(-1). With MM-kinetics a maximum degradation rate of k(max)=12 microg/L/d was determined. Although best fits were obtained by MM-kinetics, we consider the carbon stable isotope-based approach more appropriate as it is specific for biodegradation (not overall attenuation) and at the same time accounts for the dominant electron-accepting process. For o-xylene a field based isotope enrichment factor epsilon(field) of -1.4 could be determined using the Rayleigh model, which closely matched values from laboratory studies of o-xylene degradation under sulfate-reducing conditions.
Button, D K; Robertson, Betsy; Gustafson, Elizabeth; Zhao, Xiaoming
2004-09-01
A theory for solute uptake by whole cells was derived with a focus on the ability of oligobacteria to sequester nutrients. It provided a general relationship that was used to obtain the kinetic constants for in situ marine populations in the presence of naturally occurring substrates. In situ affinities of 0.9 to 400 liters g of cells(-1) h(-1) found were up to 10(3) times smaller than those from a "Marinobacter arcticus " isolate, but springtime values were greatly increased by warming. Affinities of the isolate for usual polar substrates but not for hydrocarbons were diminished by ionophores. A kinetic curve or Monod plot was constructed from the best available data for cytoarchitectural components of the isolate by using the theory together with concepts and calculations from first principles. The order of effect of these components on specific affinity was membrane potential > cytoplasmic enzyme concentration > cytoplasmic enzyme affinity > permease concentration > area of the permease site > translation coefficient > porin concentration. Component balance was influential as well; a small increase in cytoplasmic enzyme concentration gave a large increase in the effect of permease concentration. The effect of permease concentration on specific affinity was large, while the effect on K(m) was small. These results are in contrast to the Michaelis-Menten theory as applied by Monod that has uptake kinetics dependent on the quality of the permease molecules, with K(m) as an independent measure of affinity. Calculations demonstrated that most oligobacteria in the environment must use multiple substrates simultaneously to attain sufficient energy and material for growth, a requirement consistent with communities largely comprising few species.
Huang, Hsuan-Ming; Ismail-Beigi, Faramarz; Muzic, Raymond F
2011-08-01
A new model is introduced that individually resolves the delivery, transport, and phosphorylation steps of metabolism of glucose and its analogs in skeletal muscle by interpreting dynamic positron emission tomography (PET) data. The model uniquely utilizes information obtained from the competition between glucose and its radiolabeled analogs. Importantly, the model avoids use of a lumped constant which may depend on physiological state. Four basic physiologic quantities constitute our model parameters, including the fraction of total tissue space occupied by interstitial space (f(IS)), a flow-extraction product and interstitial (IS(g)) and intracellular (IC(g)) glucose concentrations. Using the values of these parameters, cellular influx (CI) and efflux (CE) of glucose, glucose phosphorylation rate (PR), and maximal transport (V(G)) and phosphorylation capacities (V(H)) can all be determined. Herein, the theoretical derivation of our model is addressed and characterizes its properties via simulation. Specifically, the model performance is evaluated by simulation of basal and euglycemic hyperinsulinemic (EH) conditions. In fitting the model-generated, synthetic data (including noise), mean estimates of all but IC(g) of the parameter values are within 5% of their values for both conditions. In addition, mean errors of CI, PR, and V(G) are less than 5% whereas those of VH and CE are not. It is concluded that under the conditions tested, the novel model can provide accurate parameter estimates and physiological quantities, except IC(g) and two quantities that are dependent on IC(g), namely CE and VH. However, the ability to estimate IC(g) seems to improve with increases in intracellular glucose concentrations as evidenced by comparing IC(g) estimates under basal vs EH conditions.
Khataee A. R.; Pourhassan M.; Ayazloo M.
2009-01-01
In recent years, the ability of microorganisms to decolorize textile wastewater has received great attention due to the environmental persistence and toxicity of these pollutants. In this paper biological decolorization of triphenylmethane dye, C.I. Basic Green 4 (BG 4), by Chlorella species was investigated. The effect of operational parameters (temperature, pH, initial dye concentration and algal concentration) on decolorization efficiency was examined. Results indicated that the desired initial pH was 9. The stability and efficiency of the algae in long-term repetitive operations were also examined. Michaelis-Menten kinetics was employed to describe the apparent correlation between the decolorization rate and dye concentration. The optimal kinetic parameters, Vmax (specific decolorization rate) and Km (maximum specific decolorization rate) were 4.6 mg dye g cell-1 h-1and 151.0 mg L-1, respectively. Fig 10, Tab 2, Ref24
Long, Cormac G; Gilbertson, John D; Vijayaraghavan, Ganesh; Stevenson, Keith J; Pursell, Christopher J; Chandler, Bert D
2008-08-06
Thiol monolayer-protected Au clusters (MPCs) were prepared using dendrimer templates, deposited onto a high-surface-area titania, and then the thiol stabilizers were removed under H2/N2. The resulting Au catalysts were characterized with transmission electron microscopy, X-ray photoelectron spectroscopy, and infrared spectroscopy of adsorbed CO. The Au catalysts prepared via this route displayed minimal particle agglomeration during the deposition and activation steps. Structural data obtained from the physical characterization of the Au catalysts were comparable to features exhibited from a traditionally prepared standard Au catalyst obtained from the World Gold Council (WGC). A differential kinetic study of CO oxidation catalysis by the MPC-prepared Au and the standard WGC catalyst showed that these two catalyst systems have essentially the same reaction order and Arrhenius apparent activation energies (28 kJ/mol). However, the MPC-prepared Au catalyst shows 50% greater activity for CO oxidation. Using a Michaelis-Menten approach, the oxygen binding constants for the two catalyst systems were determined and found to be essentially the same within experimental error. To our knowledge, this kinetic evaluation is the first experimental determination of oxygen binding by supported Au nanoparticle catalysts under working conditions. The values for the oxygen binding equilibrium constant obtained from the Michaelis-Menten treatment (ca. 29-39) are consistent with ultra-high-vacuum measurements on model catalyst systems and support density functional theory calculations for oxygen binding at corner or edge atoms on Au nanoparticles and clusters.
Parameter estimation for models of ligninolytic and cellulolytic enzyme kinetics
Wang, Gangsheng [ORNL; Post, Wilfred M [ORNL; Mayes, Melanie [ORNL; Frerichs, Joshua T [ORNL; Jagadamma, Sindhu [ORNL
2012-01-01
While soil enzymes have been explicitly included in the soil organic carbon (SOC) decomposition models, there is a serious lack of suitable data for model parameterization. This study provides well-documented enzymatic parameters for application in enzyme-driven SOC decomposition models from a compilation and analysis of published measurements. In particular, we developed appropriate kinetic parameters for five typical ligninolytic and cellulolytic enzymes ( -glucosidase, cellobiohydrolase, endo-glucanase, peroxidase, and phenol oxidase). The kinetic parameters included the maximum specific enzyme activity (Vmax) and half-saturation constant (Km) in the Michaelis-Menten equation. The activation energy (Ea) and the pH optimum and sensitivity (pHopt and pHsen) were also analyzed. pHsen was estimated by fitting an exponential-quadratic function. The Vmax values, often presented in different units under various measurement conditions, were converted into the same units at a reference temperature (20 C) and pHopt. Major conclusions are: (i) Both Vmax and Km were log-normal distributed, with no significant difference in Vmax exhibited between enzymes originating from bacteria or fungi. (ii) No significant difference in Vmax was found between cellulases and ligninases; however, there was significant difference in Km between them. (iii) Ligninases had higher Ea values and lower pHopt than cellulases; average ratio of pHsen to pHopt ranged 0.3 0.4 for the five enzymes, which means that an increase or decrease of 1.1 1.7 pH units from pHopt would reduce Vmax by 50%. (iv) Our analysis indicated that the Vmax values from lab measurements with purified enzymes were 1 2 orders of magnitude higher than those for use in SOC decomposition models under field conditions.
2012-01-01
chloroethene mineralization under nomi- nally anoxic conditions can exhibit saturation type ( Michaelis - Menten ) kinetics over the range of environmentally...relevant concentrations. The Michaelis - Menten parameters, Vmax and ks, are sensitive to a number of environmental factors and vary according to in
Zhou, Chuanzheng; Chattopadhyaya, Jyoti
2010-04-02
In this study, 12 different native or LNA, carba-LNA-modified dinucleoside phosphates were designed as simple chemical models to study how carba-LNA modifications improve the 3'-exonuclease (SVPDE in this study) resistance of internucleotidic phosphate compared to those exhibited by LNA-modified and the native counterparts. Michaelis-Menten kinetic studies for dimers 3 - 7, in which the LNA or carba-LNA modifications are located at the 5'-end, showed that (i) increased 3'-exonuclease resistance of (5')[LNA-T](p)T (3) compared to the native (5')T(p)T (1) was mainly attributed to steric hindrance imposed by the LNA modification that retards the nuclease binding (K(M)) and (ii) digestion of (5')[carba-LNA-dT](p)T (4) and (5')[LNA-T](p)T (3), however, exhibit similar K(M)s, whereas the former shows a 100x decrease in K(cat) and is hence more stable than the latter. By studying the correlation between log k(cat) and pK(a) of the departing 3'(or 6')-OHs for 3-7, we found the pK(a) of 3'-OH of carba-LNA-T was 1.4 pK(a) units higher than that of LNA-T, and this relatively less acidic character of the 3'-OH in the former leads to the 100x decrease in the catalytic efficiency for the digestion of (5')[carba-LNA-T](p)T (4). In contrast, Michaelis-Menten kinetic studies for dimers 9-12, with the LNA or carba-LNA modifications at the 3'-end, showed that the digestion of (5')T(p)[LNA-T] (9) exhibited similar K(M) but k(cat) decreased around 40 times compared to that of the native (5')T(p)T (1). Similar k(cat) values have been observed for digestion of (5')T(p)[carba-LNA-T] (10) and (5')T(p)[LNA-T] (9). The higher stability of carba-LNA modified dimer 10 compared with LNA modified dimer 9 comes solely from the increased K(M).
André Rosa Martins
2015-06-01
Full Text Available ResumoOs processos enzimáticos que seguem o modelo cinético de Michaelis-Menten foram estudados a partir de diferentes propostas para descrever a etapa de inibição reversível. As propostas de inibição foram comparadas a partir de um processo genérico, onde as constantes cinéticas receberam valores unitários e o valor numérico da concentração de substrato foi dez (10 vezes superior ao valor numérico da concentração de enzima. Para cada proposta de modelo de inibição foram obtidas soluções numéricas a partir de sistema não linear de equações diferenciais ordinárias, gerando gráficos que apresentaram, separadamente, a variação das concentrações da enzima, dos complexos enzimáticos, do substrato e do produto da reação. Foi obtido um modelo, dentre as propostas avaliadas, com desempenho indicando comportamento similar ao verificado no modelo clássico de Michaelis-Menten, onde o complexo de reação é rapidamente formado e, ao longo do processo, decai até tender a zero. Em contrapartida, diferentemente do modelo clássico, na nova proposta de modelo o efeito de inibição começa em zero e, ao longo do processo, tende ao valor nominal da concentração inicial da enzima. Tais respostas mostraram-se válidas para valores distintos de concentração de enzima e de tempo de processo, mostrando robustez e indicando uma tendência do somatório do substrato e do produto atingir o valor nominal da concentração inicial do substrato ao longo do tempo de processamento.
Effect of diet-induced obesity on kinetic parameters of amino acid uptake by rat erythrocytes.
Picó, C; Pons, A; Palou, A
1992-11-01
The effects of cafeteria diet-induced obesity upon in vitro uptake of L-Alanine, Glycine, L-Lysine, L-Glutamine, L-Glutamic acid, L-Phenylalanine and L-Leucine by isolated rat erythrocytes have been studied. The total Phe and Leu uptakes followed Michaelis-Menten kinetics. The Glu uptake was fitted to diffusion kinetics. The uptakes of Ala, Gly, Lys and Gln were best explained by a two-component transport: one saturable and one diffusion. Obesity increased the Km value for Ala, Gln and Leu, and the Vmax value for Ala, but decreased the Vmax for Lys. Kinetic parameters of Phe uptake were unaffected by obesity. In addition, the pseudo-first order rate constant (Vmax/Km) for Ala, Gly, Gln, Lys and Leu uptake decreased as a result of cafeteria diet-induced obesity. The Kd value for Ala, Gly, Gln and Glu decreased and that of Lys increased as result of obesity. These adaptations could, at least in part, explain alterations in amino acid distribution between blood cells and plasma related to overfeeding or obesity.
Valencia, Pedro L; Astudillo-Castro, Carolina; Gajardo, Diego; Flores, Sebastián
2017-04-01
We provide initial rate data from enzymatic reaction experiments and tis processing to estimate the kinetic parameters from the substrate uncompetitive inhibition equation using the median method published by Eisenthal and Cornish-Bowden (Cornish-Bowden and Eisenthal, 1974; Eisenthal and Cornish-Bowden, 1974). The method was denominated the direct linear plot and consists in the calculation of the median from a dataset of kinetic parameters Vmax and Km from the Michaelis-Menten equation. In this opportunity we present the procedure to applicate the direct linear plot to the substrate uncompetitive inhibition equation; a three-parameter equation. The median method is characterized for its robustness and its insensibility to outlier. The calculations are presented in an Excel datasheet and a computational algorithm was developed in the free software Python. The kinetic parameters of the substrate uncompetitive inhibition equation Vmax , Km and Ks were calculated using three experimental points from the dataset formed by 13 experimental points. All the 286 combinations were calculated. The dataset of kinetic parameters resulting from this combinatorial was used to calculate the median which corresponds to the statistic estimator of the real kinetic parameters. A comparative statistical analyses between the median method and the least squares was published in Valencia et al. [3].
Introducing Michaelis-Menten Kinetics through Simulation
Halkides, Christopher J.; Herman, Russell
2007-01-01
We describe a computer tutorial that introduces the concept of the steady state in enzyme kinetics. The tutorial allows students to produce graphs of the concentrations of free enzyme, enzyme-substrate complex, and product versus time in order to learn about the approach to steady state. By using a range of substrate concentrations and rate…
The Michaelis-Menten-Stueckelberg Theorem
Gorban, Alexander N.; Muhammad Shahzad
2011-01-01
We study chemical reactions with complex mechanisms under two assumptions: (i) intermediates are present in small amounts (this is the quasi-steady-state hypothesis or QSS) and (ii) they are in equilibrium relations with substrates (this is the quasiequilibrium hypothesis or QE). Under these assumptions, we prove the generalized mass action law together with the basic relations between kinetic factors, which are sufficient for the positivity of the entropy production but hold even without mic...
Introducing Michaelis-Menten Kinetics through Simulation
Halkides, Christopher J.; Herman, Russell
2007-01-01
We describe a computer tutorial that introduces the concept of the steady state in enzyme kinetics. The tutorial allows students to produce graphs of the concentrations of free enzyme, enzyme-substrate complex, and product versus time in order to learn about the approach to steady state. By using a range of substrate concentrations and rate…
Leonard, Erin M; Wood, Chris M
2013-06-01
We investigated the bioaccumulation and acute toxicity (48 h or 96 h) of Ni in four freshwater invertebrate species in two waters with hardness of 40 (soft water) and 140 mg L(-1) as CaCO(3) (hard water). Sensitivity order (most to least) was Lymnaea stagnalis > Daphnia pulex > Lumbriculus variegatus > Chironomus riparius. In all cases water hardness was protective against acute Ni toxicity with LC(50) values 3-3.5× higher in the hard water vs. soft water. In addition, higher water hardness significantly reduced Ni bioaccumulation in these organisms suggesting that competition by Ca and Mg for uptake at the biotic ligand may contribute to higher metal resistance. CBR50 values (Critical Body Residues) were less dependent on water chemistry (i.e. more consistent) than LC(50) values within and across species by ~2 fold. These data support one of the main advantages of the Tissue Residue Approach (TRA) where tissue concentrations are generally less variable than exposure concentrations with respect to toxicity. Whole body Ni bioaccumulation followed Michaelis-Menten kinetics in all organisms, with greater hardness tending to decrease B(max) with no consistent effect on K(d). Across species, acute Ni LC(50) values tended to increase with both K(d) and B(max) values - i.e. more sensitive species exhibited higher binding affinity and lower binding capacity for Ni, but there was no correlation with body size. With respect to biotic ligand modeling, log K(NiBL) values derived from Ni bioaccumulation correlated well with log K(NiBL) values derived from toxicity testing. Both whole body Na and Mg levels were disturbed, suggesting that disruption of ionoregulatory homeostasis is a mechanism of acute Ni toxicity. In L. stagnalis, Na depletion was a more sensitive endpoint than mortality, however, the opposite was true for the other organisms. This is the first study to show the relationship between Na and Ni. Copyright © 2013 Elsevier Inc. All rights reserved.
Electrochemical evaluation of glutathione S-transferase kinetic parameters.
Enache, Teodor Adrian; Oliveira-Brett, Ana Maria
2015-02-01
Glutathione S-transferases (GSTs), are a family of enzymes belonging to the phase II metabolism that catalyse the formation of thioether conjugates between the endogenous tripeptide glutathione and xenobiotic compounds. The voltammetric behaviour of glutathione (GSH), 1-chloro-2,4-dinitrobenzene (CDNB) and glutathione S-transferase (GST), as well as the catalytic conjugation reaction of GSH to CDNB by GST was investigated at room temperature, T=298.15K (25°C), at pH6.5, for low concentration of substrates and enzyme, using differential pulse (DP) voltammetry at a glassy carbon electrode. Only GSH can be oxidized; a sensitivity of 0.14nA/μM and a LOD of 6.4μM were obtained. The GST kinetic parameter electrochemical evaluation, in relation to its substrates, GSH and CDNB, using reciprocal Michaelis-Menten and Lineweaver-Burk double reciprocal plots, was determined. A value of KM~100μM was obtained for either GSH or CDNB, and Vmax varied between 40 and 60μmol/min per mg of GST.
Z. R. Yelebe
2014-03-01
Full Text Available This paper addresses the challenge of estimating various kinetic parameters for the design of an optimized enzyme catalysed batch bioreactor of high efficiency and yield. Mathematical models were developed to describe the batch reaction time in relation to the substrate, enzyme and product concentration. The results obtained from the plots generated were: 35.50gmol/l.hr for the velocity of reaction of the enzymes (Vmax, 0.10049hr-1 for the maximum specific growth rate (µmax 826.45gmol/l for the Michaelis-Menten constant (Km, 0.005402577 for maintenance coefficient (Ms, 10.104kgCx/kgCs for yield of cell weight per unit weight of substrate (Ycx/CS, 0.05436kgCp/kgCs for yield of product weight per unit weight of substrate utilized (Ycp/CS and 0.01416 for endogenous decay coefficient (Kd for the design of the batch biochemical reactor. Hence, they are useful parameters for predicting the most appropriate batch reaction conditions and the efficiency of the bioreactor. The mathematical model predictions showed that it can be considered as a good complimentary tool to real system since the simulation results of the mathematical model agrees with experimental data reported in literature.
Goudar, Chetan T
2011-10-01
We have identified an error in the published integral form of the modified Michaelis-Menten equation that accounts for endogenous substrate production. The correct solution is presented and the error in both the substrate concentration, S, and the kinetic parameters Vm , Km , and R resulting from the incorrect solution was characterized. The incorrect integral form resulted in substrate concentration errors as high as 50% resulting in 7-50% error in kinetic parameter estimates. To better reflect experimental scenarios, noise containing substrate depletion data were analyzed by both the incorrect and correct integral equations. While both equations resulted in identical fits to substrate depletion data, the final estimates of Vm , Km , and R were different and Km and R estimates from the incorrect integral equation deviated substantially from the actual values. Another observation was that at R = 0, the incorrect integral equation reduced to the correct form of the Michaelis-Menten equation. We believe this combination of excellent fits to experimental data, albeit with incorrect kinetic parameter estimates, and the reduction to the Michaelis-Menten equation at R = 0 is primarily responsible for the incorrectness to go unnoticed. However, the resulting error in kinetic parameter estimates will lead to incorrect biological interpretation and we urge the use of the correct integral form presented in this study.
Single-molecule enzymology à la Michaelis-Menten.
Grima, Ramon; Walter, Nils G; Schnell, Santiago
2014-01-01
Over the past 100 years, deterministic rate equations have been successfully used to infer enzyme-catalysed reaction mechanisms and to estimate rate constants from reaction kinetics experiments conducted in vitro. In recent years, sophisticated experimental techniques have been developed that begin to allow the measurement of enzyme-catalysed and other biopolymer-mediated reactions inside single cells at the single-molecule level. Time-course data obtained using these methods are considerably noisy because molecule numbers within cells are typically quite small. As a consequence, the interpretation and analysis of single-cell data requires stochastic methods, rather than deterministic rate equations. Here, we concisely review both experimental and theoretical techniques that enable single-molecule analysis, with particular emphasis on the major developments in the field of theoretical stochastic enzyme kinetics, from its inception in the mid-20th century to its modern-day status. We discuss the differences between stochastic and deterministic rate equation models, how these depend on enzyme molecule numbers and substrate inflow into the reaction compartment, and how estimation of rate constants from single-cell data is possible using recently developed stochastic approaches. © 2013 FEBS.
More Nuts and Bolts of Michaelis-Menten Enzyme Kinetics
Lechner, Joseph H.
2011-01-01
Several additions to a classroom activity are proposed in which an "enzyme" (the student) converts "substrates" (nut-bolt assemblies) into "products" (separated nuts and bolts) by unscrewing them. (Contains 1 table.)
Enzyme Kinetics and the Michaelis-Menten Equation
Biaglow, Andrew; Erickson, Keith; McMurran, Shawnee
2010-01-01
The concepts presented in this article represent the cornerstone of classical mathematical biology. The central problem of the article relates to enzyme kinetics, which is a biochemical system. However, the theoretical underpinnings that lead to the formation of systems of time-dependent ordinary differential equations have been applied widely to…
More Nuts and Bolts of Michaelis-Menten Enzyme Kinetics
Lechner, Joseph H.
2011-01-01
Several additions to a classroom activity are proposed in which an "enzyme" (the student) converts "substrates" (nut-bolt assemblies) into "products" (separated nuts and bolts) by unscrewing them. (Contains 1 table.)
Enzyme Kinetics and the Michaelis-Menten Equation
Biaglow, Andrew; Erickson, Keith; McMurran, Shawnee
2010-01-01
The concepts presented in this article represent the cornerstone of classical mathematical biology. The central problem of the article relates to enzyme kinetics, which is a biochemical system. However, the theoretical underpinnings that lead to the formation of systems of time-dependent ordinary differential equations have been applied widely to…
Ketobemidone prodrugs for buccal delivery
Hansen, L.B.; Christrup, Lona Louring; Bundgaard, H.
1992-01-01
conditions ensuring maximal esterase activity, was studied as a function of ester concentration at 37°C. The kinetics of hydrolysis could be accounted for in terms of the Michaelis-Menten equation and the rate parameters K(m) and V(max) were determined. Due to the occurrence of zero-order kinetics...
Bioactivation of morphine-3-propionate, a prodrug of morphine, in tissues from different species
Groth, L.; Jørgensen, A.; Steffansen, B.
1997-01-01
rabbit had higher enzymatic activity than those from rat, which again showed higher activity than those from pig. Comparison of the Michaelis-Menten parameters, K(m) and V(max), obtained using pig and rat serum respectively, suggested that morphine-3-propionate has a lower affinity for enzymes present...
Adriana Parada Dias da Silveira
2004-04-01
Full Text Available The mechanisms that determine greater P absorption by mycorrhizal plants are still not completely clear, and are attributed, in part, to an increase in the number of absorption sites promoted by the hyphae, and/or to a greater affinity of the colonized hypha or root carriers to P. The effect of mycorrhizae formed by Glomus etunicatum on the kinetic parameters of P absorption by the roots and on P influx in bean plants of the IAC-Carioca cultivar was evaluated, in two distinct plant development periods: at the onset of flowering and at the pod-filling stage (35 and 50 days after sowing, respectively. A mixture of sand and silica (9:1 was utilized as substrate and irrigated with nutrient solution. The kinetics assay was performed by the method of 32P depletion from the solution (depletion curve, using intact plants. Mycorrhization promoted greater growth and P absorption by bean plants, which was more conspicuously observed at the pod-filling stage. Mycorrhizal plants showed higher values of maximum ion uptake rate (Vmax and net P influx at the flowering stage. Lower minimum ion concentration (Cmin and Michaelis-Menten constant (Km values were verified in mycorrhizal plants at the pod-filling stage. Mycorrhizal plants also presented higher net P influx per plant, in both stages. Cmin was the kinetic parameter more intimately related to P absorption, and a significant correlation was obtained between this parameter and shoot P content and accumulation in bean plants.Os mecanismos envolvidos na maior absorção de P pela planta micorrizada ainda não estão totalmente esclarecidos, atribuindo-se, em parte, ao aumento no número de sítios de absorção promovido pela hifa e/ou maior afinidade dos carregadores da hifa ou da raiz colonizada ao P. Avaliou-se o efeito da micorriza formada por Glomus etunicatum nos parâmetros cinéticos da absorção radicular de P e no influxo de P em feijoeiro, cultivar IAC-Carioca, em duas épocas do ciclo da planta
José L. Gómez
2005-01-01
Full Text Available A new method for determining the intrinsic parameters of reaction in processes involving a high initial rate has been developed. The usefulness of this alternative, which consists of determining several sets of apparent parameters at different times and then extrapolating these to time zero, is demonstrated proved by the linear dependence obtained between the apparent parameters and the reaction time. The method permitted the values of the intrinsic parameters (enzyme specific activity and Michaelis-Menten constants of both substrates to be obtained for the system under study and was checked with experimental reaction rate data for the soybean peroxidase/phenol/hydrogen peroxide system.
Dynamics of target-mediated drug disposition: characteristic profiles and parameter identification.
Peletier, Lambertus A; Gabrielsson, Johan
2012-10-01
In this paper we present a mathematical analysis of the basic model for target mediated drug disposition (TMDD). Assuming high affinity of ligand to target, we give a qualitative characterisation of ligand versus time graphs for different dosing regimes and derive accurate analytic approximations of different phases in the temporal behaviour of the system. These approximations are used to estimate model parameters, give analytical approximations of such quantities as area under the ligand curve and clearance. We formulate conditions under which a suitably chosen Michaelis-Menten model provides a good approximation of the full TMDD-model over a specified time interval.
Optimization of enzyme parameters for fermentative production of biorenewable fuels and chemicals
Ping Liu
2012-10-01
Full Text Available Microbial biocatalysts such as Escherichia coli and Saccharomyces cerevisiae have been extensively subjected to Metabolic Engineering for the fermentative production of biorenewable fuels and chemicals. This often entails the introduction of new enzymes, deletion of unwanted enzymes and efforts to fine-tune enzyme abundance in order to attain the desired strain performance. Enzyme performance can be quantitatively described in terms of the Michaelis-Menten type parameters Km, turnover number kcat and Ki, which roughly describe the affinity of an enzyme for its substrate, the speed of a reaction and the enzyme sensitivity to inhibition by regulatory molecules. Here we describe examples of where knowledge of these parameters have been used to select, evolve or engineer enzymes for the desired performance and enabled increased production of biorenewable fuels and chemicals. Examples include production of ethanol, isobutanol, 1-butanol and tyrosine and furfural tolerance. The Michaelis-Menten parameters can also be used to judge the cofactor dependence of enzymes and quantify their preference for NADH or NADPH. Similarly, enzymes can be selected, evolved or engineered for the preferred cofactor preference. Examples of exporter engineering and selection are also discussed in the context of production of malate, valine and limonene.
OPTIMIZATION OF ENZYME PARAMETERS FOR FERMENTATIVE PRODUCTION OF BIORENEWABLE FUELS AND CHEMICALS
Laura R. Jarboe
2012-10-01
Full Text Available Microbial biocatalysts such as Escherichia coli and Saccharomyces cerevisiae have been extensively subjected to Metabolic Engineering for the fermentative production of biorenewable fuels and chemicals. This often entails the introduction of new enzymes, deletion of unwanted enzymes and efforts to fine-tune enzyme abundance in order to attain the desired strain performance. Enzyme performance can be quantitatively described in terms of the Michaelis-Menten type parameters Km, turnover number kcat and Ki, which roughly describe the affinity of an enzyme for its substrate, the speed of a reaction and the enzyme sensitivity to inhibition by regulatory molecules. Here we describe examples of where knowledge of these parameters have been used to select, evolve or engineer enzymes for the desired performance and enabled increased production of biorenewable fuels and chemicals. Examples include production of ethanol, isobutanol, 1-butanol and tyrosine and furfural tolerance. The Michaelis-Menten parameters can also be used to judge the cofactor dependence of enzymes and quantify their preference for NADH or NADPH. Similarly, enzymes can be selected, evolved or engineered for the preferred cofactor preference. Examples of exporter engineering and selection are also discussed in the context of production of malate, valine and limonene.
Development of Optimized Guidelines for Therapeutic Strategies for Organophosphate Poisoning
2011-03-01
Hoang, 1995). Metabolism is a complex mechanism, but is implemented into PBPK models in the form of zero order, first order, or Michaelis - Menten ...kinetics. The Vmax and Km required in the Michaelis - Menten equation are derived from in vitro and in vivo 22 measurements. Most PBPK models...metabolism occurs in the liver and follows Michaelis - Menten kinetics (Hoang, 1995). PBPK modeling of organophosphates The consideration of developing a
2009-01-01
with phenyl acetate and paraoxonwere determined by Michaelis - Menten steady state kinetics . The data from four or more independent experiments were fit...paraoxon was followed atA412 for 20 min at room temperature as described above. The data were fit using Michaelis - Menten steady state kinetics to derive...for 4 h at room temperature as described above. The data were fit using Michaelis - Menten steady state kinetics to derive the KM and Vmax values of
Modeling of Complex Mixtures: JP-8 Toxicokinetics
2008-10-01
diffusion, including metabolic loss via the cytochrome P-450 system, described by non-linear Michaelis - Menten kinetics as shown in the following...point. Inhalation and iv were the dose routes for the rat study. The modelers used saturable ( Michaelis - Menten ) kinetics as well as a second... Michaelis - Menten liver metabolic constants for n-decane have been measured (Km = 1.5 mg/L and Vmax = 0.4 mg/hour) using rat liver slices in a vial
Atypical cytochrome p450 kinetics: implications for drug discovery.
Tracy, Timothy S
2006-01-01
The Michaelis-Menten model is commonly used to estimate a drug's potential in vivo hepatic clearance based on in vitro data obtained during drug discovery and development. This paradigm assumes that the drug obeys 'typical' enzyme kinetics and thus can be described by this model. However, it is increasingly being recognised that a number of drugs metabolised not only by the cytochrome P450 enzymes but also by other enzymes and transporters can exhibit atypical kinetic profiles, and thus are not accurately modeled with the Michaelis-Menten model. Application of an incorrect model can then lead to mis-estimation of in vitro intrinsic clearance and thus affect the prediction of in vivo clearance. This review discusses several types of atypical kinetic profiles that may be observed, including examples of homotropic cooperativity (i.e. sigmoidal kinetics, biphasic kinetics and substrate inhibition kinetics) as well as heterotropic cooperativity (i.e. activation). Application of the incorrect kinetic model may profoundly affect estimations of intrinsic clearance. For example, incorrectly applying the Michaelis-Menten model to a kinetic profile exhibiting substrate inhibition kinetics will result in an underestimation of Km (Michaelis-Menten constant) and V(max) (maximal velocity), whereas application of the Michaelis-Menten model to sigmoidal kinetic data typically results in an overestimation of Km and V(max) at the lower substrate concentrations that are typically therapeutically relevant. One must also be careful of potential artefactual causes of atypical kinetic profiles, such as enzyme activation by solvents, buffer dependent kinetic profiles, or altered kinetic parameter estimates due to nonspecific binding of the substrate to proteins. Despite a plethora of data on the effects of atypical kinetic profiles in vitro, only modest effects have been noted in vivo (with the exception of substrate dependent inhibition). Thus, the clinical relevance of these phenomena
A new multi-wavelength model-based method for determination of enzyme kinetic parameters.
Sorouraddin, Mohammad-Hossein; Amini, Kaveh; Naseri, Abdolhossein; Vallipour, Javad; Hanaee, Jalal; Rashidi, Mohammad-Reza
2010-09-01
Lineweaver-Burk plot analysis is the most widely used method to determine enzyme kinetic parameters. In the spectrophotometric determination of enzyme activity using the Lineweaver-Burk plot, it is necessary to find a wavelength at which only the substrate or the product has absorbance without any spectroscopic interference of the other reaction components. Moreover, in this method, different initial concentrations of the substrate should be used to obtain the initial velocities required for Lineweaver-Burk plot analysis. In the present work, a multi-wavelength model-based method has been developed and validated to determine Michaelis-Menten constants for some enzyme reactions. In this method, a selective wavelength region and several experiments with different initial concentrations of the substrate are not required. The absorbance data of the kinetic assays are fitted by non-linear regression coupled to the numeric integration of the related differential equation. To indicate the applicability of the proposed method, the Michaelis-Menten constants for the oxidation of phenanthridine, 6-deoxypenciclovir and xanthine by molybdenum hydroxylases were determined using only a single initial concentration of the substrate, regardless of any spectral overlap.
Improved Methodology for Parameter Inference in Nonlinear, Hydrologic Regression Models
Bates, Bryson C.
1992-01-01
A new method is developed for the construction of reliable marginal confidence intervals and joint confidence regions for the parameters of nonlinear, hydrologic regression models. A parameter power transformation is combined with measures of the asymptotic bias and asymptotic skewness of maximum likelihood estimators to determine the transformation constants which cause the bias or skewness to vanish. These optimized constants are used to construct confidence intervals and regions for the transformed model parameters using linear regression theory. The resulting confidence intervals and regions can be easily mapped into the original parameter space to give close approximations to likelihood method confidence intervals and regions for the model parameters. Unlike many other approaches to parameter transformation, the procedure does not use a grid search to find the optimal transformation constants. An example involving the fitting of the Michaelis-Menten model to velocity-discharge data from an Australian gauging station is used to illustrate the usefulness of the methodology.
Use of Mushroom Tyrosinase to Introduce Michaelis-Menten Enzyme Kinetics to Biochemistry Students
Flurkey, William H.; Inlow, Jennifer K.
2017-01-01
An inexpensive enzyme kinetics laboratory exercise for undergraduate biochemistry students is described utilizing tyrosinase from white button mushrooms. The exercise can be completed in one or two three-hour lab sessions. The optimal amounts of enzyme, substrate (catechol), and inhibitor (kojic acid) are first determined, and then kinetic data is…
Multi-system Nernst-Michaelis-Menten model applied to bioanodes formed from sewage sludge.
Rimboud, Mickaël; Desmond-Le Quemener, Elie; Erable, Benjamin; Bouchez, Théodore; Bergel, Alain
2015-11-01
Bioanodes were formed under constant polarization at -0.2 V/SCE from fermented sewage sludge. Current densities reached were 9.3±1.2 A m(-2) with the whole fermented sludge and 6.2±0.9 A m(-2) with the fermented sludge supernatant. The bioanode kinetics was analysed by differentiating among the contributions of the three redox systems identified by voltammetry. Each system ensured reversible Nernstian electron transfer but around a different central potential. The global overpotential required to reach the maximum current plateau was not imposed by slow electron transfer rates but was due to the potential range covered by the different redox systems. The microbial communities of the three bioanodes were analysed by 16S rRNA gene pyrosequencing. They showed a significant microbial diversity around a core of Desulfuromonadales, the proportion of which was correlated with the electrochemical performance of the bioanodes. Copyright © 2015 Elsevier Ltd. All rights reserved.
The Nuts and Bolts of Michaelis-Menten Enzyme Kinetics: Suggestions and Clarifications
Silverstein, Todd
2011-01-01
Matthew Junker's recent article describes a useful and effective enzyme kinetics application and analogy in which students simulate enzyme activity by unscrewing nut-bolt "substrate molecules", thus, converting them into separate nuts and bolts "products". A number of suggestions and corrections are presented that improve the clarity and accuracy…
Michaelis-Menten reaction scheme as a unified approach towards the optimal restart problem.
Rotbart, Tal; Reuveni, Shlomi; Urbakh, Michael
2015-12-01
We study the effect of restart, and retry, on the mean completion time of a generic process. The need to do so arises in various branches of the sciences and we show that it can naturally be addressed by taking advantage of the classical reaction scheme of Michaelis and Menten. Stopping a process in its midst-only to start it all over again-may prolong, leave unchanged, or even shorten the time taken for its completion. Here we are interested in the optimal restart problem, i.e., in finding a restart rate which brings the mean completion time of a process to a minimum. We derive the governing equation for this problem and show that it is exactly solvable in cases of particular interest. We then continue to discover regimes at which solutions to the problem take on universal, details independent forms which further give rise to optimal scaling laws. The formalism we develop, and the results obtained, can be utilized when optimizing stochastic search processes and randomized computer algorithms. An immediate connection with kinetic proofreading is also noted and discussed.
Commemorating the 1913 Michaelis-Menten paper Die Kinetik der Invertinwirkung: three perspectives.
Deichmann, Ute; Schuster, Stefan; Mazat, Jean-Pierre; Cornish-Bowden, Athel
2014-01-01
Methods and equations for analysing the kinetics of enzyme-catalysed reactions were developed at the beginning of the 20th century in two centres in particular; in Paris, by Victor Henri, and, in Berlin, by Leonor Michaelis and Maud Menten. Henri made a detailed analysis of the work in this area that had preceded him, and arrived at a correct equation for the initial rate of reaction. However, his approach was open to the important objection that he took no account of the hydrogen-ion concentration (a subject largely undeveloped in his time). In addition, although he wrote down an expression for the initial rate of reaction and described the hyperbolic form of its dependence on the substrate concentration, he did not appreciate the great advantages that would come from analysis in terms of initial rates rather than time courses. Michaelis and Menten not only placed Henri's analysis on a firm experimental foundation, but also defined the experimental protocol that remains standard today. Here, we review this development, and discuss other scientific contributions of these individuals. The three parts have different authors, as indicated, and do not necessarily agree on all details, in particular about the relative importance of the contributions of Michaelis and Menten on the one hand and of Henri on the other. Rather than force the review into an unrealistic consensus, we consider it appropriate to leave the disagreements visible. © 2013 FEBS.
Specificity of non-Michaelis-Menten enzymes: necessary information for analyzing metabolic pathways.
Cornish-Bowden, Athel; Cárdenas, María Luz
2010-12-16
The specificity of an enzyme obeying the Michaelis−Menten equation is normally measured by comparing the kcat/Km for different substrates, but this is inappropriate for enzymes with a Hill coefficient h different from 1. The obvious alternative of generalizing Km in the expression as K0.5, the substrate concentration for half-saturation, is better, but it is not entirely satisfactory either, and here we show that kcat/K0.5(h) gives satisfactory results for analyzing the kinetic behavior of metabolic pathways. The importance of using kcat/K0.5(h) increases with the value of h, but even when h is small, it makes an appreciable difference, as illustrated for the mammalian hexokinases. Reinterpretation of data for the specificity of these enzymes in terms of the proposed definition indicates that hexokinase D, often believed highly specific for glucose, and accordingly called “glucokinase”, actually has the lowest preference for glucose over fructose of the four isoenzymes found in mammals.
Estimation of Michaelis-Menten constant of efflux transporter considering asymmetric permeability.
Sugano, Kiyohiko; Shirasaka, Yoshiyuki; Yamashita, Shinji
2011-10-14
It was previously reported that the apparent K(m) values of P-gp in apical to basal (A to B) and basal to apical (B to A) directions were different. The purpose of the present study was to derive a theoretical framework by which this asymmetric concentration-permeability profile can be explained using a single intrinsic K(m) value. A three compartment model was used to represent the apical, cytosol and basal compartments. The difference of passive permeability and the surface areas between the apical and basolateral membrane were explicitly taken into account. Applying the steady state approximation and considering the mass balance in the cytosol compartment, an open analytical solution was obtained. By using this equation, the asymmetric concentration-permeability profile was appropriately reproduced. In addition, the expression level dependency of apparent K(m) was also reproduced. Copyright © 2011 Elsevier B.V. All rights reserved.
Non-Michaelis-Menten kinetics model for conductance of low-conductance potassium ion channels.
Tolokh, Igor S; Tolokh, Illya I; Cho, Hee Cheol; D'Avanzo, Nazzareno; Backx, Peter H; Goldman, Saul; Gray, C G
2005-02-01
A reduced kinetics model is proposed for ion permeation in low-conductance potassium ion channels with zero net electrical charge in the selectivity filter region. The selectivity filter is assumed to be the only conductance-determining part of the channel. Ion entry and exit rate constants depend on the occupancy of the filter due to ion-ion interactions. The corresponding rates are assumed slow relative to the rates of ion motion between binding sites inside the filter, allowing a reduction of the kinetics model of the filter by averaging the entry and exit rate constants over the states with a particular occupancy number. The reduced kinetics model for low-conductance channels is described by only three states and two sets of effective rate constants characterizing transitions between these states. An explicit expression for the channel conductance as a function of symmetrical external ion concentration is derived under the assumption that the average electrical mobility of ions in the selectivity filter region in a limited range of ion concentrations does not depend on these concentrations. The simplified conductance model is shown to provide a good description of the experimentally observed conductance-concentration curve for the low-conductance potassium channel Kir2.1, and also predicts the mean occupancy of the selectivity filter of this channel. We find that at physiological external ion concentrations this occupancy is much lower than the value of two ions observed for one of the high-conductance potassium channels, KcsA.
Stability in a diffusive food chain model with Michaelis-Menten functional response
Lin, Zhigui; Pedersen, Michael
2004-01-01
This paper deals with the behavior of positive solutions to a reaction-diffusion system with homogeneous Neumann boundary conditions describing a three species food chain. A sufficient condition for the local asymptotical stability is given by linearization and also a sufficient condition...... for the global asymptotical stability is given by a Lyapunov function. Our result shows that the equilibrium solution is globally asymptotically stable if the net birth rate of the first species is big enough and the net death rate of the third species is neither too big nor too small. (C) 2004 Elsevier Ltd. All...
Michaelis-Menten reaction scheme as a unified approach towards the optimal restart problem
Rotbart, Tal; Reuveni, Shlomi; Urbakh, Michael
2015-12-01
We study the effect of restart, and retry, on the mean completion time of a generic process. The need to do so arises in various branches of the sciences and we show that it can naturally be addressed by taking advantage of the classical reaction scheme of Michaelis and Menten. Stopping a process in its midst—only to start it all over again—may prolong, leave unchanged, or even shorten the time taken for its completion. Here we are interested in the optimal restart problem, i.e., in finding a restart rate which brings the mean completion time of a process to a minimum. We derive the governing equation for this problem and show that it is exactly solvable in cases of particular interest. We then continue to discover regimes at which solutions to the problem take on universal, details independent forms which further give rise to optimal scaling laws. The formalism we develop, and the results obtained, can be utilized when optimizing stochastic search processes and randomized computer algorithms. An immediate connection with kinetic proofreading is also noted and discussed.
Estudio de bioequivalencia de teofilina considerando cinética de Michaelis-Menten
Fagiolino, Pietro; Turlier, M.; Payssé, Helena; Aiache, Jean-Marc
1994-01-01
Se presenta un estudio de bioequivalencia de dos formas farmacéuticas de Teofilina de liberación prolongada, teniendo en cuenta la cinética no lineal de eliminación de esta droga. Una dosis de 300 mg de Teofilina fue administrada a 12 voluntarios sanos, en un diseno aleatorio, cruzado y compensado. Se utilizó una forma farmacéutica elixir, a los efectos de estimar los parámetros farmacocinéticos de eliminación en cada individuo. Como parámetros de evaluación de la biodisponibilidad se utilizó...
The Nuts and Bolts of Michaelis-Menten Enzyme Kinetics: Suggestions and Clarifications
Silverstein, Todd
2011-01-01
Matthew Junker's recent article describes a useful and effective enzyme kinetics application and analogy in which students simulate enzyme activity by unscrewing nut-bolt "substrate molecules", thus, converting them into separate nuts and bolts "products". A number of suggestions and corrections are presented that improve the clarity and accuracy…
Grant, A O; Hondeghem, L M; Katzung, B G
1978-04-01
The neuroleptic drug droperidol has been shown to have clinically useful antiarrhythmic activity. Prior reports have resulted in conflicting conclusions regarding actions on ventricular myocardial fibers. The present study was carried out to determine whether droperidol did in fact affect the electrophysiological properties of guinea-pig papillary muscle fibers. By means of microelectrode recordings from preparations mounted in a single sucrose gap, the effects of concentrations from 10(-6) to 4 X 10(-5) M were studied on depolarization-induced automaticity, and on Vmax and its recovery time under several conditions of membrane potential, stimulation rate and external ion concentration. The results showed that at clinically relevant concentrations, droperidol significantly slows ventricular pacemaker activity, a depression reversible by epinephrine. Furthermore, Vmax was decreased and the time constant for Vmax recovery was significantly prolonged under several conditions which pertain to clinical arrhythmias, i.e., reduced membrane potential, elevated extracellular potassium concentrations and increased stimulation rate.
Dynamical Systems and Control Theory Inspired by Molecular Biology
2011-02-20
is odd) steady states, there never are more than 2n − 1 steady states, that for parameters near the standard Michaelis - Menten quasi-steady state...conditions, there are at most n + 1 steady states and that for parameters far from the standard Michaelis - Menten quasi-steady state conditions, there is at
Marcela Aparecida Guerreiro Machado
2008-01-01
Full Text Available Neste artigo é proposto, para o monitoramento de processos normais bivariados, um gráfico de controle baseado nas variâncias amostrais de duas características de qualidade. Os pontos plotados no gráfico correspondem ao valor da maior variância amostral. O gráfico proposto, denominado gráfico de VMAX, tem um desempenho superior ao do gráfico da variância amostral generalizada |S| e, além disso, tem uma melhor capacidade de diagnóstico, ou seja, com ele é mais fácil identificar a variável que teve sua variabilidade alterada pela ocorrência da causa especial. Quando a amostragem dupla está em uso o gráfico proposto também tem um desempenho superior ao do gráfico de |S|, exceto em alguns casos em que o tamanho da segunda amostra é muito grande.In this paper a control chart based on sample variances from two quality characteristics for monitoring bivariate normal processes is proposed. The points plotted on the chart are the maximum of the values of these two statistics. The proposed chart (VMAX chart detects process disturbances faster than the generalized variance |S| chart and has a better diagnostic feature, that is, with the VMAX chart it is easier to relate an out-of-control signal to the variable whose variability has moved away from its in-control state. When the double sampling scheme is used the proposed chart has also a better performance, except in a few cases in which the size of the samples at the second stage is very large.
Innovative Microsystems: Novel Nanostructures to Capture Circulating Breast Cancer Cells
2008-05-01
agitated by the auto shake function 5 seconds before each read. These data are then interpreted with a Michaelis - Menten model of the HRP enzyme kinetics ...Amplex Red) and fluorescent product (Resorufin) in a given micro-plate well as a function of time t; Vmax and KM are the standard Michaelis - Menten ...Molecular Probes). The fluorescence signal, generated by the action of the HRP immobilized on the chiclets, is then read in kinetic mode with excitation
[Determination of beta-mannanase activity by viscosimetric and spectrophotometric methods].
Firantas, S G; Venozhinskene, Iu I; Pauliukonis, A B
1982-01-01
The activity of beta-mannanase from Bacillus subtilis was measured viscosimetrically and spectrophotometrically. As substrate galactomannane of Ceratonia siliqua was used. Relationships between the beta-mannanase activity and the substrate concentration as well as the enzyme content were investigated. The kinetic parameters of the enzymes obeying the Michaelis-Menten equation were calculated. It was found viscosimetrically that Vmax of the commercial enzyme preparation was 1.4 mucat/g (at pH 5.8 and 40 degrees) and Km was 0.6 mM. The viscosimetric method shows high sensitivity, whereas the spectrophotometric technique suits mass-scale analyses.
Christiansen, Nina Høj; Andersen, Frede Østergaard; Jensen, Henning S.
2016-01-01
with the affinity at low Pi concentrations (Vmax/Km) were determined by fitting data to the Michaelis-Menten kinetics. L. uniflora showed the highest Vmax/Km in the root tissue and the lowest Km. M. alterniflorum showed the highest and E. canadensis and P. perfoliatus the lowest Vmax/Km in leaf tissue. M...
Optimal experiment selection for parameter estimation in biological differential equation models
Transtrum Mark K
2012-07-01
Full Text Available Abstract Background Parameter estimation in biological models is a common yet challenging problem. In this work we explore the problem for gene regulatory networks modeled by differential equations with unknown parameters, such as decay rates, reaction rates, Michaelis-Menten constants, and Hill coefficients. We explore the question to what extent parameters can be efficiently estimated by appropriate experimental selection. Results A minimization formulation is used to find the parameter values that best fit the experiment data. When the data is insufficient, the minimization problem often has many local minima that fit the data reasonably well. We show that selecting a new experiment based on the local Fisher Information of one local minimum generates additional data that allows one to successfully discriminate among the many local minima. The parameters can be estimated to high accuracy by iteratively performing minimization and experiment selection. We show that the experiment choices are roughly independent of which local minima is used to calculate the local Fisher Information. Conclusions We show that by an appropriate choice of experiments, one can, in principle, efficiently and accurately estimate all the parameters of gene regulatory network. In addition, we demonstrate that appropriate experiment selection can also allow one to restrict model predictions without constraining the parameters using many fewer experiments. We suggest that predicting model behaviors and inferring parameters represent two different approaches to model calibration with different requirements on data and experimental cost.
Moate, P J; Boston, R C; Jenkins, T C; Lean, I J
2008-02-01
Previous investigations into ruminal lipolysis of triacylglycerol and ruminal biohydrogenation (BH) of unsaturated long-chain fatty acids have generally quantified these processes with either zero-order or first-order kinetics. This investigation examined if Michaelis-Menten and other nonlinear kinetics might be useful for quantifying these processes. Data from 2 previously published in vitro experiments employing rumen fluid from sheep to investigate the lipolysis of trilinolein, the BH of cis-9, cis-12 linoleic acid (LA), and the BH of fatty acids derived from the lipolysis of trilinolein were used for the development of a multi-compartmental model. The model described the lipolysis of triacylglycerol well. The model also provided a good mathematical description of the resulting production of nonesterified fatty acids, the isomerization of nonesterified LA, and subsequent production of rumenic acid (RA), vaccenic acid (VA), and stearic acid (SA). However, the model described poorly the patterns of the concentrations of LA, RA, VA, and SA after incubation of trilinolein in rumen fluid. The model is consistent with known stoichiometry and biochemistry and is parsimonious in that it employs a minimal number of parameters to describe all of the major aspects of lipolysis and BH. The first step in the lipolysis of trilinolein was described by Michaelis-Menten kinetics (Vmax = 529 +/- 16 mg/L per h; Km = 698 +/- 41 mg/L). Both subsequent lipolysis steps were approximated by a first-order (linear kinetics) rate constant (k = 2.64 +/- 0.041 /h). Isomerization of LA to RA was modeled by simple Michaelis-Menten kinetics (Vmax = 2,421 +/- 83 mg/L per h; Km = 440 +/- 22 mg/L). The kinetics of the BH of RA to VA was described by a Michaelis-Menten-type process involving competitive inhibition by VA (Vmax = 492 +/- 6.5 mg/L per h; Km = 1 mg/L). The final step, the BH of VA to SA, was modeled by a quasi-first-order process (k = 0.533 +/- 0.021 /h), but as the concentration of
Linear parameter estimation of rational biokinetic functions
Doeswijk, T.G.; Keesman, K.J.
2009-01-01
For rational biokinetic functions such as the Michaelis-Menten equation, in general, a nonlinear least-squares method is a good estimator. However, a major drawback of a nonlinear least-squares estimator is that it can end up in a local minimum. Rearranging and linearizing rational biokinetic
Validation of the V(max) metabolic cart in a simulated pediatric model.
Wines, Kristen N; Rzepecki, Alexandra K; Andrews, Audrey L; Dechert, Ronald E
2015-03-01
The ability to accurately measure resting energy expenditure (REE) using indirect calorimetry, often referred to as the "gold standard" in nutrition needs assessment, is important given the well-established positive correlation between patient outcome and proportion of the nutrition goal met. While many studies have been done to compare various metabolic carts with one another, the literature lacks a large simulator-based validation of any metabolic cart system. In the present study, 8 specifically trained staff members independently conducted 10 simulation trials each using the V(max) Encore metabolic analyzer in conjunction with a metabolic calibration system, which simulates patient metabolic activity, to validate the accuracy of the V(max) Encore across a wide range of simulated metabolic conditions. Testing conditions consisted of incremental adjustments in calibrated gas infusion with a consistently set tidal volume and respiratory rate. There was a strong, statistically significant correlation between the predicted and actual VO2 and VCO2 data (VO2, R (2) = 0.998; VCO2, R (2) = 0.997). In addition, we observed no significant difference between individuals performing these trials (VO2, P = 1.000, F = 0.021, df = 79; VCO2, P = 1.000, F = 0.030, df = 79). This study is the first to report on such a wide spectrum of metabolic activity (50-2000 kcal REE) using a calibrated bench model and validates the accuracy, reproducibility, and use of the V(max) Encore metabolic cart. © 2014 American Society for Parenteral and Enteral Nutrition.
Oldiges Marco
2009-01-01
Full Text Available Abstract Background To understand the dynamic behavior of cellular systems, mathematical modeling is often necessary and comprises three steps: (1 experimental measurement of participating molecules, (2 assignment of rate laws to each reaction, and (3 parameter calibration with respect to the measurements. In each of these steps the modeler is confronted with a plethora of alternative approaches, e. g., the selection of approximative rate laws in step two as specific equations are often unknown, or the choice of an estimation procedure with its specific settings in step three. This overall process with its numerous choices and the mutual influence between them makes it hard to single out the best modeling approach for a given problem. Results We investigate the modeling process using multiple kinetic equations together with various parameter optimization methods for a well-characterized example network, the biosynthesis of valine and leucine in C. glutamicum. For this purpose, we derive seven dynamic models based on generalized mass action, Michaelis-Menten and convenience kinetics as well as the stochastic Langevin equation. In addition, we introduce two modeling approaches for feedback inhibition to the mass action kinetics. The parameters of each model are estimated using eight optimization strategies. To determine the most promising modeling approaches together with the best optimization algorithms, we carry out a two-step benchmark: (1 coarse-grained comparison of the algorithms on all models and (2 fine-grained tuning of the best optimization algorithms and models. To analyze the space of the best parameters found for each model, we apply clustering, variance, and correlation analysis. Conclusion A mixed model based on the convenience rate law and the Michaelis-Menten equation, in which all reactions are assumed to be reversible, is the most suitable deterministic modeling approach followed by a reversible generalized mass action kinetics
Nijland, G.O.; Schouls, J.; Goudriaan, J.
2008-01-01
Any agricultural production process is characterized by input¿output relations. In this paper we show that the production functions of Liebig, Mitscherlich and Liebscher for the relation between nutrient supply and crop production can be regarded as special variants of one 'integrated model'. The
Heering, Hendrik A
2012-10-01
Deconvolution of protein film voltammetric data by fitting multiple components (sigmoids, derivative peaks) often is ambiguous when features are partially overlapping, due to exchangeability between the width and the number of components. Here, a new method is presented to obtain the width of the components. This is based on the equivalence between the sigmoidal catalytic response as function of electrode potential, and the classical saturation curve obtained for the enzyme activity as function of the soluble substrate concentration, which is also sigmoidal when plotted versus log[S]. Thus, analysis of the catalytic voltammogram with Lineweaver-Burk, Eadie-Hofstee, and Hanes-Woolf plots is feasible. This provides a very sensitive measure of the cooperativity number (Hill coefficient), which for electrons equals the apparent (fractional) number of electrons that determine the width, and thereby the number of components (kinetic phases). This analysis is applied to the electrocatalytic oxygen reduction by Paracoccus denitrificans cytochrome aa(3) (cytochrome c oxidase). Four partially overlapping kinetic phases are observed that (stepwise) increase the catalytic efficiency with increasingly reductive potential. Translated to cell biology, the activity of the terminal oxidase stepwise adapts to metabolic demand for oxidative phosphorylation. Copyright © 2011 Elsevier B.V. All rights reserved.
Nijland, G.O.; Schouls, J.; Goudriaan, J.
2008-01-01
Any agricultural production process is characterized by input¿output relations. In this paper we show that the production functions of Liebig, Mitscherlich and Liebscher for the relation between nutrient supply and crop production can be regarded as special variants of one 'integrated model'. The mo
2014-04-04
were determined by Michaelis - Menten steady state kinetics using Prism Graphpad (Irvine, CA). Kinetic data for CMP hydrolysis was used as a metric to...against CMP, paraoxon and phenyl acetate versus G3C9 expression in E. coli (Table 1). A closer examination of the Michaelis - Menten parameters reveals...0.05% BSA 1.09 ± 0.06 45 ± 9 24 ± 5 Table 2. Michaelis - Menten parameters for G3C9 CMP hydrolysis. G3C9 expressed in mammalian cells displayed
Kinetic Study on Flooded Soil Recovery Using Soil Containing Arbuscular Mycorrhizal Fungi
Zainol N.
2016-01-01
Full Text Available The purpose of this research was to determine the kinetic parameters for flooded soil recovery via soil containing Arbuscular Mycorrhizal fungi (AMF. The general procedures of this experiment started by preparation of simulated flooded soil (FS and soil containing AMF (SA. Mixed soil was prepared by mixing FS and SA with ratio 1:1. Onion plant was chosen as a host plant and planted in the mixed soil for 14 days. The plantation was conducted in ambient temperature. The nutrients (nitrogen, phosphorus and potassium concentrations in the soil were tested using HACH Spectrophotomer. The Michaelis-Menten equation was used to study the nutrients recovery in soil. The Lineweaver-Bulk plot was used to solve the Michaelis-Menten equation. From the experiment conducted, the maximum nutrient uptake (Vmax and bonding affinity (Km obtained for nitrogen (N were 6.28mg/l.d and 82.17 mg/l, for phosphorus (P were 9.80 mg/l.d and 60.96 mg/l.d and for potassium (K were 0.07mg/l.d and 4.55mg/l. By comparing the result with other researcher, it showed that the Vmax and Km of nitrogen (N and phosphorus (P obtained were higher than other research. This was because the onion required a high level of N and P in the soil compared to other host plant.
Davis, Rebecca Anne
2008-03-01
The increase in waste disposal and energy costs has provided an incentive to convert carbohydrate-rich food waste streams into fuel. For example, dining halls and restaurants discard foods that require tipping fees for removal. An effective use of food waste may be the enzymatic hydrolysis of the waste to simple sugars and fermentation of the sugars to ethanol. As these wastes have complex compositions which may change day-to-day, experiments were carried out to test fermentability of two different types of food waste at 27 degrees C using Saccharomyces cerevisiae yeast (ATCC4124) and Genencor's STARGEN enzyme in batch simultaneous saccharification and fermentation (SSF) experiments. A mathematical model of SSF based on experimentally matched rate equations for enzyme hydrolysis and yeast fermentation was developed in Matlab Simulink. Using Simulink parameter estimation 1.1.3, parameters for hydrolysis and fermentation were estimated through modified Michaelis-Menten and Monod-type equations with the aim of predicting changes in the levels of ethanol and glycerol from different initial concentrations of glucose, fructose, maltose, and starch. The model predictions and experimental observations agree reasonably well for the two food waste streams and a third validation dataset. The approach of using Simulink as a dynamic visual model for SSF represents a simple method which can be applied to a variety of biological pathways and may be very useful for systems approaches in metabolic engineering in the future.
Davis, Rebecca Anne
The increase in waste disposal and energy costs has provided an incentive to convert carbohydrate-rich food waste streams into fuel. For example, dining halls and restaurants discard foods that require tipping fees for removal. An effective use of food waste may be the enzymatic hydrolysis of the waste to simple sugars and fermentation of the sugars to ethanol. As these wastes have complex compositions which may change day-to-day, experiments were carried out to test fermentability of two different types of food waste at 27° C using Saccharomyces cerevisiae yeast (ATCC4124) and Genencor's STARGEN™ enzyme in batch simultaneous saccharification and fermentation (SSF) experiments. A mathematical model of SSF based on experimentally matched rate equations for enzyme hydrolysis and yeast fermentation was developed in Matlab Simulink®. Using Simulink® parameter estimation 1.1.3, parameters for hydrolysis and fermentation were estimated through modified Michaelis-Menten and Monod-type equations with the aim of predicting changes in the levels of ethanol and glycerol from different initial concentrations of glucose, fructose, maltose, and starch. The model predictions and experimental observations agree reasonably well for the two food waste streams and a third validation dataset. The approach of using Simulink® as a dynamic visual model for SSF represents a simple method which can be applied to a variety of biological pathways and may be very useful for systems approaches in metabolic engineering in the future.
A Critical View on In Vitro Analysis of P-glycoprotein (P-gp) Transport Kinetics.
Saaby, Lasse; Brodin, Birger
2017-09-01
Transport proteins expressed in the different barriers of the human body can have great implications on absorption, distribution, and excretion of drug compounds. Inhibition or saturation of a transporter can potentially alter these absorbtion, distribution, metabolism and elimination properties and thereby also the pharmacokinetic profile and bioavailability of drug compounds. P-glycoprotein (P-gp, ABCB1) is an efflux transporter which is present in most of the barriers of the body, including the small intestine, the blood-brain barrier, the liver, and the kidney. In all these tissues, P-gp may mediate efflux of drug compounds and may also be a potential site for drug-drug interactions. Consequently, there is a need to be able to predict the saturation and inhibition of P-gp and other transporters in vivo. For this purpose, Michaelis-Menten steady-state analysis has been applied to estimate kinetic parameters, such as Km and Vmax, for carrier-mediated transport, whereas half-maximal inhibitor concentration (IC50) and the disassociation constant for an inhibitor/P-gp complex (Ki) have been determined to estimate P-gp inhibition. This review addresses in vitro methods commonly used to study P-gp transport kinetics and aims at providing a critical evaluation of the application of steady-state Michaelis-Menten analysis of kinetic parameters for substrate/P-gp interactions. Copyright © 2017 American Pharmacists Association®. Published by Elsevier Inc. All rights reserved.
Aishwarya Singh Chauhan
2015-01-01
Full Text Available Trichoderma spp. have been reported earlier for their excellent capacity of secreting extracellular α-galactosidase. This communication focuses on the optimization of culture conditions for optimal production of enzyme and its characterization. The evaluation of the effects of different enzyme assay parameters such as stability, pH, temperature, substrate concentrations, and incubation time on enzyme activity has been made. The most suitable buffer for enzyme assay was found to be citrate phosphate buffer (50 mM, pH 6.0 for optimal enzyme activity. This enzyme was fairly stable at higher temperature as it exhibited 72% activity at 60°C. The enzyme when incubated at room temperature up to two hours did not show any significant loss in activity. It followed Michaelis-Menten curve and showed direct relationship with varying substrate concentrations. Higher substrate concentration was not inhibitory to enzyme activity. The apparent Michaelis-Menten constant (Km, maximum rate of reaction (Vmax, Kcat, and catalytic efficiency values for this enzyme were calculated from the Lineweaver-Burk double reciprocal plot and were found to be 0.5 mM, 10 mM/s, 1.30 U mg−1, and 2.33 U mg−1 mM−1, respectively. This information would be helpful in understanding the biophysical and biochemical characteristics of extracellular α-galactosidase from other microbial sources.
Bellasio, Chandra; Beerling, David J; Griffiths, Howard
2016-06-01
Combined photosynthetic gas exchange and modulated fluorometres are widely used to evaluate physiological characteristics associated with phenotypic and genotypic variation, whether in response to genetic manipulation or resource limitation in natural vegetation or crops. After describing relatively simple experimental procedures, we present the theoretical background to the derivation of photosynthetic parameters, and provide a freely available Excel-based fitting tool (EFT) that will be of use to specialists and non-specialists alike. We use data acquired in concurrent variable fluorescence-gas exchange experiments, where A/Ci and light-response curves have been measured under ambient and low oxygen. From these data, the EFT derives light respiration, initial PSII (photosystem II) photochemical yield, initial quantum yield for CO2 fixation, fraction of incident light harvested by PSII, initial quantum yield for electron transport, electron transport rate, rate of photorespiration, stomatal limitation, Rubisco (ribulose 1·5-bisphosphate carboxylase/oxygenase) rate of carboxylation and oxygenation, Rubisco specificity factor, mesophyll conductance to CO2 diffusion, light and CO2 compensation point, Rubisco apparent Michaelis-Menten constant, and Rubisco CO2 -saturated carboxylation rate. As an example, a complete analysis of gas exchange data on tobacco plants is provided. We also discuss potential measurement problems and pitfalls, and suggest how such empirical data could subsequently be used to parameterize predictive photosynthetic models.
Kinetics of glucose transport in rat muscle
Ploug, Thorkil; Galbo, H; Vinten, J
1987-01-01
-MG concentration exhibited Michaelis-Menten kinetics. Uptake by simple diffusion could not be detected. The maximum 3-O-MG transport velocity (Vmax) was increased more by maximum isometric contractions (10- to 40-fold, depending on fiber type) than by insulin (20,000 microU/ml; 3- to 20-fold) in both red and white...
Farmacokinetiek van urethaan bij de rat
Olling M; Zeijlmans PWM
1988-01-01
De kinetiek van urethaan volgt het Michaelis-Menten model, waarbij de Vmax na intraperitoneale toediening varieert van 7,1 mg/l.h bij een toediening van 100 mg/kg tot 38,2 mg/l.h na 1,25 g/kg. De Michaelis constante, Km, blijkt ver beneden de concentraties te liggen welke tijdens dit onderzoek k
Tomlinson, Sean
2016-04-01
The calculation and comparison of physiological characteristics of thermoregulation has provided insight into patterns of ecology and evolution for over half a century. Thermoregulation has typically been explored using linear techniques; I explore the application of non-linear scaling to more accurately calculate and compare characteristics and thresholds of thermoregulation, including the basal metabolic rate (BMR), peak metabolic rate (PMR) and the lower (Tlc) and upper (Tuc) critical limits to the thermo-neutral zone (TNZ) for Australian rodents. An exponentially-modified logistic function accurately characterised the response of metabolic rate to ambient temperature, while evaporative water loss was accurately characterised by a Michaelis-Menten function. When these functions were used to resolve unique parameters for the nine species studied here, the estimates of BMR and TNZ were consistent with the previously published estimates. The approach resolved differences in rates of metabolism and water loss between subfamilies of Australian rodents that haven't been quantified before. I suggest that non-linear scaling is not only more effective than the established segmented linear techniques, but also is more objective. This approach may allow broader and more flexible comparison of characteristics of thermoregulation, but it needs testing with a broader array of taxa than those used here.
Privman, Eve; Venton, B Jill
2015-11-01
Dopamine release and uptake have been studied in the Drosophila larval ventral nerve cord (VNC) using optogenetics to stimulate endogenous release. However, other areas of the central nervous system remain uncharacterized. Here, we compare dopamine release in the VNC and protocerebrum of larval Drosophila. Stimulations were performed with CsChrimson, a new, improved, red light-activated channelrhodopsin. In both regions, dopamine release was observed after only a single, 4 ms duration light pulse. Michaelis-Menten modeling was used to understand release and uptake parameters for dopamine. The amount of dopamine released ([DA]p ) on the first stimulation pulse is higher than the average [DA]p released from subsequent pulses. The initial and average amount of dopamine released per stimulation pulse is smaller in the protocerebrum than in the VNC. The average Vmax of 0.08 μM/s in the protocerebrum was significantly higher than the Vmax of 0.05 μM/s in the VNC. The average Km of 0.11 μM in the protocerebrum was not significantly different from the Km of 0.10 μM in the VNC. When the competitive dopamine transporter (DAT) inhibitor nisoxetine was applied, the Km increased significantly in both regions while Vmax stayed the same. This work demonstrates regional differences in dopamine release and uptake kinetics, indicating important variation in the amount of dopamine available for neurotransmission and neuromodulation. We use a new optogenetic tool, red light activated CsChrimson, to stimulate the release of dopamine in the ventral nerve cord and medial protocerebrum of the larval Drosophila central nervous system. We monitored extracellular dopamine by fast scan cyclic voltammetry and used Michaelis-Menten modeling to probe the regulation of extracellular dopamine, discovering important similarities and differences in these two regions.
Wang, Gangsheng [ORNL; Post, Wilfred M [ORNL; Mayes, Melanie [ORNL
2013-01-01
We developed a Microbial-ENzyme-mediated Decomposition (MEND) model, based on the Michaelis-Menten kinetics, that describes the dynamics of physically defined pools of soil organic matter (SOC). These include particulate, mineral-associated, dissolved organic matter (POC, MOC, and DOC, respectively), microbial biomass, and associated exoenzymes. The ranges and/or distributions of parameters were determined by both analytical steady-state and dynamic analyses with SOC data from the literature. We used an improved multi-objective parameter sensitivity analysis (MOPSA) to identify the most important parameters for the full model: maintenance of microbial biomass, turnover and synthesis of enzymes, and carbon use efficiency (CUE). The model predicted an increase of 2 C (baseline temperature =12 C) caused the pools of POC-Cellulose, MOC, and total SOC to increase with dynamic CUE and decrease with constant CUE, as indicated by the 50% confidence intervals. Regardless of dynamic or constant CUE, the pool sizes of POC, MOC, and total SOC varied from 8% to 8% under +2 C. The scenario analysis using a single parameter set indicates that higher temperature with dynamic CUE might result in greater net increases in both POC-Cellulose and MOC pools. Different dynamics of various SOC pools reflected the catalytic functions of specific enzymes targeting specific substrates and the interactions between microbes, enzymes, and SOC. With the feasible parameter values estimated in this study, models incorporating fundamental principles of microbial-enzyme dynamics can lead to simulation results qualitatively different from traditional models with fast/slow/passive pools.
Marcella A. A. Carneiro
2011-04-01
Full Text Available The absorption efficiency and kinetic parameters (Vmax, Ks and Vmax:Ks of the seaweed Gracilaria cervicornis for the nutrients NH4+, NO3- and PO4(3- were evaluated. Absorption efficiency was measured by monitoring nutrient concentrations for 5 h in culture media with initial concentrations of 5, 10, 20 and 30µM. Kinetic parameters were determined by using the Michaelis-Menten formula. Absorption efficiencies for this algae were greater in treatments with lower concentrations, as evidenced by a reduction of 85.3, 97.5 and 81.2% for NH4+, NO3- and PO4(3-, respectively. Kinetic parameters show that G. cervicornis exhibits greater ability to take up high concentrations of NH4+ (Vmax=158.5µM g dw-1 h-1 and low concentrations of PO4(3- (Ks=5µM and Vmax:Ks=10.3. These results suggest that this algal species has good absorption capacity for the nutrients tested and may be a promising candidate as a bioremediator of eutrophized environments.
Chowdhury, Debashish
2014-01-01
Cytoskeletal motor proteins move on filamentous tracks by converting input chemical energy that they derive by catalyzing the hydrolysis of ATP. The ATPase site is the analogue of an engine and hydrolysis of ATP is the analogue of burning of chemical fuel. Moreover, the functional role of a segment of the motor is analogous to that of the transmission system of an automobile, which consists of a shaft, gear, clutch, etc. The operation of the engine is intrinsically 'noisy' and the motor faces a molecular 'hailstorm' in the aqueous medium. In this commemorative review, we celebrate the centenary of Michaelis and Menten's landmark paper of 1913 and the golden jubilee of Monod and colleagues classic paper of 1963 by highlighting their relevance with respect to explaining the operational mechanisms of the engine and the transmission system, respectively, of cytoskeletal motors. © 2013 FEBS.
Her, Cheenou; Alonzo, Aaron P.; Vang, Justin Y.; Torres, Ernesto; Krishnan, V. V.
2015-01-01
Enzyme kinetics is an essential part of a chemistry curriculum, especially for students interested in biomedical research or in health care fields. Though the concept is routinely performed in undergraduate chemistry/biochemistry classrooms using other spectroscopic methods, we provide an optimized approach that uses a real-time monitoring of the…
Her, Cheenou; Alonzo, Aaron P.; Vang, Justin Y.; Torres, Ernesto; Krishnan, V. V.
2015-01-01
Enzyme kinetics is an essential part of a chemistry curriculum, especially for students interested in biomedical research or in health care fields. Though the concept is routinely performed in undergraduate chemistry/biochemistry classrooms using other spectroscopic methods, we provide an optimized approach that uses a real-time monitoring of the…
Jensen, Michael Gejl; Rungby, Jørgen; Brock, Birgitte;
2014-01-01
Glucagon-like peptide-1 (GLP-1) is a potent insulinotropic incretin hormone with pancreatic and extrapancreatic effects. Studies reveal significant effects in regions of brain tissue that regulate appetite and satiety. The effects cause that mimetics of GLP-1 serves as treatment of type 2 diabete...... and in vivo, as in pancreas. The apparent neuroprotective potential of GLP-1, indirectly acting through changes of cerebral blood flow, glucose metabolism or brain glucose concentration, or all of these, is worthy of close attention....
Fogel, R; Limson, J L
2011-07-10
The method of immobilization of a protein has a great influence on the overall conformation, and hence, functioning of the protein. Thus, a greater understanding of the events undergone by the protein during immobilization is key to manipulating the immobilization method to produce a strategy that influences the advantages of immobilization while minimizing their disadvantages in biosensor design. In this, the second paper of a two-part series, we have assessed the kinetic parameters of thin-film laccase monolayers, covalently attached to SAMs differing in spacer-arm length and lateral density of spacer arms. This was achieved using chronoamperometry and an electroactive product (p-benzoquinone), which was modeled in a non-linear regressional fashion to extract the relevant parameters. Finally, comparisons between the kinetic parameters presented in this paper and the rheological parameters of laccase monolayers immobilized in the same manner (Part I of this two paper series) were performed. Improvements in the maximal enzyme-catalysed current, i(max), the apparent Michaelis-Menten constant, K(m) and the apparent biosensor sensitivity were noted for most of the surfaces with increasing linker length. Decreasing the lateral density of the spacer-arms brought about a general improvement in these parameters, which is attributed to the decrease in multiple points of immobilization undergone by functional proteins. Finally, comparisons between rheological data and kinetics data showed that the degree of viscosity exhibited by protein films has a negative influence on attached protein layers, while enhanced protein hydration levels (assessed piezoelectrically from data obtained in Paper 1) has a positive effect on those surfaces comprising rigidly bound protein layers.
Vinks, Alexander A; Den Hollander, Jan G; Overbeek, Shelley E; Jelliffe, Roger W; Mouton, Johan W
2003-02-01
The purpose of this study was to describe the nonlinear pharmacokinetics of piperacillin observed during intermittent infusion and continuous infusion by using a nonparametric population modeling approach. Data were 120 serum piperacillin concentration measurements from eight adult cystic fibrosis (CF) patients. Individual pharmacokinetic parameter estimates during intermittent infusion or continuous infusion were calculated by noncompartmental analysis and with a maximum iterative two-stage Bayesian estimator. To simultaneously describe concentration-time data during intermittent infusion and continuous infusion, nonlinear models were parameterized as two-compartment Michaelis-Menten models. Models were fit to the data with the nonparametric expectation maximization algorithm. The calculations were executed on a remote supercomputer. Nonlinear models were evaluated by log-likelihood estimates, residual plots, and R(2) values, and predictive performance was based on bias (mean weighted error [MWE]) and precision (mean weighted square error [MWSE]). A linear pharmacokinetic model could not describe combined intermittent infusion and continuous infusion data well. A good population model fit to the intermittent infusion and continuous infusion data was obtained with the constructed nonlinear models. Maximum a posteriori probability (MAP) Bayesian R(2) values for the nonlinear models were 0.96 to 0.97. Median parameter estimates for the best nonlinear model were as follows: K(m), 58 +/- 75 mg/liter (mean and standard deviation); V(max), 1,904 +/- 1,009 mg/h; volume of distribution of the central compartment, 14.1 +/- 3.0 liters; k(12), 0.63 +/- 0.41 h(-1); and k(21), 0.37 +/- 0.19 h(-1). The median bias (MWE) and precision (MWSE) values for MAP Bayesian estimation with the Michaelis-Menten model were 0.05 and 4.6 mg/liters, respectively. The developed nonlinear pharmacokinetic models can be used to optimize piperacillin therapy administered via continuous infusion in
Ultrasound mediated enzymatic hydrolysis of cellulose and carboxymethyl cellulose.
Sulaiman, Ahmad Ziad; Ajit, Azilah; Chisti, Yusuf
2013-01-01
A recombinant Trichoderma reesei cellulase was used for the ultrasound-mediated hydrolysis of soluble carboxymethyl cellulose (CMC) and insoluble cellulose of various particle sizes. The hydrolysis was carried out at low intensity sonication (2.4-11.8 W cm(-2) sonication power at the tip of the sonotrode) using 10, 20, and 40% duty cycles. [A duty cycle of 10%, for example, was obtained by sonicating for 1 s followed by a rest period (no sonication) of 9 s.] The reaction pH and temperature were always 4.8 and 50°C, respectively. In all cases, sonication enhanced the rate of hydrolysis relative to nonsonicated controls. The hydrolysis of CMC was characterized by Michaelis-Menten kinetics. The Michaelis-Menten parameter of the maximum reaction rate Vmax was enhanced by sonication relative to controls, but the value of the saturation constant Km was reduced. The optimal sonication conditions were found to be a 10% duty cycle and a power intensity of 11.8 W cm(-2) . Under these conditions, the maximum rate of hydrolysis of soluble CMC was nearly double relative to control. In the hydrolysis of cellulose, an increasing particle size reduced the rate of hydrolysis. At any fixed particle size, sonication at a 10% duty cycle and 11.8 W cm(-2) power intensity improved the rate of hydrolysis relative to control. Under the above mentioned optimal sonication conditions, the enzyme lost about 20% of its initial activity in 20 min. Sonication was useful in accelerating the enzyme catalyzed saccharification of cellulose. © 2013 American Institute of Chemical Engineers.
Reassessment of stiripentol pharmacokinetics in healthy adult volunteers.
Peigné, Sophie; Rey, Elisabeth; Le Guern, Marie-Emmanuelle; Dulac, Olivier; Chiron, Catherine; Pons, Gerard; Jullien, Vincent
2014-07-01
Because children who have been receiving stiripentol for the treatment of Dravet syndrome for more than 10 years are now becoming young adults, it is important to accurately characterize stiripentol pharmacokinetics in this age range. A double-blind placebo-controlled dose ranging study was therefore conducted to investigate the pharmacokinetics and tolerability of stiripentol in 12 healthy volunteers. Each subject received 3 single doses of stiripentol (500, 1000, and 2000 mg) separated by a wash-out period of 1 week. Pharmacokinetics of stiripentol was analyzed for each dose by non-compartmental analysis. Median area under the curve (AUC), terminal elimination half-life (t1/2,z) and maximal concentration (Cmax) were calculated for between-dose comparison. Safety was evaluated based on both clinical and biological criteria. Oppositely to previous results, there was no concentration rebounds in the elimination phase, which could be the consequence of the food intake. A more than proportional increase in the AUC was observed, associated with a significant increase in the t1/2,z, for increasing doses (median AUC of 8.3, 31 and 88 mgh/L, and median t1/2,z of 2, 7.7 and 10h for the 500, 1000, and 2000 mg doses respectively), which confirmed the Michaelis-Menten pharmacokinetics of Stiripentol. However, dose-normalized Cmax did not significantly vary between doses. Median Michaelis-Menten parameters were 117 mg/h for Vmax and 1.9 mg/L for Km. No safety concern was observed during the study. The present study allowed a better characterization of the disposition phase of stiripentol and confirmed its non-linear pharmacokinetic behaviour. Further pharmacokinetic/pharmacodynamic studies would be useful to determine the optimal dose of stiripentol for the treatment of Dravet patients in adulthood.
Enzymatic Reactions in Microfluidic Devices
Ristenpart, W. D.; Wan, J.; Stone, H. A.
2008-11-01
We establish simple scaling laws for enzymatic reactions in microfluidic devices, and we demonstrate that kinetic parameters obtained conventionally using multiple stop-flow experiments may instead be extracted from a single microfluidic experiment. Introduction of an enzyme and substrate species in different arms of a Y-shaped channel allows the two species to diffuse across the parallel streamlines and to begin reacting. Measurements of the product concentration versus distance down the channel provide information about the kinetics of the reaction. In the limit where the enzyme is much larger (and thus less diffusive) than the substrate, we show that near the entrance the total amount of product (P) formed varies as a power law in the distance x down the channel. For reactions that follow standard Michaelis-Menten kinetics, the power law takes the form P˜(Vmax/Km) x^5/2, where Vmax and Km are the maximum reaction rate and Michaelis constant respectively. If a large excess of substrate is used, then Km is identified by measuring Vmax far downstream where the different species are completely mixed by diffusion. Numerical simulations and experiments using the bioluminescent reaction between luciferase and ATP as a model system are both shown to accord with the model. We discuss the implications for significant savings in the amount of time and enzyme required for determination of kinetic parameters.
Zoe Rogers
2016-09-01
Full Text Available N-acetyltransferase 2 (NAT2 catalyzes the acetylation of isoniazid to N-acetylisoniazid. NAT2 polymorphism explains 88% of isoniazid clearance variability in adults. We examined the effects of clinical and genetic factors on Michaelis-Menten reaction kinetic constants of maximum velocity (Vmax and affinity (Km in children 0–10 years old. We measured the rates of isoniazid elimination and N-acetylisoniazid production in the blood of 30 children. Since maturation effects could be non-linear, we utilized a pharmacometric approach and the artificial intelligence method, multivariate adaptive regression splines (MARS, to identify factors predicting NAT2 Vmax and Km by examining clinical, genetic, and laboratory factors in toto. Isoniazid concentration predicted both Vmax and Km and superseded the contribution of NAT2 genotype. Age non-linearly modified the NAT2 genotype contribution until maturation at ≥5.3 years. Thus, enzyme efficiency was constrained by substrate concentration, genes, and age. Since MARS output is in the form of basis functions and equations, it allows multiscale systems modeling from the level of cellular chemical reactions to whole body physiological parameters, by automatic selection of significant predictors by the algorithm.
Christley Scott
2010-07-01
Full Text Available Abstract Background Stochastic effects can be important for the behavior of processes involving small population numbers, so the study of stochastic models has become an important topic in the burgeoning field of computational systems biology. However analysis techniques for stochastic models have tended to lag behind their deterministic cousins due to the heavier computational demands of the statistical approaches for fitting the models to experimental data. There is a continuing need for more effective and efficient algorithms. In this article we focus on the parameter inference problem for stochastic kinetic models of biochemical reactions given discrete time-course observations of either some or all of the molecular species. Results We propose an algorithm for inference of kinetic rate parameters based upon maximum likelihood using stochastic gradient descent (SGD. We derive a general formula for the gradient of the likelihood function given discrete time-course observations. The formula applies to any explicit functional form of the kinetic rate laws such as mass-action, Michaelis-Menten, etc. Our algorithm estimates the gradient of the likelihood function by reversible jump Markov chain Monte Carlo sampling (RJMCMC, and then gradient descent method is employed to obtain the maximum likelihood estimation of parameter values. Furthermore, we utilize flux balance analysis and show how to automatically construct reversible jump samplers for arbitrary biochemical reaction models. We provide RJMCMC sampling algorithms for both fully observed and partially observed time-course observation data. Our methods are illustrated with two examples: a birth-death model and an auto-regulatory gene network. We find good agreement of the inferred parameters with the actual parameters in both models. Conclusions The SGD method proposed in the paper presents a general framework of inferring parameters for stochastic kinetic models. The method is
Helms, Hans Christian
ekspressionen af EAAT-2 og -3 var uklar. L-glutamat blev opkoncentreret i endothelcellerne indenfor 5 minutter af basolateral tilsætning. Optaget blev hæmmet af en generel EAAT-hæmmer og udviste Michaelis-Menten kinetik med Vmax på 31 ± 6 pmol • cm-2 • min-1 og KM på 36 ± 25 µM. Resultaterne viser, at BBB kan...
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2007-01-01
In this paper, differential pulse voltammetry (DPV) was applied to study the effects of aluminum Al(Ⅲ) on the lactate dehydrogenase (LDH) activity. Michaelis-Menten constant (KNADHm) and maximum velocity (vmax) in the enzyme promoting catalytic reaction of "pyruvate(Pyr) + NADH + H+ LDH(=) lactate + NAD+" under different conditions by monitoring DPV reduction current of NAD+ were reported.(C) 2007 Shu Ping Bi. Published by Elsevier B.V. on behalf of Chinese Chemical Society. All rights reserved.
Kinetics of phosphorus uptake and root morphology of local and improved varieties of maize
Machado Cynthia Torres de Toledo
2004-01-01
Full Text Available Interspecific and intraspecific differences in the efficiency of utilization of soil phosphorus (P are explained, in part, by plant morphological and physiological variations, which characterize the plant for nutrient acquisition. As part of a study on maize genotypes characterization for P-uptake and use efficiency, kinetic parameters of P uptake and root morphological characters were evaluated for six local and improved maize varieties, grown in nutrient solution. The kinetic parameters related to P influx were: maximal transport rate (Vmax, the Michaelis-Menten constant (Km, and the external concentration when net uptake is zero (Cmin. Measured root morphological characters were: root length, radius, and surface area. Shoot and root dry matter yield and the P content in these parts were also determined. Diferences among varieties were observed in the kinetic parameters Vmax and Km, root length and in root/shoot dry matter ratio. Lower Km values were better indicatives of P uptake ability of the varietes and were significantly correlated to higher dry matter production and P-efficiency index.
Syahinaz Shahrazi
2013-01-01
Full Text Available This study relates to the mathematical modelling of enzymatic production of Cyclodextrins (CDs by Cyclodextrin Glucanotransferase (CGTase from Bacillus macerans. The experiments were carried out in batch mode using different starch sources and the results were used to estimate unknown parameters using linearization and dynamic simulation methods. Î±- and Î²-CD produced from tapioca were found to give the highest Michaelis-Menten constant, KM,i of 58.23 and 54.07 g L-1, respectively and maximum velocity, Vmax,i of 3.45 and 2.76 g L-1.min, respectively, while sago resulted in the highest KM,i and Vmax,i values of 342.35 g L-1 and 5.97 g L-1.min, respectively, for Î³-CD obtained by the linearization method. Value of product inhibition, K1,i and CD degradation coefficient rate, Î´CD,i, were estimated using dynamic simulation, indicating that exponential reaction kinetics could be fitted better with the experimental data. Sensitivity analysis revealed that the product inhibition parameter in the exponential reaction kinetic equation is more significant in the process. For validation, the production of CDs by fed batch method was undertaken and starch and enzyme were added into the reaction medium. Then, the predicted profiles generated by simulation were compared with the experimental values. The proposed exponential reaction kinetics shows good fitting with the experimental data.
A Qualitative Approach to Enzyme Inhibition
Waldrop, Grover L.
2009-01-01
Most general biochemistry textbooks present enzyme inhibition by showing how the basic Michaelis-Menten parameters K[subscript m] and V[subscript max] are affected mathematically by a particular type of inhibitor. This approach, while mathematically rigorous, does not lend itself to understanding how inhibition patterns are used to determine the…
KINETICS OF QUERCETIN NITRATIO N BY HORSERADISH PEROXIDASE
Andrija Šmelcerović
2013-03-01
Full Text Available In this study we investigated the kinetics of the nitration of quercetin by horseradish peroxidase. Quercetin nitration reaction was followed by recording the spectral changes over the time at 380 nm. The reaction rate increases with increasing of the quercetin concentration and follows the Michaelis-Menten type kinetics. Kinetic parameters of the studied enzymatic reaction were determined.
A Qualitative Approach to Enzyme Inhibition
Waldrop, Grover L.
2009-01-01
Most general biochemistry textbooks present enzyme inhibition by showing how the basic Michaelis-Menten parameters K[subscript m] and V[subscript max] are affected mathematically by a particular type of inhibitor. This approach, while mathematically rigorous, does not lend itself to understanding how inhibition patterns are used to determine the…
Deng, Dongyang; Weidhaas, Jennifer L; Lin, Lian-Shin
2016-03-15
The kinetics and microbial ecology in sulfidogenic bioreactors used in a novel two-stage process for co-treatment of acid mine drainage (AMD) and municipal wastewater (MWW) were investigated. Michaelis-Menten modeling of COD oxidation by sulfate reducing bacteria (SRB) (Vmax=0.33mgL(-1)min(-1), Km=4.3mgL(-1)) suggested that the Vmax can be reasonably achieved given the typical COD values in MWW and anticipated mixing with AMD. Non-competitive inhibition modeling (Ki=6.55mgL(-1)) indicated that excessive iron level should be avoided to limit its effects on SRB. The COD oxidation rate was positively correlated to COD/sulfate ratio and SRB population, as evidenced by dsrA gene copies. Phylogenetic analysis revealed diverse microbial communities dominated by sulfate reducing delta-proteobacteria. Microbial community and relative quantities of SRB showed significant differences under different COD/sulfate ratios (0.2, 1 and 2), and the highest dsrA gene concentration and most complex microbial diversity were observed under COD/sulfate ratio 2. Major species were associated with Desulfovirga, Desulfobulbus, Desulfovibrio, and Syntrophus sp. The reported COD kinetics, SRB abundances and the phylogenetic profile provide insights into the co-treatment process and help identify the parameters of concerns for such technology development. Copyright © 2015 Elsevier B.V. All rights reserved.
Use of mesoporous MnO2 as a support for immobilization of lipase from Candida rugosa
Babaei Mahsa
2014-01-01
Full Text Available In this study, immobilization of lipase from Candida rugosa on mesoporous manganese dioxide by adsorption method was carried out and the effect of three immobilization variables including temperature, process time and enzyme/support ratio on immobilization efficiency were studied. The characteristics of synthesized MnO2 and lipase-bound MnO2 were investigated by scanning electron microscopy (SEM, transmission electron microscopy (TEM and Fourier Transform Infrared Spectroscopy (FT-IR methods. The porous property of the support particles was also studied by X-ray diffraction (XRD and Brunauer, Emmett, and Teller (BET measurements. Thermal stability of immobilized lipase was determined to be better than that of free enzyme. Also the operational stability of lipase-bound MnO2 was studied and showed an almost strong attachment of enzyme to support. The Michaelis-Menten kinetic parameters (Km and Vmax were also determined for both free and immobilized lipases. It was observed that there is an increase of the Km value (672.96 mg/ml and a decrease of the Vmax value (130.99 U/mg for the immobilized enzyme comparing with the corresponding values of the free lipase.
Zaritzky, N.
2004-06-01
Full Text Available Soluble or immobilized A2 phospholipase liberates one mole of fatty acid of the C-2 position in soybean lecithin phospholipids to product lysolecithins. When using the enzyme in its immobilized form the enzymatic activity decreases due to substrate and product transport phenomenon. By comparison of the kinetic parameters of the hydrolysis reaction catalized by A2 phospholipase immobilized on alumina or on DEAE-Sephadex against those of the soluble enzyme, for soybean lecithin hydrolysis reaction, the diffusive effects were evaluated. The decrease of the reaction rate was quantified in presence of diffusive effects and the effectiveness factors were calculated. The Michaelis-Menten kinetic parameters were determined: KM = 8,2.10-2 molÂ·l-1 and 5,36.10-2 molÂ·l-1 and Vmax = 7,7.10-5 molÂ·l-1 .min-1 and 9,5.10-5 molÂ·l-1 Â·min-1 for the enzyme immobilized on alumina and on DEAE-Sephadex, respectively. The effectiveness factors were 0,277 for alumina and 0,376 for DEAE-Sephadex.La Fosfolipasa A2, soluble o inmovilizada, libera un mol de ácido graso de la posición C-2 de los fosfolípidos de la lecitina de soja para producir lisolecitinas. Cuando se utiliza la enzima en su forma inmovilizada, la actividad enzimática decrece debido al fenómeno de transporte de sustrato y de producto. Se evaluaron los efectos de difusión comparando los parámetros cinéticos de la reacción de hidrólisis de lecitina de soja catalizada por fosfolipasa A2 inmovilizada sobre alúmina o sobre DEAE-Sephadex, frente a los de enzima soluble. La disminución de la velocidad de reacción fue cuantificada en presencia de efectos difusionales y se calcularon los factores de eficiencia. Se determinaron los parámetros de Michaelis-Menten: KM = 8,2.10-2 molÂ·l-1 and 5,36.10-2 molÂ·l-1 y Vmax = 7,7.10-5 molÂ·l-1 .min-1 y 9,5.10-5 molÂ·l-1 Â·min-1 para la enzima inmovilizada sobre alúmina y sobre DEAE-Sephadex, respectivamente. El factor de eficiencia fue 0
Modeling of Bacillus spores: Inactivation and Outgrowth
2011-03-01
52 Michaelis - Menten Kinetics ...of repair mechanism [36]. These models were based on Michaelis - Menten kinetics , which is also the foundation of the work in this research Michaelis ...catalyzed reactions. Michaelis - Menten kinetics is a model of enzyme kinetics . The Michaelis - Menten equation describes the rates of enzymatic reactions by
Assessment and kinetics of soil phosphatase in Brazilian Savanna systems
ADÃO S. FERREIRA
2016-06-01
Full Text Available The activity and kinetics of soil phosphatases are important indicators to evaluate soil quality in specific sites such as the Cerrado (Brazilian Savanna. This study aimed to determine the activity and kinetic parameters of soil phosphatase in Cerrado systems. Soil phosphatase activity was assessed in samples of native Cerrado (NC, no-tillage (NT, conventional tillage (CT and pasture with Brachiaria brizantha (PBb and evaluated with acetate buffer (AB, tris-HCl buffer (TB, modified universal buffer (MUB and low MUB. The Michaelis-Menten equation and Eadie-Hofstee model were applied to obtain the kinetic parameters of soil phosphatase using different concentrations of p-nitrophenol phosphate (p-NPP. MUB showed the lowest soil phosphatase activity in all soils whereas AB in NC and NT presented the highest. Low MUB decreased interferences in the assessment of soil phosphatase activity when compared to MUB, suggesting that organic acids interfere on the soil phosphatase activity. In NC and NT, soil phosphatase activity performed with TB was similar to AB and low MUB. Km values from the Michaels-Menten equation were higher in NC than in NT, which indicate a lower affinity of phosphatase activity for the substrate in NC. Vmax values were also higher in NC than in NT. The Eadie-Hofstee model suggests that NC had more phosphatase isoforms than NT. The study showed that buffer type is of fundamental importance when assessing soil phosphatase activity in Cerrado soils.
马中良; 李艳利; 鲍真真; 王旻
2005-01-01
在生物化学试验中,酶的米氏常数的测定实验是经典的实验.通过Km 测定这一实验的改进,指导学生怎样认识和把握理论知识,并将之应用科学研究中.在生物化学实验教学中,注意提高学生的动手能力,提高解决问题和分析问题的能力,从而形成对待实验结果和教材的正确观点.
林中; 苏银法
2004-01-01
目的: 获得(一级并行)米氏消除药物静脉注射给药时的血药浓度近似解.方法: 根据四阶Runge-Kutta算法,采用Excel软件编写基于药动学参数的程序.结果:输出某周期或稳态任一次给药后的预期血药浓度.结论:方法操作简单,结果可靠,可作为(一级并行)米氏消除药物静脉注射给药时药动学方程的数值解法.
苏银法; 杜乐燕
2006-01-01
目的获得(一级并行)米氏消除药物血管外给药时的血药浓度近似值.方法根据四阶Runge-Kutta算法,采用Excel软件编写基于药动学参数的血药浓度近似解表格程序.结果通过实例演示,可以输出第n周期(或稳态)第s次血管外给药后每间隔0.005 h的预期血药浓度.结论该法是(一级并行)米氏消除药物血管外给药动力学方程的一种可靠的数值解法.
祁兵; 黄大贶
2003-01-01
@@ Michaelis-Menten消除动力学(下称米氏型消除)是非线性药物动力学中的重要部分.大量临床研究表明[1],呈药动学非线性特征的药物,尤有必要进行血药浓度监测.本文对静注多次给药情况下的稳态动力学特征进行了研究,得到了稳态浓度存在的必要条件及稳态浓度的精确表达式,为临床用药提供了理论依据.
HE Binglin(Ho Pinglum); HUANG Wenqiang
1983-01-01
As a model of serine hydrolase, the condensation polymers of salicylic acid, formaldehyde and methyl amine, n-propyl amine, n-hexyl amine or n-lauryl amine were prepared by polycondensation catalyzed by sulfuric acid. It was confirmed by potentiometric titration and infrared spectrum that the polymers containing tertiary amino group possess the structure which resembles the internal salt of amino acid in weak basic and weak acidic solution:[-OOC-OH-CH2-H+N-R-CH2-]n R=alkyl group The catalytic reaction of the above polymers for hydrolysis of active ester,p-nitrophenyl acetate (PNPA),was studied .It was found kinetically that the most efficient catalytic effect of polymer was composed of two salicylic acid groups and one tertiary amino group in the polymer chain.The rates of hydrolysis of PNPA increase with increasing of pH values and length of the alkyl group in the side chain of the polymers and the effect of the conformation of the polymer containing tertiary amino group in the buffer solution on the catalytic activity was also investigated. Hydrolysis of PNPA catalyzed by the polymer made of salicylic acid, formaldehyde and n-lauryl amine follows the simple Michaelis-Menten type mechanism . The kinetics parameters were determined as :Km 6.7×10-5 M and Vmax 2.07×10-7 M·min-1.
Effects of 2'-O-methyl nucleotide on ligation capability of T4 DNA ligase.
Zhao, Bin; Tong, Zhaoxue; Zhao, Guojie; Mu, Runqing; Shang, Hong; Guan, Yifu
2014-09-01
To further understand the ligation mechanism, effects of 2'-O-methyl nucleotide (2'-OMeN) on the T4 DNA ligation efficiency were investigated. Fluorescence resonance energy transfer assay was used to monitor the nick-joining process by T4 DNA ligase. Results showed that substitutions at 5'- and 3'-ends of the nick decreased the ligation efficiency by 48.7% ± 6.7% and 70.6% ± 4.0%, respectively. Substitutions at both 5'- and 3'-ends decreased the ligation efficiency by 76.6% ± 1.3%. Corresponding kinetic parameters, Vmax, Km, and kcat, have been determined in each case by using the Michaelis-Menten equation. The kinetic data showed that the 2'-OMeN substitutions reduced the maximal initial velocity and increased the Michaelis constant of T4 DNA ligase. Mismatches at 5'- and 3'-ends of the nick have also shown different influences on the ligation. Results here showed that the sugar pucker conformation at 3'-end impairs the ligation efficiency more profoundly than that at 5'-end. Different concentrations of Mg(2+), Ca(2+), K(+), Na(+), and ATP were also demonstrated to affect the T4 DNA ligase activity. These results enriched our knowledge about the effects of 2'-OMeN substitutions on the T4 DNA ligase.
Das, Bipasha; Bhattacharjee, Sangita; Bhattacharjee, Chiranjib
2013-09-01
In this study, ultrafiltration (UF) of pretreated casein whey was carried out in a cross-flow module fitted with 5 kDa molecular weight cut-off polyethersulfone membrane to recover whey proteins in the retentate and lactose in the permeate. Effects of processing conditions, like transmembrane pressure and pH on permeate flux and rejection were investigated and reported. The polarised layer resistance was found to increase with time during UF even in this high shear device. The lactose concentration in the permeate was measured using dinitro salicylic acid method. Enzymatic kinetic study for lactose hydrolysis was carried out at three different temperatures ranging from 30 to 50 °C using β-galactosidase enzyme. The glucose formed during lactose hydrolysis was analyzed using glucose oxidase-peroxidase method. Kinetics of enzymatic hydrolysis of lactose solution was found to follow Michaelis-Menten model and the model parameters were estimated by Lineweaver-Burk plot. The hydrolysis rate was found to be maximum (with Vmax = 5.5091 mmol/L/min) at 30 °C.
YANG,Huang-Hao(杨黄浩); LI,Dong-Hui(李东辉); CHEN,Xiao-Lan(陈小兰); QU,Hui-Ying(曲会英); DING,Ma-Tai(丁马太); XU,Jin-Gou(许金钩)
2002-01-01
The use of tetra-substituted amino aluminum phthalocyanine (TAAIPc) as a new red-region fluorescent substrate for horseradish peroxidase (HRP)-based enzyme-linked immunosorbent assay was investigated. TAAIPc displayed an excitation maximum at 610 mn and emission maximum at 678 nm in a strong acidic medium. In the presence of HRP, trace amounts of H2O2 could rapidly and significantly react with TAAIPc, thus quenching the fluorescence of TAAIPc. The Michaelis- Menten parameters Km and Vmax were measured to be 2.82×10-6 mol/L-1 amt6.0×10-9 mol.L-1.s-1, respectively. In this paper, TAAlPc was used in an HRP-based ehzyme-linked immunosorbent assay (ELISA) of a-fetoprotein (AFP) in human serum with satisfactory results. AFP could be determined in the concentration range of 0.5-200 ng/mL with a detection limit of 0.2 ng/mL, which was close to that of radioimmunoassay. The advantage of proposed method was strongly minimizing the interference resulting from background fluorescence or scattering light and had a high analytical sensitivity.
CHEN Lihua; LIU Liuzhan; SHEN Hanxi
2005-01-01
Enzyme-catalytic fluorescence determination of artemisinin (qinghaosu, QHS) was developed using pyronine B (PB) as substrate of horseradish peroxidase (HRP). The interaction between HRP and QHS was an enzyme-substrate model. The catalytic characteristic of HRP in the oxidation reaction, in which the fluorescence of PB was decreased in the presence of QHS, was studied. The steady-state catalytic rate depended upon enzyme and substrate concentrations, and the Michaelis-Menten parameters Km, Vmax and Kcat were 8.4×10-5 mol·L-1, 7.4×10-6 mol·L-1 s-1 and 50.23 s-1. The catalytic activity of enzyme was inhibited in the presence of deactivated agents and at high temperature, respectively. Under optimum conditions, linear relationship between fluorescence intensity change (F0-F) of pyronine B and concentration of QHS was in the range of 1.41×10-7―1.27×10-6 mol·L-1. The detection limit (3σ) was determined to be 2.7×10-8 mol·L-1. The proposed method was applied to the concentration determination of QHS in the media of plasma or urine samples.
Bento, H. B. S.; de Castro, H. F.; de Oliveira, P. C.; Freitas, L.
2017-03-01
Magnetized hydrophobic polymeric particles were prepared by suspension polymerization of styrene and divinylbenzene with the addition of magnetite (Fe3O4) functionalized with oleic acid (OA). The magnetic poly(STY-co-DVB) particles were characterized by Fourier transform infrared spectroscopy (FTIR), X-ray diffraction (XRD) and scanning electron microscopy (SEM). The results showed that the magnetic polymer particles fulfill the requirements for being used as matrix in the immobilization of microbial lipase from Candida rugosa by physical adsorption. The resulted immobilized derivative presented high catalytic activity in both aqueous and non-aqueous media. A comparative study between free and immobilized lipases showed a similar biochemical behavior, but with better hydrolytic activity at a pH range of 8.0-8.5. The patterns of heat stability indicated that the immobilization process also stabilizes the enzyme by a 50-fold improvement of thermal stability parameters (thermal deactivation and half-life time). Data on olive oil hydrolytic activities indicated that the Michaelis-Menten equation can be used to adjust data so as to calculate Km and Vmax, which attained values of 1766 mM and 5870 μM g-1 min-1, respectively. Such values indicated that the immobilized system was subjected to mass transfer limitations. High operational stability (t ½=1014 h) was achieved under repetitive batch runs in ester synthesis. The results indicated that the magnetized support particles can be very promising carriers for immobilizing enzymes in biotransformation reactions.
Nitrate Effect on Rice Growth and Nitrogen Absorption and Assimilation at Different Growth Stages
DUAN Ying-Hua; ZHANG Ya-Li; SHEN Qi-Rong; WANG Song-Wei
2006-01-01
The effect of nitrate (NO3-) on rice (Oryza sativa L.) growth as well as N absorption and assimilation during different growth stages was examined using three typical rice cultivars. Dry weight, yield, N uptake, nitrate reductase activity(NRA) in leaves, and glutamine synthetase activity (GSA) in roots and leaves during their entire growth periods, as well as the kinetic parameters of ammonium (NH4+) uptake at the seedling stage, were measured with solution culture experiments. Results indicated that addition of NH4+-N and NO3--N at a ratio of 75:25 (NH4++NO3- treatment) whencompared with that of NH4+-N alone (NH4+ treatment) increased the dry weight of 'Nanguang' cultivar by 30% and treatment compared to the NH4+ treatment, NRA in the leaves increased by 2.09 folds, and GSA increased by 92% in the roots and 52% in the leaves of the three cultivars. NO3- supply increased the maximum uptake rate (Vmax) in the uptake rate of NH4+ by rice. There was no effect on the apparent Michaelis-Menten constant (Km) of the three cultivars.Thus, some replacement of NH4+ with NO3- could greatly improve the growth of rice plants, mainly on account of the increased uptake of NH4+ promoted by NO3-, and future studies should focus on the molecular mechanism of the increased uptake of NH4+ by NO3-.
Srichandan, Haragobinda; Pathak, Ashish; Kim, Dong Jin; Lee, Seoung-Won
2014-01-01
A central composite design (CCD) combined with response surface methodology (RSM) was employed for maximizing bioleaching yields of metals (Al, Mo, Ni, and V) from as-received spent refinery catalyst using Acidithiobacillus thiooxidans. Three independent variables, namely initial pH, sulfur concentration, and pulp density were investigated. The pH was found to be the most influential parameter with leaching yields of metals varying inversely with pH. Analysis of variance (ANOVA) of the quadratic model indicated that the predicted values were in good agreement with experimental data. Under optimized conditions of 1.0% pulp density, 1.5% sulfur and pH 1.5, about 93% Ni, 44% Al, 34% Mo, and 94% V was leached from the spent refinery catalyst. Among all the metals, V had the highest maximum rate of leaching (Vmax) according to the Michaelis-Menten equation. The results of the study suggested that two-step bioleaching is efficient in leaching of metals from spent refinery catalyst. Moreover, the process can be conducted with as received spent refinery catalyst, thus making the process cost effective for large-scale applications.
Bai, J. P.; Hu, M.; Subramanian, P.; Mosberg, H. I.; Amidon, G. L.
1992-01-01
The feasibility of targeting prolidase as a peptide prodrug-converting enzyme has been examined. The enzymatic hydrolysis by prolidase of substrates for the peptide transporter L-alpha-methyldopa-pro and several dipeptide analogues without an N-terminal alpha-amino group (phenylpropionylproline, phenylacetylproline, N-benzoylproline, and N-acetylproline) was investigated. The Michaelis-Menten parameters Km and Vmax for L-alpha-methyldopa-pro are 0.09 +/- 0.02 mM and 3.98 +/- 0.25 mumol/min/mg protein, respectively. However, no hydrolysis of the dipeptide analogues without an N-terminal alpha-amino group is observed, suggesting that an N-terminal alpha-amino group is required for prolidase activity. These results demonstrate that prolidase may serve as a prodrug-converting enzyme for the dipeptide-type prodrugs, utilizing the peptide carrier for transport of prodrugs into the mucosal cells and prolidase, a cytosolic enzyme, to release the drug. However, a free alpha-amino group appears to be necessary for prolidase hydrolysis.
Silambarasan, Sivagnanam; Vangnai, Alisa S
2016-01-25
4-nitroaniline (4-NA) is one of the major priority pollutants generated from industrial productions and pesticide transformation; however very limited biodegradation details have been reported. This work is the first to report 4-NA biodegradation kinetics and toxicity reduction using a newly isolated plant-growth promoting bacterium, Acinetobacter sp. AVLB2. The 4-NA-dependent growth kinetics parameters: μmax, Ks and Ki, were determined to be 0.039 h(-1), 6.623 mg L(-1) and 25.57 mg L(-1), respectively using Haldane inhibition model, while the maximum biodegradation rate (Vmax) of 4-NA was at 0.541 mg L(-1) h(-1) and 0.551 mg L(-1) h(-1), following Michaelis-Menten and Hanes-Woolf models, respectively. Biodegradation pathway of 4-NA by Acinetobacter sp. AVLB2 was proposed, and successfully led to the reduction of 4-NA toxicity according to the following toxicity assessments: microbial toxicity using Escherichia coli DH5α, phytotoxicity with Vigna radiata and Crotalaria juncea, and cytogenotoxicity with Allium cepa root-tip cells. In addition, Acinetobacter sp. AVLB2 possess important plant-growth promoting traits, both in the presence and absence of 4-NA. This study has provided a new insight into 4-NA biodegradation ability and concurrent plant-growth promoting activities of Acinetobacter sp. AVLB2, which may indicate its potential role for rhizoremediation, while sustaining crop production even under 4-NA stressed environment.
Effects of 2'-O-methyl nucleotide substitution on EcoRI endonuclease cleavage activities.
Guojie Zhao
Full Text Available To investigate the effect of sugar pucker conformation on DNA-protein interactions, we used 2'-O-methyl nucleotide (2'-OMeN to modify the EcoRI recognition sequence -TGAATTCT-, and monitored the enzymatic cleavage process using FRET method. The 2'-O-methyl nucleotide has a C3'-endo sugar pucker conformation different from the C2'-endo sugar pucker conformation of native DNA nucleotides. The initial reaction velocities were measured and the kinetic parameters, Km and Vmax were derived using Michaelis-Menten equation. Experimental results showed that 2'-OMeN substitutions for the EcoRI recognition sequence decreased the cleavage efficiency for A2, A3 and T4 substitutions significantly, and 2'-OMeN substitution for T5 residue inhibited the enzymatic activity completely. In contrast, substitutions for G1 and C6 could maintain the original activity. 2'-fluoro nucleic acid (2'-FNA and locked nucleic acid (LNA having similar C3'-endo sugar pucker conformation also demonstrated similar enzymatic results. This position-dependent enzymatic cleavage property might be attributed to the phosphate backbone distortion caused by the switch from C2'-endo to C3'-endo sugar pucker conformation, and was interpreted on the basis of the DNA-EcoRI structure. These 2'-modified nucleotides could behave as a regulatory element to modulate the enzymatic activity in vitro, and this property will have potential applications in genetic engineering and biomedicine.
Application of microdialysis to study the in vitro metabolism of drugs in liver microsomes.
Gunaratna, C; Kissinger, P T
1997-10-01
Current methods for studying in vitro drug metabolism involve add-incubate-separate-measure approach. Separation of the desired analytes requires removal of protein which is typically accomplished by precipitation and centrifugation and extraction of the analytes into an organic phase. The analysis scheme then becomes more complex resulting in a decrease in precision and an increase in assay time. Microdialysis sampling circumvents these problems by allowing researchers to sample the reaction mixture periodically and obtain the complete metabolic profile. In the present study, microdialysis sampling was used to investigate Phase I metabolism of salicylic acid, diazepam and ibuprofen in rat liver microsomes. The major metabolites of these drugs were profiled by LC. Michaelis-Menten enzyme kinetic parameters, Km and Vmax were obtained for the formation of diazepam metabolites by both microdialysis and conventional microsomal incubations and were in good agreement with the values reported in the literature. This study shows that microdialysis has considerable promise as a sampling technique for in vitro drug metabolism studies. By making minor modifications to the instruments, microdialysis can be applied to other in vitro systems such as isolated hepatocytes to study the Phase II metabolism or tissue slices to study drug distribution.
Hot experience for cold-adapted microorganisms: temperature sensitivity of soil enzymes
Liu, Shibin; Razavidezfuly, Baharsadat; Kuzyakov, Yakov
2016-04-01
The temperature sensitivity of enzymes responsible for organic matter decomposition in cold environment soil, where warming is expected to be greatest is crucial. Based on Michaelis-Menten kinetics and Arrhenius function, we hypothesized that cold-adapted microorganisms will produce high efficient enzymes at cold temperatures (enzymes with lower apparent activation energy (Ea) at cold temperature ranges). To test our hypothesis, 30 g soil of Tibetan Plateau (4100 m a.s.l., annual temperature 2.4 °C) in 4 replicates were incubated for one month over a temperature range of 0-40 °C (with 5 °C steps) and determined the kinetic parameters of six enzymes involved in decomposing organics: cellobiohydrolase and β-glucosidase, which are commonly measured as enzymes responsible for consecutive stages of cellulose degradation; xylanase, which is responsible for breaking down hemicelluloses; acid phosphatase, which mineralizes organic P to phosphate by hydrolyzing phosphoric (mono) ester bonds under acidic conditions. Activities of leucine aminopeptidase and tyrosine aminopeptidase were analyzed to assess the hydrolysis of L-peptide bonds. The apparent activation energy varied between enzymes from 42 (phosphatase) to 54 (cellobiohydrolase) kJ mol-1 corresponding to the Q10 values of the enzyme reactions of 1.8-2.3. The increase of substrate affinity (Km) with temperature was gradual for most tested enzymes from 0-20 °C (enzymes involved in C cycle), (proteases) and 0-40 °C (phosphatase). However, within a high range of temperatures (25-40 °C) the hydrolytic activity was governed by enzymes with nearly constant substrate affinity. Overall, for enzymes involved in C cycle and proteases, a strong increase (30-40%) in Km at high temperatures (25 °C) reflects an expression of multiple isoenzymes each with different temperature optima and probable shift of microbial community. The general trend of catalytic efficiency (Vmax/Km) demonstrated a gradual increase with
Evaluation of rate law approximations in bottom-up kinetic models of metabolism
Du, Bin; Zielinski, Daniel C.; Kavvas, Erol S.
2016-01-01
. These approximate rate laws were: 1) a Michaelis-Menten rate law with measured enzyme parameters, 2) a Michaelis-Menten rate law with approximated parameters, using the convenience kinetics convention, 3) a thermodynamic rate law resulting from a metabolite saturation assumption, and 4) a pure chemical reaction......Background: The mechanistic description of enzyme kinetics in a dynamic model of metabolism requires specifying the numerical values of a large number of kinetic parameters. The parameterization challenge is often addressed through the use of simplifying approximations to form reaction rate laws...... with reduced numbers of parameters. Whether such simplified models can reproduce dynamic characteristics of the full system is an important question. Results: In this work, we compared the local transient response properties of dynamic models constructed using rate laws with varying levels of approximation...
Zebin Wang
2012-04-01
Full Text Available A response study and the effects of different parameters (pH, temperature and enzyme dose on kinetics of isolated soy protein hydrolysis by a trypsin-like endopeptidase (TL1 were conducted. Degree of hydrolysis (%DH data varied at different times under different hydrolysis conditions. Fitting the kinetics data to Michaelis-Menten kinetics model did not result in reasonable kinetic parameters, which implied that Michaelis-Menten kinetics was invalid for such a hydrolysis process. A kinetics model proposed by (Gonzalez-Tello, Camacho, Jurado, Paez, & Guadix, 1994 was found to fit the kinetics curve well and resulted in acceptable model parameters. A simple simulation example was performed to demonstrate the concept of how the kinetics equation could be applied in process engineering.
Sousa Jr R.
2004-01-01
Full Text Available Partial hydrolysis of whey proteins by enzymes immobilized on an inert support can either change or evidence functional properties of the produced peptides, thereby increasing their applications. The hydrolysis of sweet cheese whey proteins by alcalase, which is multipoint-immobilized on agarose gel, is studied here. A Michaelis-Menten model that takes into account competitive inhibition by the product was fitted to experimental data. The influence of pH on the kinetic parameters in the range 6.0 to 11.0 was assessed, at 50ºC. Initial reaction-rate assays in a pHstat at different concentrations of substrate were used to estimate kinetic and Michaelis-Menten parameters, k and K M. Experimental data from long-term batch assays were used to quantify the inhibition parameter, K I. The fitting of the model to the experimental data was accurate in the entire pH range.
Coexistence of steady state for a diffusive prey-predator model with harvesting
Yan Li
2016-07-01
Full Text Available In this article, we study a diffusive prey-predator model with modified Leslie-Gower term and Michaelis-Menten type prey harvesting, subject to homogeneous Dirichlet boundary conditions. Treating the prey harvesting parameter as a bifurcation parameter, we obtain the existence, bifurcation and stability of coexistence steady state solutions. We use the method of upper and lower solutions, degree theory in cones, and bifurcation theory. The conclusions show the importance of prey harvesting in the model.
Effect in vitro of propoxur on kinetics of K+ stimulated PNPPase and protection by thiol reagents.
Babu, G R; Reddy, G R; Rajendra, W; Chetty, C S
1990-09-01
Kinetics analysis of K+ stimulated PNPPase was studied in the rat brain synaptosomes in the presence of propoxur. Non-competitive inhibition with respect to activation by PNPP was seen by the decreased maximal velocity (Vmax) without change in Michaelis-Menten Constant (Km). Activation energy values (delta E) were increased suggesting the decreased catalytic potential of the enzyme. It is also observed that dithiothrietol (DTT) (76 microM), cysteine (82 microM) and glutathione (120 microM) neutralized the inhibition of K(+)-PNPPase by propoxur to different extents.
Ferley, Derek D; Osborn, Roy W; Vukovich, Matthew D
2013-06-01
Uphill running represents a frequently used and often prescribed training tactic in the development of competitive distance runners but remains largely uninvestigated and unsubstantiated as a training modality. The purpose of this investigation included documenting the effects of uphill interval training compared with level-grade interval training on maximal oxygen consumption (VO2max), the running speed associated with VO2max (Vmax), the running speed associated with lactate threshold (V(LT)), and the duration for which Vmax can be sustained (Tmax) in well-trained distance runners. Thirty-two well-trained distance runners (age, 27.4 ± 3.8 years; body mass, 64.8 ± 8.9 kg; height, 173.6 ± 6.4 cm; and VO2max, 60.9 ± 8.5 ml·min(-1)·kg(-1)) received assignment to an uphill interval training group (G(Hill) = 12), level-grade interval training group (G(Flat) = 12), or control group (G(Con) = 8). G(Hill) and G(Flat) completed 12 interval and 12 continuous running sessions over 6 weeks, whereas G(Con) maintained their normal training routine. Pre- and posttest measures of VO2max, Vmax, V(LT), and Tmax were used to assess performance. A 3 × 2 repeated measures analysis of variance was performed for each dependent variable and revealed a significant difference in Tmax in both G(Hill) and G(Flat) (p interval training can induce significant improvements in a run-to-exhaustion test in well-trained runners at the speed associated with VO2max but that traditional level-grade training produces greater gains.
Gumowski, I
1977-01-01
A class of differential equations with pure delay and a hyperbolic nonlinearity, analogous to the Michaelis-Menten term in chemical reaction kinetics, is examined. Conditions for the existence of periodic solutions are established. The amplitude and period dependences on the equation parameters are estimated analytically. A mixed analytico-numerical approach is used in the computations, because a straightforward integration of the equations is numerically ill conditioned. (11 refs).
Charge Transfer Between Quantum Dots and Peptide-Coupled Redox Complexes
2009-01-01
number of intact Ru-peptides per QD-conjugate following enzymatic digestion. This also allowed the derivation of standard Michaelis - Menten kinetic values...in each case the kinetic data agreed reasonably with the expected val- ues.2 Conclusions: We combined the electrochemi- cal properties of redox...locity versus increasing chymotrypsin concentration in the presence and absence of a specific chymostatin inhibitor. The changes in kinetic parameters
2011-03-01
interaction) for each lead candidate compound will be described by conducting Michaelis - Menten kinetic assays to derive KM and kcat for ATP and dsDNA in the...radioactively (32P) at one 5’-end and the purified yeast Mus81-Mms4 protein, we showed in kinetic experiments that the fluorescence labels do not interfere...with endonuclease activity in comparison to several control substrates (8, 9). By determining the kinetic parameters, KM and kcat, we show that there
Moran, B.; Kulkarni, S.S.; Reeves, H.W.
2007-01-01
A path-independent (conservation) integral is developed for the characterization of solute concentration and flux in a biofilm in the vicinity of a detachment or other flux limiting boundary condition. Steady state conditions of solute diffusion are considered and biofilm kinetics are described by an uptake term which can be expressed in terms of a potential (Michaelis-Menten kinetics). An asymptotic solution for solute concentration at the tip of the detachment is obtained and shown to be analogous to that of antiplane crack problems in linear elasticity. It is shown that the amplitude of the asymptotic solution can be calculated by evaluating a path-independent integral. The special case of a semi-infinite detachment in an infinite strip is considered and the amplitude of the asymptotic field is related to the boundary conditions and problem parameters in closed form for zeroth and first order kinetics and numerically for Michaelis-Menten kinetics. ?? Springer Science+Business Media, Inc. 2007.
Kim, Seung-Hyun; Chung, Jong-Bae; Jeong, Byeong-Ryong; Lee, Young-Deuk; Prasher, Shiv O
2003-01-01
During the dry season in Korea, rivers become more vulnerable to contamination by biochemical oxygen demand (BOD) and nitrogen. It is hypothesized that the natural characteristics of the streams in Korea allow the contaminated water to be treated at the tributaries. Down-stream river water quality in Korea may be improved by spraying the contaminated stream water from the tributaries over the surrounding floodplains. The consequent water filtration through the soil could remove the contaminants through aerobic and denitrifying reactions. In this study, the kinetics parameters of the denitrifying reaction in floodplain filtration were determined using contaminated stream water. For the electron donor the Monod kinetics was used, while the competitive Michaelis-Menten model was employed for the electron acceptors. The parameters to the competitive Michaelis-Menten model were found using continuous denitrifying reactions, instead of the batch reactions employed in previous studies, to match the conditions needed to apply the competitive Michaelis-Menten kinetics. From the result, it was found that continuous reactions as well as batch reactions could be used to determine the affinity coefficients in denitrification. The results of this study also showed that the affinity coefficient of NO2, using continuous reactions, was similar to that of other studies in the literature found via batch reactions, whereas the affinity coefficient of N2O was much larger than that acquired with batch reactions. The parameters obtained in this study will be used in future work to simulate the contaminant behaviors during floodplain filtration using a mathematical model.
Li, Qiang; Csanády, György András; Kessler, Winfried; Klein, Dominik; Pankratz, Helmut; Pütz, Christian; Richter, Nadine; Filser, Johannes Georg
2011-10-01
Ethylene (ET) is metabolized in mammals to the carcinogenic ethylene oxide (EO). Although both gases are of high industrial relevance, only limited data exist on the toxicokinetics of ET in mice and of EO in humans. Metabolism of ET is related to cytochrome P450-dependent mono-oxygenase (CYP) and of EO to epoxide hydrolase (EH) and glutathione S-transferase (GST). Kinetics of ET metabolism to EO and of elimination of EO were investigated in headspace vessels containing incubations of subcellular fractions of mouse, rat, or human liver or of mouse or rat lung. CYP-associated metabolism of ET and GST-related metabolism of EO were found in microsomes and cytosol, respectively, of each species. EH-related metabolism of EO was not detectable in hepatic microsomes of rats and mice but obeyed saturation kinetics in hepatic microsomes of humans. In ET-exposed liver microsomes, metabolism of ET to EO followed Michaelis-Menten-like kinetics. Mean values of V(max) [nmol/(min·mg protein)] and of the apparent Michaelis constant (K(m) [mmol/l ET in microsomal suspension]) were 0.567 and 0.0093 (mouse), 0.401 and 0.031 (rat), and 0.219 and 0.013 (human). In lung microsomes, V(max) values were 0.073 (mouse) and 0.055 (rat). During ET exposure, the rate of EO production decreased rapidly. By modeling a suicide inhibition mechanism, rate constants for CYP-mediated catalysis and CYP inactivation were estimated. In liver cytosol, mean GST activities to EO expressed as V(max)/K(m) [μl/(min·mg protein)] were 27.90 (mouse), 5.30 (rat), and 1.14 (human). The parameters are most relevant for reducing uncertainties in the risk assessment of ET and EO.
Kiriyama, Akiko; Nishiura, Tomoyuki; Yamaji, Hirokazu; Takada, Kanji
1999-01-01
KNI-272 is a tripeptide protease inhibitor for treating human immunodeficiency virus type 1 (HIV-1). In in vitro stability studies using rat tissue homogenates, KNI-272 concentrations in the liver, kidney, and brain decreased significantly with time. Moreover, in tissue distribution studies, KNI-272 distributed highly to the liver, kidney, and small intestine in vivo. From these results and reported physiological parameters such as the tissue volume and tissue blood flow rate, we considered the liver to be the main organ which takes part in the metabolic elimination of KNI-272. Then the hepatic metabolism of KNI-272 was more thoroughly investigated by using rat liver microsomes. KNI-272 was metabolized in the rat liver microsomes, and five metabolites were found. The initial metabolic rate constant (kmetabolism) tended to decrease when the KNI-272 concentration in microsomal suspensions increased. The calculated Michaelis-Menten constant (Km) and the maximum velocity of KNI-272 metabolism (Vmax), after correction for the unbound drug concentration, were 1.12 ± 0.09 μg/ml (1.68 ± 0.13 μM) and 0.372 ± 0.008 μg/mg of protein/min (0.558 ± 0.012 nmol/mg of protein per min), respectively. The metabolic clearance (CLint,metabo), calculated as Vmax/Km, was 0.332 ml/mg of protein per min. Moreover, by using selective cytochrome P-450 inhibitors and recombinant human CYP3A4 fractions, KNI-272 was determined to be metabolized mainly by the CYP3A isoform. In addition, ketoconazole, a representative CYP3A inhibitor, inhibited KNI-272 metabolism competitively, and the inhibition constant (Ki) was 4.32 μM. PMID:10049266
孔俊豪; 杨秀芳; 涂云飞; 孙庆磊; 陈小强
2011-01-01
The polyphenol oxidase activity of cryopreservation fresh tea leaves was determined by spectrophotometric method. The influence of main factors, such as substrate concentration, system pH and temperature on catalytic activities of PPO were investigated. The results showed that, the optimum pH and temperature for the enzymatic reaction was 4.6~5.0 and 35~60 ℃, respectively .The Michaelis-Menten equation of PPO from cryopreservation fresh tea leaves was established, accordingly,1/v=1.168 8/[S]+3.083 3, by which the kinetic parameters obtained were as follow: Km=0.378 mol/L,vmax=0.324 U /min.%采用分光光度法对冻存处理的茶树鲜叶的多酚氧化酶(PPO)进行了活性测定,研究了底物浓度、pH值及温度对冻存茶鲜叶PPO活性的影响,建立了茶树鲜叶冻存-萎凋过程的反应动力学方程.结果表明,冻存茶鲜叶PPO酶活的最适条件为:pH值介于4.6～5.0之间,温度35～60℃.由Michelis-Menten方程1/v=1.1688/[S]+3.083 3,得到的动力学参数为:Km=0.378mol/L,vmax=0.324U/min.
New types of experimental data shape the use of enzyme kinetics for dynamic network modeling.
Tummler, Katja; Lubitz, Timo; Schelker, Max; Klipp, Edda
2014-01-01
Since the publication of Leonor Michaelis and Maude Menten's paper on the reaction kinetics of the enzyme invertase in 1913, molecular biology has evolved tremendously. New measurement techniques allow in vivo characterization of the whole genome, proteome or transcriptome of cells, whereas the classical enzyme essay only allows determination of the two Michaelis-Menten parameters V and K(m). Nevertheless, Michaelis-Menten kinetics are still commonly used, not only in the in vitro context of enzyme characterization but also as a rate law for enzymatic reactions in larger biochemical reaction networks. In this review, we give an overview of the historical development of kinetic rate laws originating from Michaelis-Menten kinetics over the past 100 years. Furthermore, we briefly summarize the experimental techniques used for the characterization of enzymes, and discuss web resources that systematically store kinetic parameters and related information. Finally, describe the novel opportunities that arise from using these data in dynamic mathematical modeling. In this framework, traditional in vitro approaches may be combined with modern genome-scale measurements to foster thorough understanding of the underlying complex mechanisms.
Hostrup, Morten; Kalsen, A; Ortenblad, N
2014-01-01
The aim of the present study was to examine the effect of beta2-adrenergic stimulation on skeletal muscle contractile properties, sarcoplasmic reticulum (SR) rates of Ca(2+) release and uptake, and Na(+)/K(+)-ATPase-activity before and after fatiguing exercise in trained men. The study consisted......-fatigue, but terbutaline counteracted exercise-induced reductions in Vmax at time of fatigue. In conclusion, increased contractile force induced by beta2-adrenergic stimulation is associated with enhanced rate of Ca(2+) release in humans. While beta2-adrenergic stimulation elicits positive inotropic and lusitropic effects...... of two experiments (EXP1, n = 10 M, EXP2, n = 20 M), where beta2-adrenoceptor agonist (terbutaline) or placebo was randomly administered in double-blinded crossover designs. In EXP1, maximal voluntary isometric contraction of m.quadriceps (MVC) was measured, followed by exercise to fatigue at 120% of Vo2...
2017-01-01
The specific consumption rate of substrate, as well as the associated specific growth rate, is an essential parameter in the mathematical description of substrate-limited microbial growth. In this paper we develop a completely new kinetic model of substrate transport, based on recent knowledge on the structural biology of transport proteins, which correctly describes very accurate experimental results at near-zero substrate concentration values found in the literature, where the widespread Michaelis-Menten model fails. Additionally, our model converges asymptotically to Michaelis-Menten predictions as substrate concentration increases. Instead of the single active site enzymatic reaction of Michaelis-Menten type, the proposed model assumes a multi-site kinetics, simplified as an apparent all-or-none mechanism for the transport, which is controlled by means of the local substrate concentration in the close vicinity of the transport protein. Besides, the model also assumes that this local concentration is not equal to the mean substrate concentration experimentally determined in the culture medium. Instead, we propose that it fluctuates with a mostly exponential distribution of Weibull type. PMID:28187189
Canceling effect: a natural mechanism to reduce the effects of global warming
Razavi, Bahar S.; Blagodatskaya, Evgenia; kuzyakov, Yakov
2016-04-01
The temperature sensitivity of enzymes responsible for organic matter decomposition in soil is crucial for predicting the effects of global warming on the carbon cycle and sequestration. We tested the hypothesis that differences in temperature sensitivity of enzyme kinetic parameters Vmax and Km will lead to a canceling effect: strong reduction of temperature response of catalytic reactions. Short-term temperature response of Vmax and Km of three hydrolytic enzymes responsible for decomposition of cellulose (β-glucosidase, cellobiohydrolase) and hemicelluloses (xylanase) were analyzed in situ from 0 to 40 °C. The apparent activation energy varied between enzymes from 20.7 to 35.2 kJ mol-1 corresponding to the Q10 values of the enzyme activities of 1.4-1.9 (with Vmax-Q10 1.0-2.5 and Km-Q10 0.94-2.3). Temperature response of all tested enzymes fitted well to the Arrhenius equation. Despite that,the fitting of Arrhenius model revealed the non-linear increase of two cellulolytic enzymes activities with two distinct thresholds at 10-15 °C and 25-30 °C, which were less pronounced for xylanase. The nonlinearity between 10 and 15 °C was explained by 30-80% increase in Vmax. At 25-30 °C, however, the abrupt decrease of enzyme-substrate affinity was responsible for non-linear increase of enzyme activities. Our study is the first demonstrating nonlinear response of Vmax and Km to temperature causing canceling effect, which was most strongly pronounced at low substrate concentrations and at temperatures above 15 °C. Under cold climate, however, the regulation of hydrolytic activity by canceling in response to warming is negligible because canceling was never observed below 10 °C. The canceling, therefore, can be considered as natural mechanism reducing the effects of global warming on decomposition of soil organics at moderate temperatures. The non-linearity of enzyme responses to warming and the respective thresholds should therefore be investigated for other enzymes
Le Deunff, Erwan; Tournier, Pierre-Henri; Malagoli, Philippe
2016-01-01
The ion influx isotherms obtained by measuring unidirectional influx across root membranes with radioactive or stable tracers are mostly interpreted by enzyme-substrate-like modeling. However, recent analyses from ion transporter mutants clearly demonstrate the inadequacy of the conventional interpretation of ion isotherms. Many genetically distinct carriers are involved in the root catalytic function. Parameters Vmax and Km deduced from this interpretation cannot therefore be regarded as microscopic parameters of a single transporter, but are instead macroscopic parameters (V[Formula: see text] and K[Formula: see text], apparent maximum velocity and affinity constant) that depend on weighted activities of multiple transporters along the root. The flow-force interpretation based on the thermodynamic principle of irreversible processes is an alternative macroscopic modeling approach for ion influx isotherms in which macroscopic parameters Lj (overall conductance of the root system for the substrate j) and πj (thermodynamic parameter when Jj = 0) have a straightforward meaning with respect to the biological sample studied. They characterize the efficiency of the entire root catalytic structure without deducing molecular characteristics. Here we present the basic principles of this theory and how its use can be tested and improved by changing root pre- and post-wash procedures before influx measurements in order to come as close as possible to equilibrium conditions. In addition, the constant values of Vm and Km in the Michaelis-Menten (MM) formalism of enzyme-substrate interpretation do not reflect variations in response to temperature, nutrient status or nutrient regimes. The linear formalism of the flow-force approach, which integrates temperature effect on nutrient uptake, could usefully replace MM formalism in the 1-3-dimension models of plants and phytoplankton. This formalism offers a simplification of parametrization to help find more realistic analytical
胡绵好; 奥岩松; 杨肖娥
2008-01-01
水体中的营养元素过多(特别是氮、磷)所导致的富营养化现象已是全球性的环境问题.近来利用大型维管束植物对富营养化水体的修复已备受关注.然而,水体中氮的去除受到包括氮的离子形态及其在水体中浓度等各种因素的影响.研究通过Michaelis-Menten动力学方程来研究植物根系表面氮的浓度与植物吸收氮的相互关系.该方程包括2个参数:吸收最大速率(Vmax)和米氏常数(Km),其分别表示植物吸收不同氮形态的最大速率和对不同氮形态亲和力的高低.利用加权回归分析结果表明,生长在不同浓度营养液水浮莲(Pistia stratiotes L.)吸收速率拟和Michaelis-Menten方程.水浮莲对NH4+-N的Km很高,表明其对NH4+-N亲和力高;在NO3--N单一氮源提供下,水浮莲对NO3--N的吸收动力学与NH4+-N相似.然而,在营养液中同时存在NH4+-N和NO3--N时,NO3--N吸收的最大速率明显降低,但对其Km的影响不大,这种抑制作用看来属于非竞争性的.在NH4+-NN和NO3--N的同时存在下,由于植物吸收NO3--N能力的降低可能导致植物对氮的利用率下降.%Eutrophication, which overenrich with nutrients (principally nitrogens and phosphorus) in water bodies, has been recognized as a global problem. Macrophytes play a major role in nutrient removal. However, nitrogen removal is affected by many factors including the N-ion species and its concentration in water bodies. In the present study, the relation between N concentration at the root surface and N uptake was characterized using Michaelis-Menten kinetics. The equation involves two parameters, Vmax and Km, which are measures of the maximum rate of uptake and the affinity of the uptake sites for the nutrient, respectively. Uptake rates of water lettuce (Pistia stratiotes L.) growing in a different concentration nutrient solution system were fitted to the Michaelis-Menten model using a weighted regression analysis. For NH4+-N the Km values
Miyamoto, Hirotaka; Matsueda, Satoshi; Moritsuka, Akihiro; Shimokawa, Kenta; Hirata, Haruna; Nakashima, Mikiro; Sasaki, Hitoshi; Fumoto, Shintaro; Nishida, Koyo
2015-10-01
The effect of hypothermia on the in vivo pharmacokinetics of midazolam was evaluated, with a focus on altered metabolism in the liver and binding to serum proteins. Rat primary hepatocytes were incubated with midazolam (which is metabolized mainly by CYP3A2) at 37, 32 or 28 °C. The Michaelis-Menten constant (Km) and maximum velocity (Vmax) of midazolam were estimated using the Michaelis-Menten equation. The Km of CYP3A2 midazolam remained unchanged, but the Vmax decreased at 28 °C. In rats, whose temperature was maintained at 37, 32 or 28 °C by a heat lamp or ice pack, the plasma concentrations of midazolam were higher, whereas those in the brain and liver were unchanged at 28 °C. The tissue/plasma concentration ratios were, however, increased significantly. The unbound fraction of midazolam in serum at 28 °C was half that at 37 °C. These pharmacokinetic changes associated with hypothermic conditions were due to reductions in CYP3A2 activity and protein binding.
Hezbollah: The Dynamics of Recruitment
2011-05-19
fundamental Michaelis - Menten kinetic interaction of the enzyme- substrate complex over time. As substrates are converted by enzymes 0 to the intermediate... Michaelis - Menten , Sensitivity Analysis, Nonlinear Differential Equations 16. PRICE CODE 17. SECURITY CLASSIFICATION UNCLASSIFIED OF REPORT 18...Illustrations Figures Figure 1. Concentration over time for the Michaelis - Menten equations. ...................................... 38 Figure 2
Kinetics of inhibition of acetylcholinesterase in the presence of acetonitrile.
Pietsch, Markus; Christian, Leonie; Inhester, Therese; Petzold, Susanne; Gütschow, Michael
2009-04-01
The hydrolysis of acetylthiocholine by acetylcholinesterase from Electrophorus electricus was investigated in the presence of the inhibitors tacrine, gallamine and compound 1. The interaction of the enzyme with the substrate and the inhibitors was characterized by the parameters K(I), alpha', b or beta, K(m) and V(max), which were determined directly and simultaneously from nonlinear Michaelis-Menten plots. Tacrine was shown to act as a mixed-type inhibitor with a strong noncompetitive component (alpha' approximately 1) and to completely block deacylation of the acyl-enzyme. In contrast, acetylcholinesterase inhibition by gallamine followed the 'steric blockade hypothesis', i.e. only substrate association to as well as substrate/product dissociation from the active site were reduced in the presence of the inhibitor. The relative efficiency of the acetylcholinesterase-gallamine complex for the catalysis of substrate conversion was determined to be 1.7-25% of that of the free enzyme. Substrate hydrolysis and the inhibition of acetylcholinesterase were also investigated in the presence of 6% acetonitrile, and a competitive pseudo-inhibition was observed for acetonitrile (K(I) = 0.25 m). The interaction of acetylcholinesterase with acetonitrile and tacrine or gallamine resulted in a seven- to 10-fold increase in the K(I) values, whereas the principal mode of inhibition was not affected by the organic solvent. The determination of the inhibitory parameters of compound 1 in the presence of acetonitrile revealed that the substance acts as a hyperbolic mixed-type inhibitor of acetylcholinesterase. The complex formed by the enzyme and the inhibitor still catalysed product formation with 8.7-9.6% relative efficiency.
Ferey, Justine; Da Silva, David; Bravo-Veyrat, Sophie; Lafite, Pierre; Daniellou, Richard; Maunit, Benoît
2016-12-16
This paper presents a kinetic study of invertase, a specific fructofuranosidase cloned from the Leishmania major genome. The kinetic parameters of the β-d-fructofuranosidase from Leishmania major (BfrA) were determined using Thin-Layer Chromatography (TLC) and UV-densitometry (TLC@UV) specifically developed for the separation and detection of three carbohydrates namely sucrose, glucose and fructose. Separation was performed on TLC silica gel 60 F254 plates impregnated with sodium bisulphate and citrate and heated prior to development. This fast and easy separation was performed with two successive developments using ACN/H2O 80/20 (v/v) as mobile phase. Sensitive and repeatable derivatization of sugars was achieved by dipping the plates in a solution of 4-aminobenzoic acid. Quantification was performed by UV-detection. The method was validated according to ICH guidelines Q2(R1) in terms of specificity, limits of detection and quantification, precision and robustness (with n=3 replicates and CV ≤10%). The characterization of BfrA reaction kinetic was performed by monitoring the accumulation of either glucose or fructose detected by TLC@UV. Hydrolysis of sucrose was described by the Michaelis-Menten kinetic parameters (KM; Vmax) respectively equal to 63.09±7.590mM; 0.037±0.00094mM/min using glucose production and 83.01±14.39mM; 0.031±0.0021mM/min monitoring fructose. Hydrolyses of three alternative substrates, raffinose, stachyose and inulin, were also compared and the regiospecificity of the reaction was characterized. This TLC@UV method is shown to be suitable for the refined kinetic analysis of different reactions related to the hydrolysis of sugars. Copyright © 2016. Published by Elsevier B.V.
Kinetic study of enzymatic hydrolysis of potato starch
Óscar Fernando Castellanos Domínguez
2010-04-01
Full Text Available This article describes the kinetic study of potato starch enzymatic hydrolysis using soluble enzymes (Novo Nordisk. Different assays divided into four groups were used: reaction time (with which it was possible to reduce the 48-72 hour duration reported in the literature to 16 hours with comparable productivity levels; selecting the set of enzymes to be used (different types were evaluated - BAN and Termamyl as alfa-amylases during dextrinisation stage, and AMG, Promozyme and Fungamyl for sacarification reaction- identifying those presenting the best performance during hydrolysis. Reaction conditions were optimised for the process's two stages (destrinisation and sacarification. Enzyme dose, calcium cofactor concentration, pH, temperature and agitation speed were studied for the first stage. Enzyme ratio, pH and agitation speed were studied for sacarification; the latter parameter reported values having no antecedents in the literature (60 rpm and 30 rpm for first and second reactions, respectively. Michaelis Menten kinetics were calculated once conditions had been optimised, varying substrate from 10-50% P/V, obtaining km and Vmax kinetic parameters for each reaction. A kinetic model was found according to local working conditions which was able to explain potato starch conversion to glucose syrup, achieving 96 dextrose equivalents by the end of the reaction, being well within the maximum range reported in the literature (94-98. Laboratory equipment was constructed prior to carrying out assays which was able to reproduce and improve the conditions reported in the literature, making it a useful, reliable tool for use in assays returning good results.
Hartwig, S; Frister, T; Alemdar, S; Li, Z; Scheper, T; Beutel, S
2015-03-20
An uncharacterized plant cDNA coding for a polypeptide presumably having sesquiterpene synthase activity, was expressed in soluble and active form. Two expression strategies were evaluated in Escherichia coli. The enzyme was fused to a highly soluble SUMO domain, in addition to being produced in an unfused form by a cold-shock expression system. Yields up to ∼325 mg/L(-1) were achieved in batch cultivations. The 6x-His-tagged enzyme was purified employing an Ni(2+)-IMAC-based procedure. Identity of the protein was established by Western Blot analysis as well as peptide mass fingerprinting. A molecular mass of 64 kDa and an isoelectric point of pI 4.95 were determined by 2D gel electrophoresis. Cleavage of the fusion domain was possible by digestion with specific SUMO protease. The synthase was active in Mg(2+) containing buffer and catalyzed the production of (+)-zizaene (syn. khusimene), a precursor of khusimol, from farnesyl diphosphate. Product identity was confirmed by GC-MS and comparison of retention indices. Enzyme kinetics were determined by measuring initial reaction rates for the product, using varying substrate concentrations. By assuming a Michaelis-Menten model, kinetic parameters of KM = 1.111 μM (±0.113), vmax = 0.3245 μM min(-1) (±0.0035), kcat = 2.95 min(-1), as well as a catalytic efficiency kcat/KM = 4.43 × 10(4) M(-1)s(-1) were calculated. Fusion to a SUMO moiety can substantially increase soluble expression levels of certain hard to express terpene synthases in E. coli. The kinetic data determined for the recombinant synthase are comparable to other described plant sesquiterpene synthases and in the typical range of enzymes belonging to the secondary metabolism. This leaves potential for optimizing catalytic parameters through methods like directed evolution. Copyright © 2015 Elsevier Inc. All rights reserved.
Phytotoxicity of sodium fluoride and uptake of fluoride in willow trees.
Clausen, Lauge Peter Westergaard; Karlson, Ulrich Gosewinkel; Trapp, Stefan
2015-01-01
The willow tree (Salix viminalis) toxicity test and a cress seed germination test (Lepidium sativum) were used to determine uptake of F and phytotoxicity of NaF. Concentrations in hydroponic solutions were 0-1000 mg F/L and 0-400 mg F/L in the preliminary and definitive test. A third test was done with soils collected from a fluoride-contaminated site at Fredericia, Denmark. The EC10, EC20 and EC50-values for inhibition of transpiration were determined to 38.0, 59.6 and 128.7 mg F/L, respectively. The toxicity test with soil showed strong inhibition for the sample with the highest fluoride concentration (405 mg free F per kg soil, 75 mg F per L soil solution). The seed germination and root elongation test with cress gave EC10, EC20 and EC50-values of 61.4, 105.0 and 262.8 mg F/L, respectively. At low external concentrations, fluoride was taken up more slowly than water and at high external concentrations at the same velocity. This indicates that an efflux pump becomes overloaded at concentrations above 210 mg F/L. Uptake kinetics were simulated with a non-linear mathematical model, and the Michaelis-Menten parameters were determined to half-saturation constant KM near 2 g F/L and maximum enzymatic removal rate vmax at 9 g/(kg d).
Yu, Jian; Han, Jing-Chun; Hua, Li-Min; Gao, Ya-Jie
2013-09-01
Vanillin is a food flavoring agent widely utilized in foods, beverages, drugs, and perfumes and has been demonstrated to exhibit multiple pharmacological activities. Given the importance of glucuronidation in the metabolism of vanillin, the UDP-glucuronosyltransferase conjugation pathway of vanillin was investigated in this study. Vanillin glucuronide was identified by high-performance liquid chromatography-tandem mass spectrometry (HPLC-MS/MS) and a hydrolysis reaction catalyzed by β-glucuronidase. The kinetic study showed that vanillin glucuronidation by HLMs and HIMs followed Michaelis-Menten kinetics and the kinetic parameters were as follows: 134.9 ± 13.5 μM and 81.3 ± 11.3 μM for K(m) of HLMs and HIMs, 63.8 ± 2.0 nmol/min/mg pro and 13.4 ±2.0 nmol/min/mg pro for Vmax of HLMs and HIMs. All UDP-glucuronosyltransferase (UGT) isoforms except UGT1A4, 1A9, and 2B7 showed the capability to glucuronidate vanillin, and UGT1A6 exerted the higher V(max)/K(m) values than other UGT isoforms for the glucuronidation of vanillin when assuming expression of isoforms is similar in recombinant UGTs. Kinetic analysis using liver microsomes from six studied speices indicated that vanillin had highest affinity for the monkey liver microsomes enzyme (K(m) = 25.6 ± 3.2 μM) and the lowest affinity for the mice liver microsomes enzyme (K(m) = 149.1 ± 18.4 μM), and intrinsic clearance was in the following order: monkey > dog > minipig > mice > rat ~ human. These data collectively provided important information for understanding glucuronidation of vanillin.
Scarpellini, Marciela; Neves, Ademir; Hörner, Rosmari; Bortoluzzi, Adailton J; Szpoganics, Bruno; Zucco, César; Nome Silva, René A; Drago, Valderes; Mangrich, Antônio S; Ortiz, Wilson A; Passos, Wagner A C; de Oliveira, Maurício C B; Terenzi, Hernán
2003-12-15
The tridentate Schiff base [(2-(imidazol-4-yl)ethyl)(1-methylimidazol-2-yl)methyl)imine (HISMIMI) and its reduced form HISMIMA were synthesized and characterized, as well their mononuclear cis-dihalo copper(II) complexes 1 and 2, respectively. In addition, the dinuclear [CuII(mu-OH)2CuII](2+) complexes (3) and (4) obtained from complexes 1 and 2, respectively, were also isolated and characterized by several physicochemical techniques, including magnetochemistry, electrochemistry, and EPR and UV-vis spectroscopies. The crystal structures of 1 and 2 were determined by X-ray crystallography and revealed two neutral complexes with their tridentate chelate ligands meridionally coordinated. Completing the coordination spheres of the square-pyramidal structures, a chloride ion occupies the apical position and another is bonded in the basal plane. In addition, complexes 1 and 2 were investigated by infrared, electronic, and EPR spectroscopies, cyclic voltammetry, and potentiometric equilibrium studies. The hydrolytic activity on phosphate diester cleavage of 1 and 2 was investigated utilizing 2,4-BDNPP as substrate. These experiments were carried out at 50 degrees C, and the data treatment was based on the Michaelis-Menten approach, giving the following kinetic parameters (complex 1/complex 2): vmax (mol L(-1) s(-1))=16.4x10(-9)/7.02x10(-9); KM (mol L(-1))=17.3x10(-3)/3.03x10(-3); kcat (s(-1))=3.28x10(-4)/1.40x10(-4). Complex 1 effectively promoted the hydrolytic cleavage of double-strand plasmid DNA under anaerobic and aerobic conditions, with a rate constant of 0.28 h(-1) for the decrease of form I, which represents about a 10(7) rate increase compared with the estimated uncatalyzed rate of hydrolysis.
Noguchi, Kengo; Morishima, Yoshiyuki; Takahashi, Shinichi; Ishihara, Hiroaki; Shibano, Toshiro; Murata, Mitsuru
2015-03-01
Edoxaban is an oral direct factor Xa (FXa) inhibitor and its efficacy as an oral anticoagulant is less subject to drug-food and drug-drug interaction than existing vitamin K antagonists. Although this profile of edoxaban suggests it is well suited for clinical use, it is not clear whether genetic variations of factor X influence the activity of edoxaban. Our aim was to investigate a possible impact of single-nucleotide polymorphisms (SNPs) in the factor X gene on the functions of factor X and the activity of edoxaban. Two nonsynonymous SNPs within mature factor X, Ala152Thr and Gly192Arg, were selected as possible candidates that might affect the functions of FXa and the activity of edoxaban. We measured catalytic activities of wild type and mutant FXas in a chromogenic assay using S-2222 and coagulation times including prothrombin time (PT) and activated partial thrombin time (aPTT) of plasma-containing recombinant FXs in the presence and absence of edoxaban. Michaelis-Menten kinetic parameters of FXas, Km and Vmax values, PT and aPTT were not influenced by either mutation indicating these mutations do not affect the FXa catalytic and coagulation activities. The Ki values of edoxaban for the FXas and the concentrations of edoxaban required to double PT and aPTT were not different between wild type and mutated FXas indicating that both mutations have little impact on the activity of edoxaban. In conclusion, these data suggest that edoxaban has little interpatient variability stemming from SNPs in the factor X gene.
Johnen, G; Kowlessur, D; Citron, B A; Kaufman, S
1995-01-01
The characterization of 4a-carbinolamine dehydratase with the enzymatically synthesized natural substrate revealed non-Michaelis-Menten kinetics. A Hill coefficient of 1.8 indicates that the dehydratase exists as a multisubunit enzyme that shows cooperativity. A mild form of hyperphenylalaninemia with high 7-biopterin levels has been linked to mutations in the human 4a-carbinolamine dehydratase gene. We have now cloned and expressed two mutant forms of the protein based on a patient's DNA sequences. The kinetic parameters of the mutant C82R reveal a 60% decrease in Vmax but no change in Km (approximately 5 microM), suggesting that the cysteine residue is not involved in substrate binding. Its replacement by arginine possibly causes a conformational change in the active center. Like the wild-type enzyme, this mutant is heat stable and forms a tetramer. The susceptibility to proteolysis of C82R, however, is markedly increased in vitro compared with the wild-type protein. We have also observed a decrease in the expression levels of C82R protein in transfected mammalian cells, which could be due to proteolytic instability. The 18-amino acid-truncated mutant GLu-87--> termination could not be completely purified and characterized due to minute levels of expression and its extremely low solubility as a fusion protein. No dehydratase activity was detected in crude extracts from transformed bacteria or transfected mammalian cells. Considering the decrease in specific activity and stability of the mutants, we conclude that the patient probably has less than 10% residual dehydratase activity, which could be responsible for the mild hyperphenylalaninemia and the high 7-biopterin levels. PMID:8618906
Kinetics of Phosphatase of Regenerating Liver-3 (PRL-3) Inhibition by Small-molecular Inhibitors
无
2006-01-01
Phosphatase of Regenerating Liver-3 (PRL-3) is a newly identified colorectal cancer metastasis-related protein,which isa 22 kDa non-classical protein tyrosine phosphatase with a C-terminal prenylation motif. In this study, the inhibition kinetics of protein tyrosine phosphatases (PTPs) by a fluorescent substrate, 6,8-difluoro-4-methylumbelliferyl phosphate (DiFMUP) was evaluated. PRL-3 exhibits classical Michaelis-Menten kinetics with a vmax value of the inhibitor magnolol can cause Km to increase, but does not alter the vmax value, which suggests the competitive inhibition of PRL-3. At the same time, it was found that DiFMUP is a more sensitive substrate for PRL-3 than para-nitrophenyl phosphate(pNPP) that is more frequently used at present. Furthermore, the method of screening for PTPs by the use of DiFMUP was developed, which studied the acceptance of DiFMUP by other PTPs.
Entrapment of glucoamylase by sol-gel technique in PhTES/TEOS hybrid matrixes
B. Vlad-Oros
2007-12-01
Full Text Available Mesoporous silica particles were prepared by the sol-gel method from different alkoxysilane precursors and used as a host matrix for encapsulation of glucoamylase, an enzyme widely used in fermentative industry. The aim was to investigate the physico-chemical properties of the different silica powders and their effect on the enzyme kinetics. The encapsulated enzymes followed Michaelis-Menten kinetics. The Michaelis constant (KM and the maximum rate of starch hydrolysis reaction (Vmax were calculated according to the Michaelis-Menten and Lineweaver-Burke plots. The values of the Michaelis constant (KM of the encapsulated enzymes were higher than those of the free enzyme. The temperature and pH inﬂ uence on the activity of free and immobilized glucoamylase were also compared. The results of this study show that the enzymes immobilized in organic/inorganic hybrid silica matrixes (obtained by the sol-gel method, allowing the entrapped glucoamylase to retain its biological activity, are suitable for many different applications, (medicinal, clinical, analytical.
Urmeela Taukoorah
2016-01-01
Full Text Available Aloe vera gel (AVG is traditionally used in the management of diabetes, obesity, and infectious diseases. The present study aimed to investigate the inhibitory potential of AVG against α-amylase, α-glucosidase, and pancreatic lipase activity in vitro. Enzyme kinetic studies using Michaelis-Menten (Km and Lineweaver-Burk equations were used to establish the type of inhibition. The antioxidant capacity of AVG was evaluated for its ferric reducing power, 2-diphenyl-2-picrylhydrazyl hydrate scavenging ability, nitric oxide scavenging power, and xanthine oxidase inhibitory activity. The glucose entrapment ability, antimicrobial activity, and total phenolic, flavonoid, tannin, and anthocyanin content were also determined. AVG showed a significantly higher percentage inhibition (85.56±0.91 of pancreatic lipase compared to Orlistat. AVG was found to increase the Michaelis-Menten constant and decreased the maximal velocity (Vmax of lipase, indicating mixed inhibition. AVG considerably inhibits glucose movement across dialysis tubes and was comparable to Arabic gum. AVG was ineffective against the tested microorganisms. Total phenolic and flavonoid contents were 66.06±1.14 (GAE/mg and 60.95±0.97 (RE/mg, respectively. AVG also showed interesting antioxidant properties. The biological activity observed in this study tends to validate some of the traditional claims of AVG as a functional food.
Jin-Bo Li
2016-01-01
Objective:To study the differences in superior thyroid artery and inferior thyroid artery blood flow spectrum parameters in subacute thyroiditis. Methods:A Total of 40 cases of patients with subacute thyroiditis and 40 cases of healthy volunteers were selected for study and enrolled in pathology group and control group respectively, color Doppler ultrasonography was conducted to detect peak blood flow velocities (Vmax) of superior thyroid artery and inferior thyroid artery as well as resistance index (RI), and serum was collected to detect thyroid hormone contents, infection indexes and oxidative stress indexes. Results:Peak blood flow velocities Vmax of superior thyroid artery and inferior thyroid artery of pathology group were significantly higher than those of control group, and resistance index RI was not different from that of control group;FT3, FT4, TT3, TT4, ESR, CRP, PCT and MDA of pathology group were significantly higher than those of control group, and SOD and TAOC were significantly lower than those of control group;Vmax of superior thyroid artery and inferior thyroid artery were positively correlated with FT3, FT4, TT3, TT4, ESR, CRP, PCT and MDA, and negatively correlated with SOD and TAOC. Conclusion:Peak blood flow velocities (Vmax) of superior thyroid artery and inferior thyroid artery in subacute thyroiditis are significantly accelerated, Vmax has good consistency with thyroid hormone contents, infection indexes and oxidative stress indexes, and it can accurately assess the severity of the disease.
Xiaorong Dai
Full Text Available Ammonia emission from animal production is a major environmental problem and has impacts on the animal health and working environment inside production houses. Ammonia is formed in manure by the enzymatic degradation of urinary urea and catalyzed by urease that is present in feces. We have determined and compared the urease activity in feces and manure (a urine and feces mixture from pigs and cattle at 25°C by using Michaelis-Menten kinetics. To obtain accurate estimates of kinetic parameters Vmax and K'm, we used a 5 min reaction time to determine the initial reaction velocities based on total ammoniacal nitrogen (TAN concentrations. The resulting Vmax value (mmol urea hydrolyzed per kg wet feces per min was 2.06±0.08 mmol urea/kg/min and 0.80±0.04 mmol urea/kg/min for pig feces and cattle feces, respectively. The K'm values were 32.59±5.65 mmol urea/l and 15.43±2.94 mmol urea/l for pig feces and cattle feces, respectively. Thus, our results reveal that both the Vmax and K'm values of the urease activity for pig feces are more than 2-fold higher than those for cattle feces. The difference in urea hydrolysis rates between animal species is even more significant in fresh manure. The initial velocities of TAN formation are 1.53 mM/min and 0.33 mM/min for pig and cattle manure, respectively. Furthermore, our investigation shows that the maximum urease activity for pig feces occurs at approximately pH 7, and in cattle feces it is closer to pH 8, indicating that the predominant fecal ureolytic bacteria species differ between animal species. We believe that our study contributes to a better understanding of the urea hydrolysis process in manure and provides a basis for more accurate and animal-specific prediction models for urea hydrolysis rates and ammonia concentration in manures and thus can be used to predict ammonia volatilization rates from animal production.
Characterization of the penicillin G acylase from Bacillus megaterium ATCC 14945
Vanessa Ribeiro de Souza
2005-06-01
Full Text Available The purpose of this work was to characterize the enzyme penicillin G acylase (PGA produced by Bacillus megaterium. Purification of the enzyme by ultra/diafiltration did not allow the detection of the PGA band by SDS-PAGE electrophoresis due to the high content of remaining proteins. However, using the DNA of the microorganism, it was possible to replicate the genes of the two B. megaterium PGA reported in literature, showing that the enzyme consisted of two sub-units, having 245 and 537 amino acids each and an average molecular mass of 26950 and 59070 Da, respectively. The parameters studied were: 1 the influence of temperature in the 25-60(0C range, 2 pH in the 5-10 range and 3 substrate concentration, this was tested to obtain results on the Penicillin G hydrolysis reaction rate, using the initial velocities approach. The maximum hydrolysis rate was obtained at 37ºC and pH 8.0. The Michaelis-Menten model fitted well, resulting in estimated Km and Vmax parameters values of 1.83 mM and 0.165*10-3 mmol/min/UI, respectively.O objetivo deste trabalho foi caracterizar a enzima penicilina G acilase (PGA produzida por Bacillus megaterium, uma importante enzima industrial que catalisa a hidrólise de penicilina G, para produção de antibióticos semi-sintéticos. Purificação da enzima por ultra/diafiltração não permitiu detectar a banda de PGA por eletroforese SDS-PAGE devido ao elevado conteúdo de outras proteínas remanescentes. Contudo, utilizando DNA do microrganismo que vem sendo estudado, foi possível amplificar os genes das duas sub-unidades de PGA previstas na literatura, mostrando que a enzima em estudo é também constituída de duas sub-unidades, 245 e 537 aminoácidos cada, com massas moleculares médias de 26950 e 59070 Da, respectivamente. Foram estudadas as influências da temperatura 25-60(0C, pH 5-10, e concentração do substrato na velocidade da reação de hidrólise da penicilina G. A temperatura e pH ótimos foram de 37
Julius Kwagh-Har Ikya
2014-02-01
Full Text Available The ability of Commercial Native Linamarase (CNLIN and Engineered Linamarase (GELIN extracts from Saccharomyces cerevisiae to hydrolyse cassava linamarin was challenged. CNLIN acting as control was used together with GELIN extracts from Saccharomyces cerevisiae to evaluate the kinetic data for test enzymes at pH 3.5, 6.8 and 10.5, respectively and ambient temperature (35°C. Data obtained from the varying activity versus substrate concentrations were fitted with the Michaelis-Menten plots and Lineweaver-Burk model to obtain maximum velocity (Vmax, affinity coefficient (Km, physiological efficiency (Vmax/Km and r2 (linear regressing coefficient. The results indicated that the engineered linamarase conferred different enzyme kinetic data showing degradation of cassava linamarin by CNLIN and GELIN from Saccharomyces cerevisiae at the optimum pH and temperature. The relation was best described by the characteristic sigmoid Michaelis-Menten plots and Lineweaver-Burk model evidence from the high coefficient of linear regression (r2>0.976. Vmax and Km derived from the Lineweaver-Burk model varied from 10.0 to 13.0 µmol/min and 0.5 to 0.9 &muM respectively for engineered enzymes and 0.0-10.0 mol/min and 0.0 to 0.9 &muM respectively for CNLIN. The kinetics profiles of the studied enzymes showed their actions on cassava linamarin were influenced by degree of genetic manipulation, purification and pH at ambient temperature. The wide pH tolerance in the degradation of linamarin suggests a possible use of the engineered linamarase from Saccharomyces cerevisiae in detoxifying linamarin in cassava for the production of cyanide-free cassava-based food products.
Armstrong, Robert A.
2008-10-01
Pasciak and Gavis were first to propose a model of nutrient uptake that includes both physical transport by diffusion and active biological transport across the cell membrane. While the Pasciak-Gavis model is not complicated mathematically (it can be expressed in closed form as a quadratic equation), its parameters are not so easily interpretable biologically as are the parameters of the Michaelis-Menten uptake model; this lack of transparency is probably the main reason the Pasciak-Gavis model has not been adopted by ecologically oriented modelers. Here I derive a Michaelis-like approximation to the Pasciak-Gavis model, and show how the parameters of the latter map to those of the Michaelis-like model. The derived approximation differs from a pure Michaelis-Menten model in a subtle but potentially critical way: in a pure Michaelis-Menten model, the half-saturation constant for nutrient uptake is independent of the density of transporter (or "porter") proteins on the cell surface, while in the Pasciak-Gavis model and its Michaelis-like approximation, the half-saturation constant does depend on the density of porter proteins. The Pasciak-Gavis model predicts a unique relationship between cell size, nutrient concentration in the medium, the half-saturation constant of porter-limited nutrient uptake, and the resulting rate of uptake; the Michaelis-like approximation preserves the most important feature of that relationship, the size at which porter limitation gives way to diffusion limitation. Finally I discuss the implications for community structure that are implied by the Pasciak-Gavis model and its Michaelis-like approximation.
Is oral absorption of vigabatrin carrier-mediated?
Nøhr, M. K.; Juul, R. V.; Thale, Z. I.
2015-01-01
by mechanistic non-linear mixed effects modelling, evaluating PAT1-ligands as covariates on the PK parameters with a full covariate modelling approach. The oral absorption of vigabatrin was adequately described by a Michaelis-Menten type saturable absorption. Using a Michaelis constant of 32.8 mM, the model...... by significant increases in the apparent Michaelis constant. Based on the mechanistic model, a high capacity low affinity carrier is proposed to be involved in intestinal vigabatrin absorption. PAT1-ligands increased the Michaelis constant of vigabatrin after oral co-administration indicating that this carrier...
Oakes, Jesse; Nguyen, Tina; Britt, B Mark
2003-06-01
Ellman's method was used to determine the Michaelis-Menten parameters for the hydrolysis of acetylthiocholine by Electrophorus electricus acetylcholinesterase from 12 to 37 degrees C. Arrhenius analysis revealed that the activation energy for formation of the enzyme/substrate complex is 22.2 +/- 1.1 kJ/mole. The Arrhenius plot of k(cat) is markedly curved and attributed to comparable rates of acylation and deacylation due to the absence of evidence for a temperature-dependent enzyme conformational change by differential scanning calorimetry.
2012-01-01
This article reports a first contribution for the elucidation of catalytic mechanism of Lipase from porcine pancreas, type VI-s (PPL), in hydrolyzing an ester substrate in aqueous media. The conclusions were based on the pH-profiles of Michaelis-Menten parameters k cat/Km, k cat and Km, as well as on the absolute temperature profile of k cat/Km, obtained during the hydrolysis of p-nitrophenyl laurate by PPL. It was found that (a) PPL performs catalysis by means of ion pairs formed either as S...
Takayanagi, Toshiaki
2013-12-01
The basic model for chronic hepatitis B virus (HBV) or hepatitis C virus (HCV) infection during therapy enables us to analyze short-term viral kinetics. However, the model is not useful for analyzing long-term viral kinetics. Here, I suggest a new model that was obtained by introducing Michaelis-Menten kinetics into the basic model. The new model can exhibit long-term viral kinetics without rebound and oscillation, unlike the basic model. The value of the parameter K in the new model is analogous to the Michaelis constant Km and is predicted to be approximately less than 10(10)/ml.
张灵; 杨晓兰; 白婧; 廖娟; 刘红博; 廖飞
2011-01-01
Objective:To establish a method based on analysis of the changes of kinetic parameters to characterize an inhibitor of glutathione-S-transferase (glutathione-S-transferases,GST). Methods:The acidic GST isozyme was purified from the porcine liver via anion-exchange chromatography and affinity chromatography. The reaction of glutathione (glutathione, GSH) and 1 -chloro-2,4-dini-trobenzene( 1, - chloro- 2,4- dinitrobenzene,CDNB) gave S-(2,4 -dinitrobenzyl) -glutathione (GS-DNB) as a candidate inhibitor. Michaelis-Menten constant(Km) and maximal reaction rate(Vm) were estimated to determine the inhibition constant (Ki) of GS-DNB. Results: Specific activity of GST was increased by more than 146 times with overall activity yield of about 30%. GST followed random bi-substrate kinetics and had Km of 42 |xmol/L for GSH,and Km of 0.86 mmol/L for CDNB. The competitive Ki of GS-DNB was (21 ± 1)μmol/L (n=2) against CDNB,and (17 ± 1) μmol/L (ra=2) against GSH. Conclusion:GS-DNB is an effective competitive inhibitor of GST;the estimation of Ki from responses of Km and Vm to inhibitor concentrations can be a conventional method to screen GST inhibitors.%目的:测定谷胱甘肽-S-转移酶(Glutathione-S-transferases,GST)动力学参数变化,建立表征其抑制剂的方法.方法:从猪肝经阴离子交换层析和亲和层析制备GST酸性同工酶,用还原型谷胱甘肽(Glutathione,GSH)和1-氯-2,4-二硝基苯(1,-chloro-2,4-dinitrobenzene,CDNB)合成S-(2,4-二硝基苯基)-谷胱甘肽(GS-DNB)为候选抑制剂,以GSH与CDNB为底物测定GST在GS-DNB作用下的米氏常数(Km)和最大反应速度(Vm),从而确定GS-DNB对GST的抑制常数(Ki).结果:此GST被纯化146倍以上,活性总收率近30％.该GST对GSH和CDNB的Km分别为42 μmol/L和0.86 mmol/L,属于随机双底物动力学模型.GS-DNB对CDNB竞争性Ki为(21±1)μmol/L (n=2)；对GSH竞争性Ki为(17±1)μmol/L (n=2).结论:产物GS-DNB是GST的高亲和力竞争性抑制剂；测定GST动力学
李华; 霍瑞贞
2000-01-01
In experiment,the polyphenoloxidase was extracted from mushroom by using acetone precipitating method threetimes. And then, it was immobilized by using the absorbentdeposition method with porous glass powder as carriers,It wasstudied to catalize p-chlorophenol oxidizing reaction inchloroform, complys with Michaelis-Menten dynamicmodel.And themoisture content in organic solvent directly affected thecatalytic activity of mushroom polyphenoloxidase. Theoptimum reaction condition for the catalyrtic oxidation of p-chlorophenol in chloroform was determined: pH:7, temperature:25°C, moisture content: 0.5%(v/v).The measured value of dynamic parameters was 29.45kJ. mol-1 for apparent activationenergy,1.058mol. L-1 for Michaelis-Menten kinetics and 9.074×10-2 min-1 for the maximum reaction rate.% 本文用丙酮沉淀法从蘑菇中提取多酚氧化酶,以多孔玻璃粉为载体,用吸附沉积法将酶固定,研究了该酶在氯仿介质中催化对氯苯酚氧化反应的机理遵循米氏(Michaelis-Menten)动力学方程；而且,在有机介质中含水率大小直接影响酶的催化活性.实验测得反应的最佳条件为pH=7.0,温度为25°C,含水率为0.5%(v/v)；表观活化能Ea=29.54kJ . mol-1,米氏常数Km=1.058mol . dm-3,最大反应速率rmax=90.74×10-3min-1.
STUDI KINETIKA REAKSI ESTERIFIKASI ENZIMATIS ASAM MIRISTAT DENGAN OLEIL ALKOHOL
Emmy Yuanita
2013-05-01
Full Text Available Studi kinetika reaksi esterifikasi enzimatisasam miristat dan oleil alkohol telah dilakukan. Penelitian ini bertujuan untuk mendapatkan hasil sintesis yang optimal, sehingga meningkatkan konversi dan kecepatan reaksi pembentukan wax ester. Analisis kualitatif wax ester yang terbentuk dilakukan secara TLC dan GC, sedangkan analisis secara kuantitatif dilakukan secara titrasi asam-basa. Dari hasil penelitian diperoleh % konversi wax ester dengan menggunakan enzim tanpa perlakuan sebesar 94,44%. Nilai Km dan Vmax untuk asam miristat sebesar 2,5649 dan 14,3823 mmol x10-5 mmol/menit.mg katalis sedangkan untuk oleil alkohol sebesar 7,0345 dan 29,2292 mmol x10-mmol/menit.mg katalis. Sehingga dapat disimpulkan bahwa kinetika reaksi esterifikasi asam miristat dengan oleil Alkohol yang dikatalisis oleh enzim lipase tanpa perlakuan mengikuti Model Michaelis-Menten sedangkan mekanisme reaksi esterifikasi mengikuti mekanisme Bi Bi Ping-Pong
In vitro inhibition by stiripentol of rat brain cytochrome P-450-mediated naphthalene hydroxylation.
Mesnil, M; Testa, B; Jenner, P
1988-09-01
1. The formation of 1-naphthol from naphthalene was investigated in rat brain 105,000 g particulate fraction. The reaction showed NADPH dependency and was inhibited by carbon monoxide. Michaelis-Menten kinetics were apparent with Vmax = 0.264 pmol/mg protein per min and Km = 22.6 microM. 2. Stiripentol, an antiepileptic drug containing a methylenedioxybenzene moiety, proved to be a potent inhibitor of the reaction, with an IC50 value close to 1 microM under the conditions of study and without preincubation. 3. The inhibitory activity of stiripentol was seen mainly after metabolic activation of the drug. The inhibitory effect appeared progressively when substrate and inhibitor were added together to the incubates, whereas its appearance was more rapid following preincubation of stiripentol.
Modelling the Effects of Ageing Time of Starch on the Enzymatic Activity of Three Amylolytic Enzymes
Nelson P. Guerra
2012-01-01
Full Text Available The effect of increasing ageing time (t of starch on the activity of three amylolytic enzymes (Termamyl, San Super, and BAN was investigated. Although all the enzymatic reactions follow michaelian kinetics, vmax decreased significantly (P<0.05 and KM increased (although not always significantly with the increase in t. The conformational changes produced in the starch chains as a consequence of the ageing seemed to affect negatively the diffusivity of the starch to the active site of the enzymes and the release of the reaction products to the medium. A similar effect was observed when the enzymatic reactions were carried out with unaged starches supplemented with different concentrations of gelatine [G]. The inhibition in the amylolytic activities was best mathematically described by using three modified forms of the Michaelis-Menten model, which included a term to consider, respectively, the linear, exponential, and hyperbolic inhibitory effects of t and [G].
Gravitropism in higher plant shoots. V - Changing sensitivity to auxin
Salisbury, Frank B.; Gillespie, Linda; Rorabaugh, Patricia
1988-01-01
The relationship in plants between the sensitivity to auxin and differential growth and bending was investigated experimentally. Decapitated and marked sunflower hypocotyl sections were immersed in buffered auxin solutions of different concentrations (0, 10 to the -8th, or 0.001 molar) and were photographed at 1/2 hr intervals; the negatives were analyzed with a digitizer/computer to evaluate surface-length changes in terms of Michaelis-Menten enzyme kinetics. It was found that bending decreased with increasing concentration of auxin. Increasing the auxin concentration inhibits the elongation growth of lower surfaces but promotes upper-surface growth, indicating that the lower surfaces have a greater Km sensitivity to applied auxin than the upper surfaces. At optimum auxin levels (maximum growth), the growth of bottom surfaces exceeded that of top surfaces, indicating that bottom tissues had a greater Vmax sensitivity.
Faure, Mathilde; Sotta, Bruno; Gamby, Jean
2014-08-15
Real time monitoring of electrolyte resistance changes during hydrolysis of 4-nitrophenylphosphate (pNPP) by alkaline phosphatase (ALP) bound on paramagnetic-beads was performed into a small dielectric channel. The reaction kinetic fit with a non-competitive substrate-inhibition equation. Michaelis-Menten apparent constant, KM(app), was determined as 0.33±0.06mM and the maximum apparent rate, Vmax(app) as 98±5pMs(-1). The detection limits were 15fM for ALP and 0.75mM for pNPP. This miniaturized device constitutes a powerful tool for analysis of interaction between ligands. Copyright © 2014 Elsevier B.V. All rights reserved.
谢晶; 刘晓丹
2006-01-01
对香菇分别在273 K、283 K和293 K的密闭容器中氧气和二氧化碳随时间、浓度的变化进行了测定,根据酶动力学原理,利用非线性估计法、多重回归分析分别获得气体成分的变化率曲线和米式方程,从而获得相应的参数,求得反映呼吸状态的呼吸熵动态变化规律以及温度影响参数--活化能,并以此求出在任意温度、有氧呼吸气体环境条件下果蔬的最大呼吸速率,为气调包装系统设计提供理论依据.
2011-03-01
interactions [9] at the Michaelis - Menten state [14]. These interactions enable the protonation of the adenine ring at N3 [9] by the cationic Arg180 of RTA...bound and unbound states. a (top left): overlay of the apo RTA (green, 1IFT [32]) with the oligonucleotide-bound RTA at the Michaelis - Menten state...box atop in the less populated bound conformation (1IFS [32]); d (bottom right): overlay of the oligonucleotide-bound RTA at the Michaelis - Menten state
On the number of steady states in a multiple futile cycle.
Wang, Liming; Sontag, Eduardo D
2008-07-01
The multisite phosphorylation-dephosphorylation cycle is a motif repeatedly used in cell signaling. This motif itself can generate a variety of dynamic behaviors like bistability and ultrasensitivity without direct positive feedbacks. In this paper, we study the number of positive steady states of a general multisite phosphorylation-dephosphorylation cycle, and how the number of positive steady states varies by changing the biological parameters. We show analytically that (1) for some parameter ranges, there are at least n + 1 (if n is even) or n (if n is odd) steady states; (2) there never are more than 2n - 1 steady states (in particular, this implies that for n = 2, including single levels of MAPK cascades, there are at most three steady states); (3) for parameters near the standard Michaelis-Menten quasi-steady state conditions, there are at most n + 1 steady states; and (4) for parameters far from the standard Michaelis-Menten quasi-steady state conditions, there is at most one steady state.
Effects of Four Pesticides on Grain Growth Parameters of Rice
WU Jin-cai; DONG Bo; LI Dong-hu; QIU Hui-min; YANG Guo-qing
2004-01-01
Effect of four commonly used pesticides, triadlmefon, jingganmycin, triazoplos and imidacloprid, on grain growth parameters was examined using a growth equation in the present paper. Two hundreds of spikes, not damaged by pests were simultaneously marked per plot during the heading stage of rice. Rice plants were sprayed at 1 d after marking.Thereafter, 20 spikes were sampled at 4 d intervals and dried in an oven. Then, 10 superior and inferior grains were picked from each spike, and brown rice was weighed after shelling, respectively. First, second and third order derivates were deduced from the following grain growth formula:W=K/1+ea-bt , where W was the weight of 100 grains brown rice at time t; K was maximum of grain growth; a and b were parameters of the formula. The parameters were calculated as following:R0=Kbea/ (1 + ea)2 ,△ t=t2-t1,GT=bk/4(t2-t1)=Vmax(t2-t1),Vmax=bk/4Where R0, △t, GT and Vmax were initial growth power, active growth stage, accumulative weight of dried content during △ t and maximum growth rate, respectively. The result showed that GT and K of superior grain following 22.5 and 45 ga.i. ha-1 of imidacloprid sprays were significantly reduced, and △t was significantly decreased for 112.5 and 225ga.i. ha-1 jingganmycin treatments. In addition, the high dose of imidacloprid significantly reduced the weight of 1 000 rice grains by 9.77%. However, there was no significant difference for the weight of 1 000 grains between the high dose of jingganmycin and thecontrol, indicating that effective duration of jingganmycin on grain filling was shorterthan that of imidacloprid.
Robust Nonlinear Regression in Enzyme Kinetic Parameters Estimation
Maja Marasović
2017-01-01
Full Text Available Accurate estimation of essential enzyme kinetic parameters, such as Km and Vmax, is very important in modern biology. To this date, linearization of kinetic equations is still widely established practice for determining these parameters in chemical and enzyme catalysis. Although simplicity of linear optimization is alluring, these methods have certain pitfalls due to which they more often then not result in misleading estimation of enzyme parameters. In order to obtain more accurate predictions of parameter values, the use of nonlinear least-squares fitting techniques is recommended. However, when there are outliers present in the data, these techniques become unreliable. This paper proposes the use of a robust nonlinear regression estimator based on modified Tukey’s biweight function that can provide more resilient results in the presence of outliers and/or influential observations. Real and synthetic kinetic data have been used to test our approach. Monte Carlo simulations are performed to illustrate the efficacy and the robustness of the biweight estimator in comparison with the standard linearization methods and the ordinary least-squares nonlinear regression. We then apply this method to experimental data for the tyrosinase enzyme (EC 1.14.18.1 extracted from Solanum tuberosum, Agaricus bisporus, and Pleurotus ostreatus. The results on both artificial and experimental data clearly show that the proposed robust estimator can be successfully employed to determine accurate values of Km and Vmax.
Study on Characteristics of Polyphenol Oxidase from Yacon%天山雪莲果多酚氧化酶的特性研究
刘姝; 王渊; 方佳; 刘冬志; 韩丽丽
2012-01-01
In this study,with fresh material of Tianshan Yacon,The optimum polyphenol oxidase(PPO),optimum pH,optimum temperature,the fitting of the Michaelis-Menten equation and obtained the Km and Vmax,and explore the different inhibitionagents on PPO activity.Using catechol as substrate,the Km and Vmax were 0.061mol/L,776.4U/g·min respectively.The four inhibitors had different effects on inhibiting enzymatic browning and the inhibiting effect are as follow: citric acid〉L-cysteine〉ascorbic acid〉acetic acid.%以新鲜的天山雪莲果为材料,研究了多酚氧化酶（PPO）的最适pH、最适温度,拟合了米氏方程并求得了Km、Vmax,并探讨了不同抑制剂对PPO的活性影响。结果表明：天山雪莲果多酚氧化酶最适反应pH为6.5,最适温度为45℃;以邻苯二酚为底物,km=0.061mol/L,Vmax=776.4U/min·g;在选定的浓度范围内抑制剂对PPO的抑制作用大小为：NaHSO3﹥L-cys﹥Vc﹥柠檬酸。
Kinetics of trypsin-catalyzed hydrolysis determined by isothermal titration calorimetry.
Maximova, Ksenia; Trylska, Joanna
2015-10-01
Isothermal titration calorimetry (ITC) was applied to determine enzymatic activity and inhibition. We measured the Michaelis-Menten kinetics for trypsin-catalyzed hydrolysis of two substrates, casein (an insoluble macromolecule substrate) and Nα-benzoyl-dl-arginine β-naphthylamide (a small substrate), and estimated the thermodynamic parameters in the temperature range from 20 to 37°C. The inhibitory activities of reversible (small molecule benzamidine) and irreversible (small molecule phenylmethanesulfonyl fluoride and macromolecule α1-antitrypsin) inhibitors of trypsin were also determined. We showed the usefulness of ITC for fast and direct measurement of inhibition constants and half-maximal inhibitory concentrations and for predictions of the mechanism of inhibition. ITC kinetic assays could be an easy and straightforward way to estimate Michaelis-Menten constants and the effectiveness of inhibitors as well as to predict the inhibition mechanism. ITC efficiency was found to be similar to that of classical spectrophotometric enzymatic assays. Copyright © 2015 Elsevier Inc. All rights reserved.
Exploration of two-enzyme coupled catalysis system using scanning electrochemical microscopy.
Wu, Zeng-Qiang; Jia, Wen-Zhi; Wang, Kang; Xu, Jing-Juan; Chen, Hong-Yuan; Xia, Xing-Hua
2012-12-18
In biological metabolism, a given metabolic process usually occurs via a group of enzymes working together in sequential pathways. To explore the metabolism mechanism requires the understanding of the multienzyme coupled catalysis systems. In this paper, an approach has been proposed to study the kinetics of a two-enzyme coupled reaction using SECM combining numerical simulations. Acetylcholine esterase and choline oxidase are immobilized on cysteamine self-assembled monolayers on tip and substrate gold electrodes of SECM via electrostatic interactions, respectively. The reaction kinetics of this two-enzyme coupled system upon various separation distance precisely regulated by SECM are measured. An overall apparent Michaelis-Menten constant of this enzyme cascade is thus measured as 2.97 mM at an optimal tip-substrate gap distance of 18 μm. Then, a kinetic model of this enzyme cascade is established for evaluating the kinetic parameters of individual enzyme by using the finite element method. The simulated results demonstrate the choline oxidase catalytic reaction is the rate determining step of this enzyme cascade. The Michaelis-Menten constant of acetylcholine esterase is evaluated as 1.8 mM. This study offers a promising approach to exploring mechanism of other two-enzyme coupled reactions in biological system and would promote the development of biosensors and enzyme-based logic systems.
Pugh, C. Preston; Pouncey, Dakota L; Hartman, Jessica H.; Nshimiyimana, Robert; Desrochers, Linda P.; Goodwin, Thomas E.; Boysen, Gunnar; Miller, Grover P.
2014-01-01
The widely used anticoagulant Coumadin (R/S-warfarin) undergoes oxidation by cytochromes P450 into hydroxywarfarins that subsequently become conjugated for excretion in urine. Hydroxywarfarins may modulate warfarin metabolism transcriptionally or through direct inhibition of cytochromes P450 and thus, UGT action toward hydroxywarfarin elimination may impact levels of the parent drugs and patient responses. Nevertheless, relatively little is known about conjugation by UDP-glucuronosyltransferases in warfarin metabolism. Herein, we identified probable conjugation sites, kinetic mechanisms and hepatic UGT isoforms involved in microsomal glucuronidation of R- and S-7-hydroxywarfarin. Both compounds underwent glucuronidation at C4 and C7 hydroxyl groups based on elution properties and spectral characteristics. Their formation demonstrated regio- and enantioselectivity by UGTs and resulted in either Michaelis-Menten or substrate inhibition kinetics. Glucuronidation at the C7 hydroxyl group occurred more readily than at the C4 group, and the reaction was overall more efficient for R-7-hydroxywarfarin due to higher affinity and rates of turnover. The use of these mechanisms and parameters to model in vivo clearance demonstrated that contributions of substrate inhibition would lead to underestimation of metabolic clearance than that predicted by Michaelis-Menten kinetics. Lastly, these processes were driven by multiple UGTs indicating redundancy in glucuronidation pathways and ultimately metabolic clearance of R- and S-7-hydroxywarfarin. PMID:25447818
Minatti, Gheise; Mello, Josiane M.M. de; Souza, Selene M.A. Guelli Ulson de; Antonio Augusto Ulson de [Universidade Federal de Santa Catarina (UFSC), Florianopolis, SC (Brazil)
2008-07-01
The compounds BTX inside of the petrochemical effluent have presented a high potential of pollution, representing a serious risk to the environment and to the human. The great improvements in the field of biological treatment of liquid effluent were reached through the process using biofilm capable of degrading toxic compounds. The objective of this paper is to determine the degradation kinetics of BTX using biofilm. The experimental data were compared with two kinetic models, kinetic of first order and model of Michaelis-Menten. The kinetic parameters of BTX compounds were experimentally obtained in a bioreactor in batch with biomass immobilized in activated-carbon, being fed daily with solution of nutrients and BTX. For the kinetic models studied in this paper, the best performance was achieved with the model of Michaelis-Menten showing a good correlation coefficient for the three compounds. The biomass amount in these bioreactors was 49.18, 28.35 and 5.15 mg of SSV per gram of support for the toluene, benzene and o-xylene, respectively. The experimental tests showed that the biomass inside of bioreactor is capable to degrade all compounds in a time of approximately 300 minutes. (author)
A mathematical model of liver metabolism: from steady state to dynamic
Calvetti, D; Kuceyeski, A [Case Western Reserve University, Department of Mathematics, 10900 Euclid Avenue, Cleveland, OH 44106 (United States); Somersalo, E [Helsinki University of Technology, Institute of Mathematics, P. O. Box 1100, FIN-02015 HUT (Finland)], E-mail: daniela.calvetti@case.edu, E-mail: amy.kuceyeski@case.edu, E-mail: erkki.somersalo@hut.fi
2008-07-15
The increase in Type 2 diabetes and other metabolic disorders has led to an intense focus on the areas of research related to metabolism. Because the liver is essential in regulating metabolite concentrations that maintain life, it is especially important to have good knowledge of the functions within this organ. In silico mathematical models that can adequately describe metabolite concentrations, flux and transport rates in the liver in vivo can be a useful predictive tool. Fully dynamic models, which contain expressions for Michaelis-Menten reaction kinetics can be utilized to investigate different metabolic states, for example exercise, fed or starved state. In this paper we describe a two compartment (blood and tissue) spatially lumped liver metabolism model. First, we use Bayesian Flux Balance Analysis (BFBA) to estimate the values of flux and transport rates at steady state, which agree closely with values from the literature. These values are then used to find a set of Michaelis-Menten parameters and initial concentrations which identify a dynamic model that can be used for exploring different metabolic states. In particular, we investigate the effect of doubling the concentration of lactate entering the system via the hepatic artery and portal vein. This change in lactate concentration forces the system to a new steady state, where glucose production is increased.
Zhu, Rencheng; Li, Shunyi; Bao, Xiaofeng; Dumont, Éric
2017-02-01
The performances of two identical biofilters, filled with a new composite packing material (named CM-5) embedded with functional microorganisms or sterilized CM-5 without microorganisms, were investigated for H2S treatment. Running parameters in terms of microbial counts, pressure drops, and inlet and outlet H2S concentrations were measured. The results show that the microbial count of the CM-5 was approximately ×105 CFU/g before being filled into the biofilter, while that of the sterilized CM-5 was negligible. The functional microorganisms embedded in CM-5 adapted to the environment containing H2S quickly. In most cases, pressure drops of the CM-5 biofilter were slightly higher than those of the sterilized CM-5 biofilter when the gas flow rate was 0.6-2.5 m3/h. The maximum elimination capacity (EC) of the CM-5 biofilter in treating H2S could reach up to 65 g/(m3·h) when the loading rate (LR) was approximately 80 g/(m3·h). If the LR was much higher, the measured EC showed a slight downward trend. The experimental ECs of biofilters were fitted by two typical dynamic models: the Michaelis-Menten model and the Haldane model. Compared with the Michaelis-Menten model, the Haldane model fit the experimental ECs better for the two biofilters because of the presence of the substrate inhibition behaviour.
Kinetic study of the enzymatic hydrolysis of sugarcane bagasse
M. L. Carvalho
2013-09-01
Full Text Available This work presents a kinetic study of the enzymatic hydrolysis of three cellulosic substrates: filter paper (FP, used as a low recalcitrance substrate model; steam exploded sugarcane bagasse (SB; and weak acid pretreated SB (1:20 dry bagasse:H2SO4 solution 1% w/w, the last two delignified with 4% NaOH (w/w. The influence of substrate concentration was assessed in hydrolysis experiments in a shaker, using Accellerase® 1500, at pH 4.8, in 50 mM sodium citrate buffer. Cellulose loads (weight substrate/weight total were changed between 0.5%-13% (for FP and 0.99%-9.09% (for SB. For FP and low loads of steam exploded SB, it was possible to fit pseudo-homogeneous Michaelis-Menten models (with inhibition. For FP and higher loads of steam exploded SB, modified Michaelis-Menten models were fitted. Besides, it was observed that, after retuning of the model parameters, it is possible to apply a model fitted for one situation to a different case. Chrastil models were also fitted and they were the only feasible approach for the highly recalcitrant acid-treated SB.
Use of CdSe/ZnS luminescent quantum dots incorporated within sol-gel matrix for urea detection
Duong, Hong Dinh [School of Applied Chemical Engineering, Research Center for Biophotonics, Chonnam National University, Yong-Bong dong 300, 500-757 Gwangju (Korea, Republic of); Rhee, Jong Il [School of Applied Chemical Engineering, Research Center for Biophotonics, Chonnam National University, Yong-Bong dong 300, 500-757 Gwangju (Korea, Republic of)], E-mail: jirhee@chonnam.ac.kr
2008-09-19
In this work, urea detection techniques based on the pH sensitivity of CdSe/ZnS QDs were developed using three types of sol-gel membranes: a QD-entrapped membrane, urease-immobilized membrane and double layer consisting of a QD-entrapped membrane and urease-immobilized membrane. The surface morphology of the sol-gel membranes deposited on the wells in a 24-well microtiter plate was investigated. The linear detection range of urea was in the range of 0-10 mM with the three types of sol-gel membranes. The urea detection technique based on the double layer consisting of the QD-entrapped membrane and urease-immobilized membrane resulted in the highest sensitivity to urea due to the Michaelis-Menten kinetic parameters. That is, the Michaelis-Menten constant (K{sub m} =2.0745 mM) of the free urease in the QD-entrapped membrane was about 4-fold higher than that (K{sub m} =0.549 mM) of the immobilized urease in the urease-immobilized membrane and about 12-fold higher than that (K{sub m} =0.1698 mM) of the immobilized urease in the double layer. The good stability of the three sol-gel membranes for urea sensing over 2 months showed that the use of sol-gel membranes immobilized with QDs or an enzyme is suitable for biomedical and environmental applications.
Zhu, Rencheng; Li, Shunyi; Bao, Xiaofeng; Dumont, Éric
2017-01-01
The performances of two identical biofilters, filled with a new composite packing material (named CM-5) embedded with functional microorganisms or sterilized CM-5 without microorganisms, were investigated for H2S treatment. Running parameters in terms of microbial counts, pressure drops, and inlet and outlet H2S concentrations were measured. The results show that the microbial count of the CM-5 was approximately ×105 CFU/g before being filled into the biofilter, while that of the sterilized CM-5 was negligible. The functional microorganisms embedded in CM-5 adapted to the environment containing H2S quickly. In most cases, pressure drops of the CM-5 biofilter were slightly higher than those of the sterilized CM-5 biofilter when the gas flow rate was 0.6–2.5 m3/h. The maximum elimination capacity (EC) of the CM-5 biofilter in treating H2S could reach up to 65 g/(m3·h) when the loading rate (LR) was approximately 80 g/(m3·h). If the LR was much higher, the measured EC showed a slight downward trend. The experimental ECs of biofilters were fitted by two typical dynamic models: the Michaelis-Menten model and the Haldane model. Compared with the Michaelis-Menten model, the Haldane model fit the experimental ECs better for the two biofilters because of the presence of the substrate inhibition behaviour. PMID:28198800
Studies on the kinetics of plasminogen activation by tissue plasminogen activator.
Rånby, M
1982-06-24
The steady-state rate of plasminogen activation by tissue plasminogen activator has been determined at various plasminogen concentrations. A plasmin substrate method similar to that presented by Christensen and Müllertz (Biochim. Biophys. Acta 480 (1977) 257-281) was used. The reaction was studied using one-chain type and two-chain type tissue plasminogen activator, N-terminal glutamic acid and N-terminal lysine plasminogen in the presence and in the absence of fibrin (eight studies). The kinetic data were fitted to a general Wong-Hanes equation and the simplest equation with significant parameters was found. In the absence of fibrin N-terminal glutamic acid plasminogen activation obeyed the Michaelis-Menten rate equation (Km 4.9 and 7.6 micro M and kcat 0.0013 and 0.0078 s-1 for one-chain type and two-chain type tissue plasminogen activator, respectively. In the absence of fibrin the activation of N-terminal lysine plasminogen activation failed to obey the Michaelis-Menten rate equation. Fibrin was found to stimulate greatly (up to 1000-fold) the steady-state activation rate. A theory for the fibrin stimulating mechanism is presented.
Catalytic Behavior of Lipase Immobilized onto Congo Red and PEG-Decorated Particles
Rubens A. Silva
2014-06-01
Full Text Available Poly(ethylene glycol (PEG-decorated polystyrene (PS nanoparticles with mean hydrodynamic diameter (D and zeta–potential (ζ of (286 ± 15 nm and (−50 ± 5 mV, respectively, were modified by the adsorption of Congo red (CR. The PS/PEG/CR particles presented D and ζ values of (290 ± 19 nm and (−36 ± 5 mV, respectively. The adsorption of lipase onto PS/PEG or PS/PEG/CR particles at (24 ± 1 °C and pH 7 changed the mean D value to (380 ± 20 and (405 ± 11 nm, respectively, and ζ value to (−32 ± 4 mV and (−25 ± 2 mV, respectively. The kinetic parameters of the hydrolysis of p-nitrophenyl butyrate were determined for free lipase, lipase immobilized onto PS/PEG and PS/PEG/CR particles. Lipase on PS/PEG/CR presented the largest Michaelis-Menten constant (KM, but also the highest Vmax and kcat values. Moreover, it could be recycled seven times, losing a maximum 10% or 30% of the original enzymatic activity at 40 °C or 25 °C, respectively. Although lipases immobilized onto PS/PEG particles presented the smallest KM values, the reactions were comparatively the slowest and recycling was not possible. Hydrolysis reactions performed in the temperature range of 25 °C to 60 °C with free lipases and lipases immobilized onto PS/PEG/CR particles presented an optimal temperature at 40 °C. At 60 °C free lipases and lipases immobilized onto PS/PEG/CR presented ~80% and ~50% of the activity measured at 40 °C, indicating good thermal stability. Bioconjugation effects between CR and lipase were evidenced by circular dichroism spectroscopy and spectrophotometry. CR molecules mediate the open state conformation of the lipase lid and favor the substrate approaching.
王周俊; 李翔; 王琛琛; 唐颐; 张亚红
2011-01-01
通过在毛细管内层层组装纳米沸石并固定脂肪酶来构建纳米沸石修饰的固定化酶微反应器通道,将纳米沸石良好的生物相容性和高的酶固定能力与微反应器反应效率高和扩散传质快等优点相结合,以对硝基苯棕榈酸酯的水解作为探针反应,对该微反应器内固定化酶催化水解反应动力学进行了研究和计算,并与普通反应器内同样的反应进行比较.通过对比米氏方程参数,证实在微反应器内酶催化水解反应效率比普通反应器内提高3倍以上,并可提高酶和反应底物的亲和能力.%Nanozeolite modified microchannel reactors were constructed by assembling zeolite nanocrystals into capillary using layer-by-layer assemble method. And then lipase CRL was immobilized on the nanozeolites assembled in the microreactors. The nanozeolite modified microreactors could incorporate excellent biocaptibility and large external area of nanozeolites and high efficiency and fast mass diffusion of microreactors together.Hydrolysis of 4-nitrophenyl palmitate (4-NPP) was carried out as a probe reaction to study the hydrolysis kinetics catalyzed by immobilized CRL in the microreactors. By comparing the characteristic parameters (Km and Vmax) of Michaelis-Menten equation, it is found that efficiency of enzymatic hydrolysis in such nanozeolite modified microchannel reactors could be 3 or more times higher than that of the same reaction in conventional reactors. In addition, affinity between enzyme and substrates is also enhanced in the nanozeolite modified microchannel reactors.
Dunlop, J; Lou, Z; Zhang, Y; McIlvain, H B
1999-12-01
1. In this study we have examined the use of the ecdysone-inducible mammalian expression system (Invitrogen) for the regulation of expression of the predominant L-glutamate transporter EAAT2 (Excitatory Amino Acid Transporter) in HEK 293 cells. 2. HEK 293 cells which were stably transformed with the regulatory vector pVgRXR (EcR 293 cells) were used for transfection of the human EAAT2 cDNA using the inducible vector pIND and a clone designated HEK/EAAT2 was selected for further characterization. 3. Na+-dependent L-glutamate uptake activity (3.2 pmol min-1 mg-1) was observed in EcR 293 cells and this was increased approximately 2 fold in the uninduced HEK/EAAT2 cells, indicating a low level of basal EAAT2 activity in the absence of exogenous inducing agent. Exposure of HEK/EAAT2 cells to the ecdysone analogue Ponasterone A (10 microM for 24 h) resulted in a > or = 10 fold increase in the Na+-dependent activity. 4. L-glutamate uptake into induced HEK/EAAT2 cells followed first-order Michaelis-Menten kinetics and Eadie-Hofstee transformation of the saturable uptake data produced estimates of kinetic parameters as follows; Km 52.7+/-7.5 microM, Vmax 3.8+/-0.9 nmol min-1 mg-1 protein. 5. The pharmacological profile of the EAAT2 subtype was characterized using a series of L-glutamate transport inhibitors and the rank order of inhibitory potency was similar to that described previously for the rat homologue GLT-1 and in synaptosomal preparations from rat cortex. 6. Addition of the EAAT2 modulator arachidonic acid resulted in an enhancement (155+/-5% control in the presence of 30 microM) of the L-glutamate transport capacity in the induced HEK/EAAT2 cells. 7. This study demonstrates that the expression of EAAT2 can be regulated in a mammalian cell line using the ecdysone-inducible mammalian expression system.
Duhamel, Marie-Claude; Troncy, Eric; Beaudry, Francis
2010-08-01
Medetomidine is a potent and selective alpha2-adrenergic agonist. The activation of alpha2-adrenergic receptor mediates a variety of effects including sedation, analgesia, relief of anxiety, vasoconstriction and bradycardia. However, our main interest is the sedative effects of medetomidine when used as a premedicant prior surgery in companion animals, especially in dogs. Recently, data suggested that following intravenous infusion at six dosing regiments non-linear pharmacokinetics was observed. Major causes of non-linear pharmacokinetics are the elimination of the drug not following a simple first-order kinetics and/or the elimination half-life changing due to saturation of an enzyme system. The goal of this study was to establish the metabolic stability and determine the metabolic pathway of medetomidine in dog liver microsomes. Consequently, Michaelis-Menten parameters (V(max), K(m)), T(1/2) and CL(i) were determined. The incubations were performed in a microcentrifuge tube and containing various concentrations of medetomidine (10-5000 nM), 1 mg/mL of microsomal proteins suspended in 0.1 M phosphate buffer, pH 7.4. Microsomal suspensions were preincubated with NADPH (1 mM) for 5 min at 37 degrees C prior to fortification with medetomidine. Samples were taken at various time points for kinetic information and the initial velocity (v(i)) was determined after 10 min incubation. The reaction was stopped by the addition of an internal standard solution (100 ng/mL of dextrometorphan in acetone). Medetomidine concentrations were determined using a selective and sensitive HPLC-ESI/MS/MS method. Using non-linear regression, we determined a K(m) value of 577 nM, indicating relatively low threshold enzyme saturation consistent with previous in vivo observation. The metabolic stability was determined at a concentration of 100 nm (dog liver microsomes, also consistent with previous in vivo data. Moreover, results suggest that principally medetomidine is metabolized by the
Hadamard Transform Time-of-Flight Mass Spectrometry
2010-01-26
determined by direct fitting of the initial rates data to the Michaelis - Menten equation. Excellent agreement is shown amongst the values indicating that...of VGVKVR by trypsin at pH 8.5. The dashed red line in the figure shows a best fit to the Michaelis - Menten equation for the data collected. The
Hadamard Transform Time-of-Flight Spectroscopy
2010-01-26
system presented in Figure 13 were determined by direct fitting of the initial rates data to the Michaelis - Menten equation. Excellent agreement is...trypsin at pH 8.5. The dashed red line in the figure shows a best fit to the Michaelis - Menten equation for the data collected. The error bars in
Jensen, Michael Gejl; Lerche, Susanne; Egefjord, Lærke
2013-01-01
hypoglycemia study and our previous hyperglycemia study to estimate the Michaelis-Menten constants of glucose transport and metabolism. The GLP-1 treatment lowered the vascular volume of brain tissue. Loading data from hypo- to hyperglycemia into the Michaelis-Menten equation, we found increased maximum...
The total quasi-steady-state approximation for complex enzyme reactions
Pedersen, Morten Gram; Bersani, A. M.; Bersani, E.
2008-01-01
Biochemistry in general and enzyme kinetics in particular have been heavily influenced by the model of biochemical reactions known as Michaelis-Menten kinetics. Assuming that the complex concentration is approximately constant after a short transient phase leads to the usual Michaelis-Menten (MM...
Plankton Dynamics and Mesoscale Turbulence
2010-06-29
dependending on available nutri- ents through a Holling type-II (or Michaelis - Menten ) functional response, by a Holling type III grazing by zooplankton, by...phytoplankton, using a Michaelis - Menten (or Monod) functional form. The con- stants ρ1 and ρ2 are used to transform phytoplankton biomass into nutrient
2011-01-01
of optimisation techniques coupled with dynamic solution of the underlying model. Linear and nonlinear approaches to parameter estimation are investigated. There is also the application of maximum likelihood principles in the estimation of parameters, as well as the use of orthogonal collocation to generate a set......In this chapter the importance of parameter estimation in model development is illustrated through various applications related to reaction systems. In particular, rate constants in a reaction system are obtained through parameter estimation methods. These approaches often require the application...... of algebraic equations as the basis for parameter estimation.These approaches are illustrated using estimations of kinetic constants from reaction system models....
Macromolecular crowding and the steady-state kinetics of malate dehydrogenase.
Poggi, Christopher G; Slade, Kristin M
2015-01-20
To understand how macromolecular crowding affects enzyme activity, we quantified the Michaelis-Menten kinetics of mitochondrial malate dehydrogenase (MDH) in the presence of hen egg white (HEW), lysozyme, bovine serum albumin (BSA), gum arabic, poly(vinylpyrrolidone) (PVP), and dextrans of various molecular weights. Although crowding tended to decrease Km and Vmax values, the magnitude depended on the crowding agent, reaction direction, and isozyme (mitochondrial porcine heart or thermophlic TaqMDH from Thermus flavus). Crowding slowed oxaloacetate reduction more significantly than malate oxidation, which may suggest that mitochondrial enzymes have evolved to function optimally under the crowded constraints in which they are immersed. Since direct comparisons of neutral to charged crowders are underrepresented in the literature, we performed these studies and found that neutral crowding agents lowered Vmax values more than charged crowders of similar size. The exception was hen egg white, a mixture of charged proteins that caused the largest observed decreases in both Km and Vmax. Finally, the data provide insight about the mechanism by corroborating MDH subunit dependence.
Pedro L. Valencia
2017-04-01
Full Text Available We provide initial rate data from enzymatic reaction experiments and tis processing to estimate the kinetic parameters from the substrate uncompetitive inhibition equation using the median method published by Eisenthal and Cornish-Bowden (Cornish-Bowden and Eisenthal, 1974; Eisenthal and Cornish-Bowden, 1974. The method was denominated the direct linear plot and consists in the calculation of the median from a dataset of kinetic parameters Vmax and Km from the Michaelis–Menten equation. In this opportunity we present the procedure to applicate the direct linear plot to the substrate uncompetitive inhibition equation; a three-parameter equation. The median method is characterized for its robustness and its insensibility to outlier. The calculations are presented in an Excel datasheet and a computational algorithm was developed in the free software Python. The kinetic parameters of the substrate uncompetitive inhibition equation Vmax, Km and Ks were calculated using three experimental points from the dataset formed by 13 experimental points. All the 286 combinations were calculated. The dataset of kinetic parameters resulting from this combinatorial was used to calculate the median which corresponds to the statistic estimator of the real kinetic parameters. A comparative statistical analyses between the median method and the least squares was published in Valencia et al. [3].
Ladefoged, Peter
1980-01-01
Summarizes the 16 parameters hypothesized to be necessary and sufficient for linguistic phonetic specifications. Suggests seven parameters affecting tongue shapes, three determining the positions of the lips, one controlling the position of the velum, four varying laryngeal actions, and one controlling respiratory activity. (RL)
Sales-Cruz, Mauricio; Heitzig, Martina; Cameron, Ian;
2011-01-01
of optimisation techniques coupled with dynamic solution of the underlying model. Linear and nonlinear approaches to parameter estimation are investigated. There is also the application of maximum likelihood principles in the estimation of parameters, as well as the use of orthogonal collocation to generate a set...
Chance, B; Leigh, J S; Kent, J; McCully, K; Nioka, S; Clark, B J; Maris, J M; Graham, T
1986-12-01
Three types of metabolic control of oxidative metabolism are observed in the various tissues that have been studied by phosphorous magnetic resonance spectroscopy. The principal control of oxidative metabolism in skeletal muscle is by ADP (or Pi/phosphocreatine). This conclusion is based upon studies of arm muscles of humans during steady-state exercise. A work-cost (Vm vs. Pi/phosphocreatine) relationship follows a Michaelis-Menten rectangular hyperbola, where Km values from 0.5 to 0.6 and Vmax values from 50 to 200 (at nearly constant pH) are found in linearized plots of the equation V/Vmax = 1/(1 + 0.6 phosphocreatine/Pi) where V is work level (which is equal to the velocity of the enzymatic reaction) and Vmax is the maximal work capacity that is a measure of the enzyme activity (E) of oxidative metabolism. Adaptation to exercise enhances the slope of the work-cost relationship and causes large changes in Vmax or E. A second metabolic control may enhance the slope of the work-cost relationship but not Vmax. For example, the initiation of exercise can lead to an improved characteristic that can be explained by 2-fold increased substrate delivery, for example, increased oxygen delivery by microcirculatory control. Cardiac tissue of the adult dog affords an example of optimal endurance performance adaptation and exhibits the steepest work-cost relationship observed and is attributed to a coordinated control of substrate delivery that may involve Ca2+ and inorganic phosphate control of NADH; control of O2 delivery may also be involved. The calculated work-cost relationship is similar to that observed in the beagle heart. The theoretical curve illustrates that the liability of multiple controls is a sharp break point in metabolic control at the end of the multiple control range--a possible cause of instability of cardiac performance at high V/Vmax.
Kim, Eun Young [Dept. of Radiology, Chonbuk National University Medical School and Hospital, Research Institute of Clinical Medicine, Jeonju (Korea, Republic of); Seo, Joon Beom; Oh, Sang Young; Lee, Choong Wook; Lee, Sang Min [Dept. of Radiology and Research Institute of Radiology, University of Ulsan College of Medicine, Asan Medical Center, Seoul (Korea, Republic of); Hwang, Hye Jeon [Dept. of Radiology, Hallym University College of Medicine, Hallym University Sacred Heart Hospital, Anyang (Korea, Republic of); Lee, Young Kyung [Dept. of Radiology, Seoul Medical Center, Seoul (Korea, Republic of)
2014-04-15
To assess perfusion patterns on a dual-energy pulmonary CT angiography (DECTA) of pulmonary hypertension (PHT) with variable causes and to assess whether the extent of perfusion defect can be used in the severity assessment of PHT. Between March 2007 and February 2011, DECTA scans of 62 consecutive patients (24 men, 38 women; mean age, 58.5 ± 17.3 [standard deviation] years; range, 19-87 years) with PHT were retrospectively included with following inclusion criteria; 1) absence of acute pulmonary thromboembolism, 2) maximal velocity of tricuspid regurgitation jet (TR Vmax) above 3 m/s on echocardiography performed within one week of the DECTA study. Perfusion patterns of iodine map were divided into normal (NL), diffuse heterogeneously decreased (DH), multifocal geographic and multiple peripheral wedging patterns. The extent of perfusion defects (PD), the diameter of main pulmonary artery (MPA) and the ratio of ascending aorta diameter/MPA (aortopulmonary ratio, APR) were measured. Pearson correlation analysis was performed between TR Vmax on echocardiography and CT imaging parameters. Common perfusion patterns of primary PHT were DH (n = 15) and NL (n = 12). The perfusion patterns of secondary PHT were variable. On the correlation analysis, in primary PHT, TR Vmax significantly correlated with PD, MPA and APR (r = 0.52, r = 0.40, r = -0.50, respectively, all p < 0.05). In secondary PHT, TR Vmax significantly correlated with PD and MPA (r = 0.38, r = 0.53, respectively, all p < 0.05). Different perfusion patterns are observed on DECTA of PHT according to the causes. PD and MPA are significantly correlated with the TR Vmax.
Sharma, Sanjay
2017-01-01
This book provides a detailed overview of various parameters/factors involved in inventory analysis. It especially focuses on the assessment and modeling of basic inventory parameters, namely demand, procurement cost, cycle time, ordering cost, inventory carrying cost, inventory stock, stock out level, and stock out cost. In the context of economic lot size, it provides equations related to the optimum values. It also discusses why the optimum lot size and optimum total relevant cost are considered to be key decision variables, and uses numerous examples to explain each of these inventory parameters separately. Lastly, it provides detailed information on parameter estimation for different sectors/products. Written in a simple and lucid style, it offers a valuable resource for a broad readership, especially Master of Business Administration (MBA) students.
Analysis of mathematical modelling on potentiometric biosensors.
Mehala, N; Rajendran, L
2014-01-01
A mathematical model of potentiometric enzyme electrodes for a nonsteady condition has been developed. The model is based on the system of two coupled nonlinear time-dependent reaction diffusion equations for Michaelis-Menten formalism that describes the concentrations of substrate and product within the enzymatic layer. Analytical expressions for the concentration of substrate and product and the corresponding flux response have been derived for all values of parameters using the new homotopy perturbation method. Furthermore, the complex inversion formula is employed in this work to solve the boundary value problem. The analytical solutions obtained allow a full description of the response curves for only two kinetic parameters (unsaturation/saturation parameter and reaction/diffusion parameter). Theoretical descriptions are given for the two limiting cases (zero and first order kinetics) and relatively simple approaches for general cases are presented. All the analytical results are compared with simulation results using Scilab/Matlab program. The numerical results agree with the appropriate theories.
Bringing metabolic networks to life: convenience rate law and thermodynamic constraints
Klipp Edda
2006-12-01
Full Text Available Abstract Background Translating a known metabolic network into a dynamic model requires rate laws for all chemical reactions. The mathematical expressions depend on the underlying enzymatic mechanism; they can become quite involved and may contain a large number of parameters. Rate laws and enzyme parameters are still unknown for most enzymes. Results We introduce a simple and general rate law called "convenience kinetics". It can be derived from a simple random-order enzyme mechanism. Thermodynamic laws can impose dependencies on the kinetic parameters. Hence, to facilitate model fitting and parameter optimisation for large networks, we introduce thermodynamically independent system parameters: their values can be varied independently, without violating thermodynamical constraints. We achieve this by expressing the equilibrium constants either by Gibbs free energies of formation or by a set of independent equilibrium constants. The remaining system parameters are mean turnover rates, generalised Michaelis-Menten constants, and constants for inhibition and activation. All parameters correspond to molecular energies, for instance, binding energies between reactants and enzyme. Conclusion Convenience kinetics can be used to translate a biochemical network – manually or automatically - into a dynamical model with plausible biological properties. It implements enzyme saturation and regulation by activators and inhibitors, covers all possible reaction stoichiometries, and can be specified by a small number of parameters. Its mathematical form makes it especially suitable for parameter estimation and optimisation. Parameter estimates can be easily computed from a least-squares fit to Michaelis-Menten values, turnover rates, equilibrium constants, and other quantities that are routinely measured in enzyme assays and stored in kinetic databases.
Kim, Tae Hwan; Shin, Soyoung; Bulitta, Jürgen B; Youn, Yu Seok; Yoo, Sun Dong; Shin, Beom Soo
2017-01-03
Establishing a level A in vitro-in vivo correlation (IVIVC) for a drug with complex absorption kinetics is challenging. The objective of the present study was to develop an IVIVC approach based on population pharmacokinetic (POP-PK) modeling that incorporated physiologically relevant absorption kinetics. To prepare three extended release (ER) tablets of loxoprofen, three types of hydroxypropyl methylcellulose (HPMC 100, 4000, and 15000 cps) were used as drug release modifiers, while lactose and magnesium stearate were used as the diluent and lubricant, respectively. An in vitro dissolution test in various pH conditions showed that loxoprofen dissolution was faster at higher pH. The in vivo pharmacokinetics of loxoprofen was assessed following oral administration of the different loxoprofen formulations to Beagle dogs (n = 22 in total). Secondary peaks or shoulders were observed in many of the individual plasma concentration vs time profiles after ER tablet administration, which may result from secondary absorption in the intestine due to a dissolution rate increase under intestinal pH compared to that observed at stomach pH. In addition, in vivo oral bioavailability was found to decrease with prolonged drug dissolution, indicating site-specific absorption. Based on the in vitro dissolution and in vivo absorption data, a POP-PK IVIVC model was developed using S-ADAPT software. pH-dependent biphasic dissolution kinetics, described using modified Michaelis-Menten kinetics with varying Vmax, and site-specific absorption, modeled using a changeable absorbed fraction parameter, were applied to the POP-PK IVIVC model. To experimentally determine the biphasic dissolution profiles of the ER tablets, another in vitro dissolution test was conducted by switching dissolution medium pH based on an in vivo estimate of gastric emptying time. The model estimated, using linear regression, that in vivo initial maximum dissolution rate (Vmax(0)in vivo) was highly correlated (r(2) > 0
Kinetics of methane oxidation in selected mineral soils
Walkiewicz, A.; Bulak, P.; Brzeziñska, M.; Włodarczyk, T.; Polakowski, C.
2012-10-01
The kinetic parameters of methane oxidation in three mineral soils were measured under laboratory conditions. Incubationswere preceded by a 24-day preincubationwith 10%vol. of methane. All soils showed potential to the consumption of added methane. None of the soils, however, consumed atmospheric CH4. Methane oxidation followed the Michaelis-Menten kinetics, with relatively low values of parameters for Eutric Cambisol, while high values for Haplic Podzol, and especially for Mollic Gleysol which showed the highest methanotrophic activity and much lower affinity to methane. The high values of parameters for methane oxidation are typical for organic soils and mineral soils from landfill cover. The possibility of the involvement of nitrifying microorganisms, which inhabit the ammonia-fertilized agricultural soils should be verified.
Lemoine, Sandrine; Rouet, René; Manrique, Alain; Hanouz, Jean-Luc
2014-10-01
Lipid emulsions are used in the reversal of local anesthetic toxicity. The aim of this study was to investigate the cellular electrophysiological effects of long-chain triglyceride lipid emulsion (LCTE) on cardiac action potential characteristics and conduction disturbances induced by bupivacaine. Purkinje fibers were dissected from the left ventricle of New Zealand white rabbit hearts and superfused with either Tyrode's solution during 30 min (control group), with bupivacaine 10(-6) M, 10(-5) M, and 5.10(-5) M alone, or in the presence of LCTE 0.5%, in addition, LCTE at 0.1%, 0.5%, and 1% was perfused alone. Electrophysiological parameters were recorded using the conventional microelectrode technique (37 °C, 1 Hz frequency). Bupivacaine 5.10(-5) M-induced conduction blocks (8/8 preparations): LCTE 0.5% suppressed the bupivacaine 5.10(-5) M-induced conduction blocks (1/8 preparations). Exposure to bupivacaine 10(-6) M, 10(-5) M, and 5.10(-5) M resulted in a significant decrease in the maximal rate of depolarization (Vmax) (respectively, 25%, 55%, 75%; P bupivacaine 10(-6) M did not significantly decreased Vmax (13%; P = 0.10 vs. control group). The decrease in Vmax resulting from bupivacaine 10(-5) M alone was significantly less in the presence of LCTE 0.5% (P bupivacaine 10(-5) M alone). Exposure to bupivacaine 10(-6) M, 10(-5) M, and 5.10(-5) M alone or in the presence of LCTE 0.5% resulted in a significant decrease in action potential duration measured at 50% and 90% repolarization (APD50 and APD90; P bupivacaine. Moreover, LCTE 0.5% attenuates the decrease in Vmax induced by bupivacaine 10(-6) M and 10(-5) M.
A. Agah
2012-12-01
Full Text Available Risk-based assessment methods are commonly used at the contaminated sites by hydrocarbon pollutants. This paper presents the results of a two-dimensional finite volume model of reactive transport of biodegradable BTEX which have been developed for the saturated zone of an unconfined aquifer in the Pump station area of Tehran oil refinery, Iran. The model governing equations were numerically solved by modification of a general commercial software called PHOENICS. To reduce costs in general, many input parameters of a model are often approximated based on the used values in the contaminated sites with same conditions. It was not fully recognised the effect of errors in these inputs on modelling outputs. Thus, a sensitivity analysis was carried out to determine the influence of parameters variability on the results of model. For this analysis, the sensitivity of the model to changes in the dispersivity, distribution coefficient, parameters of Monod, Michaelis-Menten, first- and zero- order kinetics modes on the BTEX contaminant plume were examined by performing several simulations. It was found that the model is sensitive to changes in dispersivity and parameters of Michaelis-Menten, first- and zero- order kinetics model. On the other hand, the predictions for plumes assuming Monod kinetics are similar, even if different values for parameterization are chosen. The reason for this insensibility is that degradation is not limited by microbial kinetics in the simulation, but by dispersive mixing. Quantifying the effect of changes in model input parameters on the modelling results is essential when it is desired to recognise which model parameters are more vital on the fate and transport of reactive pollutants. Furthermore, this process can provide an insight into understanding pollutant transportation mechanisms.
Stiripentol kinetics in epilepsy: nonlinearity and interactions.
Levy, R H; Loiseau, P; Guyot, M; Blehaut, H M; Tor, J; Moreland, T A
1984-11-01
Stiripentol kinetics during oral therapy were assessed in six patients with epilepsy who were receiving other antiepileptic drugs. Steady-state levels at 600, 1200, and 2400 mg/day increased in a nonlinear fashion, indicating Michaelis-Menten kinetics. Oral clearance of stiripentol at 600 mg/day was 41.5 +/- 23.4 l/day/kg (mean +/- SD), greater than that at 1200 mg/day (20.3 +/- 8.8 l/day/kg; P less than 0.05) or 2400 mg/day (8.5 +/- 3.8 l/day/kg; P less than 0.01). The apparent in vivo Michaelis-Menten parameters were determined from three mean steady-state concentrations. The average velocity of conversion of stiripentol to its metabolites (Vm), Michaelis constant (Km), and the ratio Vm/Km were 49.3 +/- 13.1 mg/day/kg, 1.35 +/- 1.08 mg/l, and 50.2 +/- 27.5 l/day/kg. Stiripentol reduced the elimination clearances of concomitant antiepileptic drugs. Phenytoin clearance was reduced in all five subjects who received this drug, from a mean control of 29.5 +/- 13.4 l/day to 18.5 +/- 4.6 l/day at a stiripentol dose of 1200 mg/day (P = 0.05) and to 6.48 +/- 2.59 l/day at 2400 mg/day (P less than 0.01). Stiripentol reduced the clearance of carbamazepine in one subject from a control value of 209 l/day to 128 l/day (1200 mg/day) and 61 l/day (2400 mg/day). Stiripentol reduced phenobarbital clearance in two subjects from 3.8 and 5.1 l/day to 2.3 and 3.4 l/day (2400 mg/day). The Michaelis-Menten kinetics of stiripentol, as well as its interactions with other antiepileptic drugs, have important implications in the designing of controlled clinical trials.
A simple theory of motor protein kinetics and energetics. II.
Qian, H
2000-01-10
A three-state stochastic model of motor protein [Qian, Biophys. Chem. 67 (1997) pp. 263-267] is further developed to illustrate the relationship between the external load on an individual motor protein in aqueous solution with various ATP concentrations and its steady-state velocity. A wide variety of dynamic motor behavior are obtained from this simple model. For the particular case of free-load translocation being the most unfavorable step within the hydrolysis cycle, the load-velocity curve is quasi-linear, V/Vmax = (cF/Fmax-c)/(1-c), in contrast to the hyperbolic relationship proposed by A.V. Hill for macroscopic muscle. Significant deviation from the linearity is expected when the velocity is less than 10% of its maximal (free-load) value--a situation under which the processivity of motor diminishes and experimental observations are less certain. We then investigate the dependence of load-velocity curve on ATP (ADP) concentration. It is shown that the free load Vmax exhibits a Michaelis-Menten like behavior, and the isometric Fmax increases linearly with ln([ATP]/[ADP]). However, the quasi-linear region is independent of the ATP concentration, yielding an apparently ATP-independent maximal force below the true isometric force. Finally, the heat production as a function of ATP concentration and external load are calculated. In simple terms and solved with elementary algebra, the present model provides an integrated picture of biochemical kinetics and mechanical energetics of motor proteins.
Kinetics of platelet 5-hydroxytryptamine uptake in headache patients.
Hannah, P; Jarman, J; Glover, V; Sandler, M; Davies, P T; Clifford Rose, F
1991-07-01
Platelet 5-hydroxytryptamine (5-HT) uptake was measured in asymptomatic headache patients attending a specialist migraine clinic, and in hospital staff who did not suffer from regular or severe headache. Current levels of anxiety and depression were assessed in all subjects using the Hospital Anxiety and Depression (HAD) scale and their possible influence on the uptake kinetics taken into account during the analysis of results. The Michaelis-Menten constant (Km) was significantly raised in common migraine and tension headache compared with controls (p less than 0.001 and p less than 0.01, respectively), but not in classical migraine or cluster headache. The increase remained significant after adjusting for differences in age, sex, presence of anxiety or depression (HAD sub-scale score greater than or equal to 8), drug intake during the week before testing, time elapsed since last attack and time of assay (am or pm). No differences were observed between patients and controls in the maximal rate of uptake (Vmax) or platelet count, and previous reports of a reduction in Vmax in patients experiencing attack within 5 days prior to testing could not be confirmed. The cause and significance of an increased Km are not clear, but plasma factors acting as competitive inhibitors for the uptake site or an alteration in the configuration of the uptake site are possible explanations. If confirmed, the shared biochemical abnormality may suggest that common migraine and tension headache have a common pathogenesis.
Narayani, M; Vidya Shetty, K
2014-04-01
A Gram negative hexavalent chromium (Cr(VI)) reducing bacteria, Ochrobactrum sp. Cr-B4 (genbank accession number: JF824998) was isolated from the aerator water of an activated sludge process of a wastewater treatment facility of a dye and pigment based specialty chemical industry. It showed a resistance for 1000 mg L(-1) Cr(VI). It exhibited resistance against other heavy metal ions like Ni(2+) (900 mg L(-1) ), Cu(2+) (500 mg L(-1) ), Pb(2+) (800 mg L(-1) ), and Cd(2+) (250 mg L(-1) ), Zn(2+) (700 mg L(-1) ), Fe(3+) (800 mg L(-1) ), and against selected antibiotics. Cr-B4 could efficiently reduce 200 mg L(-1) Cr(VI) completely in nutrient and LB media and could convert Cr(VI) to Cr(III) efficiently. Cr(VI) reduction in nutrient media followed allosteric enzyme kinetics with Km values of 59.39 mg L(-1) and Vmax values of 47.03 mg L(-1) h(-1) . The reduction in LB media followed Michaelis-Menten kinetics with Km values of 99.52 mg L(-1) and Vmax of 77.63 mg L(-1) h(-1) . Scanning electron micrograms revealed the presence of extracellular polymeric secretions.
Elif Cerrahoğlu
2016-08-01
Full Text Available Bu çalışmada, Lamium purpureum (eflatun çiçekli ballıbaba bitkisinden elde edilen polifenol oksidaz (PPO enziminin kinetik özellikleri incelenmiştir. Karakterizasyon çalışmalarında substrat olarak 4-metil katekol kullanılmıştır. 4-metil katekol için Michaelis-Menten sabiti (KM ve maksimum reaksiyon hızı (Vmax hesaplanmıştır. Enziminin optimum pH değeri 7,5, optimum sıcaklık değerleri ise 10 °C bulunmuştur. Vmax ve KM değerleri ise sırasıyla 2,9977 mM ve 0,0087 EU/dak olarak hesaplanmıştır. PPO enzimi için sodyum azid, tiyoüre, L-Sistein, askorbik asit, sitrik asit, benzoik asit, 2-merkaptoetanol ile inhibisyon çalışması yapılmış, her bir inhibitör için I50 değeri hesaplanmıştır.
Competition between roots and microorganisms for nitrogen: mechanisms and ecological relevance.
Kuzyakov, Yakov; Xu, Xingliang
2013-05-01
Demand of all living organisms on the same nutrients forms the basis for interspecific competition between plants and microorganisms in soils. This competition is especially strong in the rhizosphere. To evaluate competitive and mutualistic interactions between plants and microorganisms and to analyse ecological consequences of these interactions, we analysed 424 data pairs from 41 (15)N-labelling studies that investigated (15)N redistribution between roots and microorganisms. Calculated Michaelis-Menten kinetics based on K(m) (Michaelis constant) and V(max) (maximum uptake capacity) values from 77 studies on the uptake of nitrate, ammonia, and amino acids by roots and microorganisms clearly showed that, shortly after nitrogen (N) mobilization from soil organic matter and litter, microorganisms take up most N. Lower K(m) values of microorganisms suggest that they are especially efficient at low N concentrations, but can also acquire more N at higher N concentrations (V(max)) compared with roots. Because of the unidirectional flow of nutrients from soil to roots, plants are the winners for N acquisition in the long run. Therefore, despite strong competition between roots and microorganisms for N, a temporal niche differentiation reflecting their generation times leads to mutualistic relationships in the rhizosphere. This temporal niche differentiation is highly relevant ecologically because it: protects ecosystems from N losses by leaching during periods of slow or no root uptake; continuously provides roots with available N according to plant demand; and contributes to the evolutionary development of mutualistic interactions between roots and microorganisms.
Sahoo, Banalata; Sahu, Sumanta Kumar; Bhattacharya, Dipsikha; Dhara, Dibakar; Pramanik, Panchanan
2013-01-01
In the present study, a facile functionalization of magnetic nanoparticles has been described for the immobilization of enzyme that offers many advantages for reuse and excellent efficiencies. The magnetic gold nanocomposites have been fabricated for the successful immobilization of an industrially important enzyme "papain". For immobilization of papain on magnetic gold nanocomposites, magnetic nanoparticles were modified with 3-(mercaptopropyl) trimethoxy silane (MPTS). Further, the citrate stabilized gold nanoparticles were chemisorbed on these thiol coated magnetic nanoparticles to fabricate the desired magnetic gold nanocomposites. Papain containing net positive charge (isoelectric point of papain=8.75) in PBS buffer (pH 7.4) has immobilized on the surface of the negatively charged magnetic gold nanocomposites through the ionic or electrostatic interaction. The Michaelis-Menten kinetic constant (K(m)) and maximum reaction velocity (V(max)) for free papain were 0.236×10(5) g ml(-1) and 4.08 g ml(-1)/s respectively whereas for immobilized papain, K(m) and V(max) values were 0.308×10(5) g ml(-1) and 5.4 g ml(-1)/s respectively. The loading amount of papain on magnetic gold nanocomposites was 54 mg/g support and the activity recovery of the immobilized papain reached to 47 (±5)% compared to native papain. The main advantage of this papain nanobiocatalyst is the easy isolation of enzyme from the reaction medium.
Emanuele Ricca
2014-01-01
Full Text Available The present paper addresses two crucial features in the industrial development of fructose production by enzymatic hydrolysis of inulin: the use of immobilized biocatalyst in the hydrolysis of crude extracts of chicory roots and the evaluation of the effect of degree of polymerization of inulin on the overall reaction rate. The immobilized biocatalyst consisted of inulinase covalently bound to Sepabeads® supports. It was demonstrated that its catalytic activity towards crude inulin extract (real substrate was much higher than that exhibited towards pure inulin (synthetic solution. Experiments revealed that, in applications of practical interest with real substrate, the activity of immobilized enzyme was as high as 63 % of that of free enzyme in homogeneous solution. This certainly was a driving force to potential industrial application of this immobilized enzyme preparation. Therefore, the effect of pure and crude substrates on the kinetics of the reaction catalysed by the immobilized enzyme was investigated. The kinetic analysis revealed a Michaelis-Menten dependence of the reaction rate on substrate concentration for both pure (high molecular mass and crude (low molecular mass inulin. Interesting results were derived from the comparison of Km and vmax values in the two cases. In particular, it was found that increasing degree of polymerization of the substrate caused vmax decrease and Km increase. After evaluation of mass transport effects, this was mainly associated with a different substrate/ enzyme affinity when exploiting inulin characterized by different (low or high degree of polymerization.
Root Morphology and Zn2+ Uptake Kinetics of the Zn Hyperaccumulator of Sedum alfredii Hance
Ting-Qiang LI; Xiao-E YANG; Zhen-Li HE; Jin-Yan YANG
2005-01-01
Root morphology and Zn2+ uptake kinetics of the hyperaccumulating ecotype (HE) and nonhyperaccumulating ecotype (NHE) of Sedum alfredii Hance were investigated using hydroponic methods and the radiotracer flux technique. The results indicate that root length, root surface area, and root volume of NHE decreased significantly with increasing Zn2+ concentration in growth media, whereas the root growth of HE was not adversely affected, and was even promoted, by 500 μmol/L Zn2+. The concentrations of Zn2+ in both ecotypes of S. alfredii were positively correlated with root length, root surface area and root volumes, but no such correlation was found for root diameter. The uptake kinetics for 65Zn2+ in roots of both ecotypes of S. alfredii were characterized by a rapid linear phase during the first 6 h and a slower linear phase during the subsequent period of investigation. The concentration-dependent uptake kinetics of the two ecotypes of S. alfredii could be characterized by the Michaelis-Menten equation, with the Vmax for 65Zn2+ influx being threefold greater in HE compared with NHE, indicating that enhanced absorption into the root was one of the mechanisms involved in Zn hyperaccumulation. A significantly larger Vmax value suggested that there was a higher density of Zn transporters per unit membrane area in HE roots.
Desempenho da matriz híbrida SiO2-quitosana na imobilização da lipase microbiana de Candida rugosa
Aline S Simões
2011-01-01
Full Text Available Lipase from Candida rugosa was immobilized by covalent attachment on hybrid SiO2-chitosan obtained by sol-gel technique. A comparative study between free and immobilized lipase was provided in terms of pH, temperature, kinetic parameters and thermal stability on the olive oil hydrolysis. The pH and temperature for maximum activity shifted from 7.0 and 45 ºC for the free lipase to 7.5 and wide range of temperature (40-50 ºC after immobilization. Kinetics parameters were found to obey Michaelis-Menten equation and K M values indicated that immobilization process reduced the affinity of enzyme-substrate; however Kd values revealed an increase of thermal stability of lipase.
Extended kinetic model of real-time polymerase chain reaction process
Fedorov, A. A.; Sochivko, D. G.; Varlamov, D. A.; Kurochkin, V. E.
2016-11-01
Real-time polymerase chain reaction (real-time PCR) is the main molecular genetic method used for qualitative and quantitative analysis of specific nucleic acid sequences in many areas of biomedical research. Theoretical study of pCr models allows to estimate the influence of various reaction components and parameters, and to determine the unknown parameter values by approximating the experimental real-time PCR curves. An extended kinetic model of real-time PCR is presented. The model takes into account the enzyme activity based on Michaelis-Menten kinetics, the hybridization of complementary DNA fragments, the presence of a fluorescent probe used for detection of the reaction products, and the temperature dependence of primers and probe hybridization.
S. Sheik Mansoor
2016-09-01
Full Text Available The kinetics of oxidation of some organic diols by tripropylammonium fluorochromate (TriPAFC have been studied in dimethylsulfoxide (DMSO. The main product of oxidation is the corresponding hydroxy aldehydes. The reaction is first order with respect to TriPAFC and exhibited Michaelis-Menten type kinetics with respect to organic diols. The reaction is catalyzed by hydrogen ions. The hydrogen ion dependence has the form: kobs = a + b[H+]. Various thermodynamic parameters for the oxidation have been reported and discussed along with the validity of isokinetic relationship. Oxidation of diols was studied in 18 different organic solvents. The rate data are showing satisfactory correlation with Kamlet–Taft solvotochromic parameters (α, β and π∗. A suitable mechanism of oxidation has been proposed.
Delineamentos experimentais eficientes para estudos de cinética química
Iuri E. P. Ferreira
2014-01-01
Full Text Available In this paper we show how to obtain efficient designs of experiments for fitting Michaelis-Menten and Hill equations useful in chemical studies. The search of exact D-optimal designs by using local and pseudo-Bayesian approaches is considered. Optimal designs were compared to those commonly used in practice using an efficiency measure and theoretical standard errors of the kinetic parameter estimates. In conclusion, the D-optimal designs based on the Hill equation proved efficient for estimating the parameters of both models. Furthermore, these are promising with respect to practical issues, allowing efficient estimation as well as goodness-of-fit tests and comparisons between some kinetic models.
Effect of hydrodynamics on kinetics of gluconic acid enzymatic production in bubble column reactor
Ramezani Mohammad
2013-01-01
Full Text Available Oxidation of glucose by homogeneous glucose oxidase was performed in rectangular bubble column reactor at 40°C, ambient pressure and pH of 5.5 while superficial gas (oxygen velocity was varied in the homogeneous and transition regime in the range of 0.0014 - 0.0112 m s-1. Effect of superficial gas (oxygen velocity on the apparent reaction rate and its parameters was determined and it was observed that the apparent reaction rate on the basis of volume of the liquid increased with increasing the superficial gas (oxygen velocity. The apparent reaction rate was assumed to be in the form of Michaelis-Menten equation and its apparent kinetic parameters were evaluated by the nonlinear regression method.
Vadapalli Chandrasekhar; Venkatasubbiah Krishnan; Ramachandran Azhakar; C Madhavaiah; Sandeep Verma
2005-03-01
Catalytic activity of [L2.Zn][NO3]2 (L = spiro-N3P3[O2C12H8][N(CH3)NH2]) towards the hydrolysis of two phosphodiesters, [bis(-nitrophenyl)phosphate, bNPP] and [2-(hydroxypropyl)-p-nitrophenyl phosphate, hNPP] has been examined. While the rate of hydrolysis of the former is accelerated over a million-fold, the rate of hydrolysis of the latter also is enhanced considerably. Detailed kinetic evaluation of these reactions has been carried out and all the kinetic parameters including the Michaelis-Menten parameters are reported. The catalyst [L2.Zn][NO3]2 has also been found to be an effective nuclease. Relaxation of supercoiled plasmid DNA, pBR322, occurs in presence of [L2.Zn][NO3]2 without the need for any exogenous reagents.
Chaudhury, Srabanti; Cao, Jianshu; Sinitsyn, Nikolai A
2013-01-17
We consider a generic stochastic model of ion transport through a single channel with arbitrary internal structure and kinetic rates of transitions between internal states. This model is also applicable to describe kinetics of a class of enzymes in which turnover events correspond to conversion of substrate into product by a single enzyme molecule. We show that measurement of statistics of single molecule transition time through the channel contains only restricted information about internal structure of the channel. In particular, the most accessible flux fluctuation characteristics, such as the Poisson indicator (P) and the Fano factor (F) as function of solute concentration, depend only on three parameters in addition to the parameters of the Michaelis-Menten curve that characterizes average current through the channel. Nevertheless, measurement of Poisson indicator or Fano factor for such renewal processes can discriminate reactions with multiple intermediate steps as well as provide valuable information about the internal kinetic rates.
Udayashankar, Paniveni
2016-07-01
I study the complexity of supergranular cells using intensity patterns from Kodaikanal solar observatory. The chaotic and turbulent aspect of the solar supergranulation can be studied by examining the interrelationships amongst the parameters characterizing supergranular cells namely size, horizontal flow field, lifetime and physical dimensions of the cells and the fractal dimension deduced from the size data. The findings are supportive of Kolmogorov's theory of turbulence. The Data consists of visually identified supergranular cells, from which a fractal dimension 'D' for supergranulation is obtained according to the relation P α AD/2 where 'A' is the area and 'P' is the perimeter of the supergranular cells. I find a fractal dimension close to about 1.3 which is consistent with that for isobars and suggests a possible turbulent origin. The cell circularity shows a dependence on the perimeter with a peak around (1.1-1.2) x 105 m. The findings are supportive of Kolmogorov's theory of turbulence.
Schwab, Nicole; Skopp, Gisela
2014-04-01
Ethyl glucuronide (EtG), a minor metabolite of ethanol, is used as a marker of alcohol consumption in a variety of clinical and forensic settings. At present there are very few studies of UDP-glucuronosyltransferases (UGT), responsible for catalyzing EtG formation, and the possible effect of nutritional components, e.g. flavonoids, which are extensively glucuronidated, on EtG formation has not been addressed at all. The following incubation conditions were optimized with regard to previously published conditions: buffer, substrate concentration, and incubation time. Isolation of EtG from the incubation mixture was also optimized. Recombinant UGT enzymes (UGT1A1, 1A3, 1A4, 1A6, 1A9, 2B7, 2B10, 2B15) were screened for their activity towards ethanol, and kinetic data were then established for all enzymes. It was decided to study the effect of the flavonoids quercetin and kaempferol on glucuronidation of ethanol. Isolation was by solid-phase extraction (SPE) to minimize matrix effects. Analysis was performed by liquid chromatography-tandem mass spectrometry (LC-MS-MS), with EtG-d5 as the internal standard. SPE was vital to avoid severe ion suppression after direct injection of the incubation solution. EtG formation was observed for all enzymes under investigation; their kinetics followed the Michaelis-Menten model, meaning the maximum reaction rate achieved at saturating substrate concentrations (V(max)) and the substrate concentration at which the reaction rate is half of V(max) (Michaelis-Menten constant, K(m)) could be calculated. The highest rate of glucuronidation was observed with UGT1A9 and 2B7. After co-incubation with both flavonoids, formation of EtG was significantly reduced for all enzymes except for UGT2B15, whose activity did not seem to be affected. Results reveal that multiple UGT isoforms are capable of catalyzing glucuronidation of ethanol; nevertheless, the effect of UGT polymorphism on glucuronidation of ethanol needs further study. Formation of Et
Sidelmann, U. G.; Cornett, Claus; Tjornelund, J.
1996-01-01
, whereas the intrinsic clearance with respect to formation of the glucuronic acid conjugate was lower in slices compared with hepatocytes. 4. The metabolism of metronidazole in liver slices, in hepatocytes in primary monolayer culture, in hepatocytes incubated in suspension, and in liver microsomes...... higher in microsomes than in the other liver preparations. The metabolic rates in hepatocytes in primary culture and in suspension with respect to the oxidative metabolites were higher than in liver slices. The metabolic turnover observed in liver slices was predicted to correlate with in vivo data...... have been investigated. 3. An incubation system where liver slices are incubated in 12-well culture plates was evaluated with respect to metabolism of metronidazole. Optimal viability was observed for a time period of up to 24 h. The Michaelis-Menten parameters for the metabolism of metronidazole...
Removing Iron and Manganese Simultaneously from Ground Water Using One-stage Biological Filter
XUE Gang; GAO Pin; GONG Qing-jie
2009-01-01
A novel process for removing iron and manganese simultaneously in ground water, which consisted of simple aeration and one-stage filtration, was developed in this research. It was found that the biological process had much higher manganese removal efficiency than chemical contact oxidation process. At the same time, the optimal operation parameters of aeration and biological filtration such as DO concentration and pH after aeration, filtration rate before and after startup, filtration operation cycle and backwashing rate, etc., were also obtained by experiments. By analyzing water quafity in different positions of filter bed, it was found that the oxidation of Fe2+ in biological filter bed adapted to first-order reaction, whereas the oxidation of Mn2+ conformed to zero-order reaction, which could be explained by Michaelis-Menten enzyme reaction equation when substrate concentration was far more than bacteria amount.
Aza Cope Rearrangement of Propargyl Enammonium Cations Catalyzed By a Self-Assembled `Nanozyme
Hastings, Courntey J.; Fiedler, Dorothea; Bergman, Robert G.; Raymond, Kenneth N.
2008-02-27
The tetrahedral [Ga{sub 4}L{sub 6}]{sup 12-} assembly (L = N,N-bis(2,3-dihydroxybenzoyl)-1,5-diaminonaphthalene) encapsulates a variety of cations, including propargyl enammonium cations capable of undergoing the aza Cope rearrangement. For propargyl enammonium substrates that are encapsulated in the [Ga{sub 4}L{sub 6}]{sup 12-} assembly, rate accelerations of up to 184 are observed when compared to the background reaction. After rearrangement, the product iminium ion is released into solution and hydrolyzed allowing for catalytic turnover. The activation parameters for the catalyzed and uncatalyzed reaction were determined, revealing that a lowered entropy of activation is responsible for the observed rate enhancements. The catalyzed reaction exhibits saturation kinetics; the rate data obey the Michaelis-Menten model of enzyme kinetics, and competitive inhibition using a non-reactive guest has been demonstrated.
Performance of a Pectinase from Bacillus Subtilis WSHB04-02 Used in Bioscouring of Cotton Fabrics
无
2007-01-01
A pectinase produced by Bacillus subtilis WSHB04-02 isolated from soil with lyase activity operating at alkaline pH was studied. The MichaelisMenten kinetic parameters of this newly isolated pectinase on different substrates, such as citrus pectin and polygalacturonic acid (PGA), were determined, and pectin proved to be the most suitable substrate. The effects of temperature and pH on pectinase activity and stability were also investigated. The optimal temperature for pectinase was 55℃ with a stable range of 45℃- 55℃. In general,pectinase was pH insensitive and the stable pH ranged from 8.6 to 10.0. Ultimately the bioscouring effects of cotton fabrics using this pectinase were evaluated and some promising results were obtained.
Degradation kinetics and metabolites in continuous biodegradation of isoprene.
Srivastva, Navnita; Singh, Ram S; Upadhyay, Siddh N; Dubey, Suresh K
2016-04-01
The kinetic parameters of isoprene biodegradation were studied in a bioreactor, comprising of bioscrubber and polyurethane foam packed biofilter in series and inoculated with Pseudomonas sp., using a Michaelis-Menten type model. The maximum elimination capacity, ECmax; substrate constant, Ks and ECmax/Ks values for bioscrubber were found to be 666.7 g m(-3) h(-1), 9.86 g m(-3) and 67.56 h(-1), respectively while those for biofilter were 3333 g m(-3) h(-1), 13.96 g m(-3) and 238.7 h(-1), respectively. The biofilter section exhibited better degradation efficiency compared to the bioscrubber unit. Around 62-75% of the feed isoprene got converted to carbon dioxide, indicating the efficient capability of bacteria to mineralize isoprene. The FTIR and GC-MS analyses of degradation products indicated oxidative cleavage of unsaturated bond of isoprene. These results were used for proposing a plausible degradation pathway for isoprene.
Chitosan-g-polyaniline: a creatine amidinohydrolase immobilization matrix for creatine biosensor
2009-09-01
Full Text Available A novel matrix composed of chitosan-graft-polyaniline (CHIT-g-PANI was electrochemically prepared to investigate the immobilization of creatine amidinohydrolase (CAH. CAH enzyme was covalently immobilized with the CHIT-g-PANI matrix using glutaraldehyde as a linker. The resulting CAH/CHIT-g-PANI biomatrix was characterized with Fourier transform infrared spectroscopy (FTIR, atomic force microscopy (AFM, contact angle measurement and cyclic voltammetry (CV taking CHIT-g-PANI as a reference. The influence of various parameters on CAH enzyme activity within the matrix was investigated including pH, temperature, and time. The Michaelis-Menten constant and apparent activities for the CAH enzyme were calculated to be 0.51 mM and 83.59 mg/cm2, respectively; indicating CHIT-g-PANI matrix has a high affinity to immobilize CAH enzyme.
Cotton cellulose: enzyme adsorption and enzymic hydrolysis
Beltrame, P.L.; Carniti, P.; Focher, B.; Marzetti, A.; Cattaneo, M.
1982-01-01
The adsorption of a crude cellulase complex from Trichoderma viride on variously pretreated cotton cellulose samples was studied in the framework of the Langmuir approach at 2-8 degrees. The saturation amount of adsorbed enzyme was related to the susceptibility of the substrates to hydrolysis. In every case the adsorption process was faster by 2-3 orders of magnitude than the hydrolysis step to give end products. For ZnCl/sub 2/-treated cotton cellulose the Langmuir parameters correlated fairly well with the value of the Michaelis constant, measured for its enzymic hydrolysis, and the adsorptive complex was indistinguishable from the complex of the Michaelis-Menten model for the hydrolysis.
Karakhim, S A
2012-01-01
The article is dedicated to analysis of equation which expresses apparent Michaelis constant K(m)app) of enzyme-catalysed reactions with activator participation by means of the substrate constant K(s) and rate constant of enzyme-substrate complex decomposition k(cat). It has been shown that although it is possible to record the mechanisms of such reactions as a scheme similar to Michaelis-Menten model and to derive equation of apparent Michaelis constant as K(m(app) = K(s) + k(cat)/k(1), but this approach cannot be used for investigation of all reactions with activator participation. The equation mentioned above is not obeyed in the general case, it may be true for some mechanisms only or under certain ratio of kinetic parameters of enzyme-catalysed reactions.
A multivariate nonlinear mixed effects method for analyzing energy partitioning in growing pigs
Strathe, Anders Bjerring; Danfær, Allan Christian; Chwalibog, André
2010-01-01
Simultaneous equations have become increasingly popular for describing the effects of nutrition on the utilization of ME for protein (PD) and lipid deposition (LD) in animals. The study developed a multivariate nonlinear mixed effects (MNLME) framework and compared it with an alternative method...... for estimating parameters in simultaneous equations that described energy metabolism in growing pigs, and then proposed new PD and LD equations. The general statistical framework was implemented in the NLMIXED procedure in SAS. Alternative PD and LD equations were also developed, which assumed...... that the instantaneous response curve of an animal to varying energy supply followed the law of diminishing returns behavior. The Michaelis-Menten function was adopted to represent a biological relationship in which the affinity constant (k) represented the sensitivity of PD to ME above maintenance. The approach...
Peroxidase-like catalytic activity of Ag3PO4 nanocrystals prepared by a colloidal route.
Yuanjun Liu
Full Text Available Nearly monodispersed Ag3PO4 nanocrystals with size of 10 nm were prepared through a colloidal chemical route. It was proven that the synthesized Ag3PO4 nanoparticles have intrinsic peroxidase-like catalytic activity. They can quickly catalyze oxidation of the peroxidase substrate 3, 3, 5, 5-tetramethylbenzidine (TMB in the presence of H2O2, producing a blue color. The catalysis reaction follows Michaelis-Menten kinetics. The calculated kinetic parameters indicate a high catalytic activity and the strong affinity of Ag3PO4 nanocrystals to the substrate (TMB. These results suggest the potential applications of Ag3PO4 nanocrystals in fields such as biotechnology, environmental chemistry, and medicine.
Ruthenium(III Catalysis in Perborate Oxidation of 5-Oxoacids
S. Shree Devi
2014-01-01
Full Text Available Ruthenium(III catalyzes perborate oxidation of substituted 5-oxoacids in acidic solution. The catalyzed oxidation is first order with respect to the oxidant and catalyst. The rate of ruthenium(III catalyzed oxidation displays the Michaelis-Menten kinetics on the reductant and is independent of [H+] of the medium. Hydrogen peroxide is the reactive species of perborate and the kinetic results reveal formation of ruthenium(III peroxo species-5-oxoacid complex. Electron-releasing substituents accelerate the reaction rate and electron-withdrawing substituents retard it. The order of reactivity among the studied 5-oxoacids is p-methoxy ≫ p-methyl > p-phenyl > −H > p-chloro > p-bromo > m-nitro. Activation parameters are evaluated using Arrhenius and Eyring’s plots. A mechanism consistent with the observed kinetic data is proposed and discussed. A suitable rate law is derived based on the mechanism.
Permeation study of the potassium channel from streptomyces Lividans
XU Xiuzhi; ZHAN Yong; ZHAO Tongjun
2004-01-01
A three-state hopping model is established according to experiments to study permeation of an open-state potassium channel from Streptomyces Lividans (KcsA potassium channel). The master equations are used to characterize the dynamics of the system. In this model, ion conduction involves transitions of three states, with one three-ion state and two two-ion states in the selectivity filter respectively. In equilibrium, the well-known Nernst equation is deduced. It is further shown that the current follows Michaelis-Menten kinetics in steady state. According to the parameters provided by Nelson, the current-voltage relationship is proved to be ohmic and the current-concentration relationship is also obtained reasonably. Additional validation of the model in the characteristic time to reach the steady state for the potassium channel is also discussed. This model lays a possible physical basis for the permeation of ion channel, and opens an avenue for further research.
Nerve Agent Hydrolysis Activity Designed into a Human Drug Metabolism Enzyme
2011-03-18
inhibition, Michaelis - Menten constants, and rates of reactivation for wild-type and V146H/ L363E hCE1 against racemic cyclosarin and stereoisomers of...0017441.t002 Table 3. Inhibition and Michaelis - Menten constants for wild-type and V146H/L363E hCE1 against stereoisomers of sarin and soman model...6 | Issue 3 | e17441 where Km was the nerve agent model Michaelis - Menten constant, k2 the unimolecular phosphonylation rate constant, v the remaining
Kinetics of atrazine, deisopropylatrazine, and deethylatrazine soil biodecomposers.
la Cecilia, Daniele; Maggi, Federico
2016-12-01
Twenty-two experimental sets were used to determine the biodecomposition parameters of atrazine (ATZ), deisopropylatrazine (DIATZ), and deethylatrazine (DEATZ) by inverse solution of Michaelis-Menten-Monod kinetic equations. The averaged maximum specific growth rate (μ), Michaelis-Menten half-saturation concentration (K), and biomass yield (Y) ranged between 2.00 × 10(-7) and 4.62 × 10(-5) 1/s, 3.43 × 10(-6) and 1.39 × 10(1) mol/L, and 1.20 × 10(2) and 2.98 × 10(5) mg-wet-Bio/mol-Subs, respectively. Parameters grouped by reaction pathway appeared clustered by aerobic and anaerobic catabolic breakdown, and were poorly correlated between each other (R ranging from -0.27 to 0.63, p ≥ 0.05). The tested bacterial strains decomposed ATZ, DIATZ, and DEATZ relatively rapidly in laboratory conditions, with an half-life (t1/2) ranging between 3 and 6 days. Numerical modeling showed that ATZ, DIATZ, and DEATZ half-lives were particularly sensitive to their initial concentration and the initial microbial biomass concentration. This study suggests that these bacterial strains can effectively be used or enhanced for bioremediation of agricultural soils where atrazine has been applied as long as these bacteria already coexist in or can integrate with the local soil microbial population at a given location. Copyright © 2016 Elsevier Ltd. All rights reserved.
Canceling effect leads temperature insensitivity of hydrolytic enzymes in soil
Razavi, Bahar S.; Blagodatskaya, Evgenia; Kuzyakov, Yakov
2015-04-01
Extracellular enzymes are important for decomposition of many macromolecules abundant in soil such as cellulose, hemicelluloses and proteins (Allison et al., 2010; Chen et al., 2012). The temperature sensitivity of enzymes responsible for organic matter decomposition is the most crucial parameter for prediction of the effects of global warming on carbon cycle. Temperature responses of biological systems are often expressed as a Q10 functions; The Q10 describes how the rate of a chemical reaction changes with a temperature increase for 10 °C The aim of this study was to test how the canceling effect will change with variation in temperature interval, during short-term incubation. We additionally investigated, whether canceling effect occurs in a broad range of concentrations (low to high) and whether it is similar for the set of hydrolytic enzymes within broad range of temperatures. To this end, we performed soil incubation over a temperature range of 0-40°C (with 5°C steps). We determined the activities of three enzymes involved in plant residue decomposition: β-glucosidase and cellobiohydrolase, which are commonly measured as enzymes responsible for degrading cellulose (Chen et al., 2012), and xylanase, which degrades xylooligosaccharides (short xylene chain) in to xylose, thus being responsible for breaking down hemicelluloses (German et al., 2011). Michaelis-Menten kinetics measured at each temperature allowed to calculate Q10 values not only for the whole reaction rates, but specifically for maximal reaction rate (Vmax) and substrate affinity (Km). Subsequently, the canceling effect - simultaneous increase of Vmax and Km with temperature was analyzed within 10 and 5 degree of temperature increase. Three temperature ranges (below 10, between 15 and 25, and above 30 °C) clearly showed non-linear but stepwise increase of temperature sensitivity of all three enzymes and allowed to conclude for predominance of psychrophilic, mesophilic and thermophilic
Depuración aerobia de los efluentes resultantes del proceso de biometanización del alpechín
Borja Padilla, R.
1992-02-01
Full Text Available A study of aerobic treatment in batch regime of the effluents produced in the olive mill wastewater biomethanation process was carried out.
An 83% of effluents organic substances was removal after the third day of fermentation.
The substrate removal rate follows a zero-order kinetic for high concentrations, and a first-order kinetic for low organic matter concentration, during the last days of fermentation.
The kinetic parameters (q_{máx} and K were obtained from Michaelis- Menten model.
Se ha efectuado un estudio del proceso de depuración aerobia, en régimen discontinuo, de los efluentes procedentes del proceso de depuración anaerobia o biometanización del alpechín.
Se comprueba que el 83% de la materia orgánica presente en este efluente se elimina a partir del tercer día de fermentación.
La eliminación de sustrato sigue una cinética de orden cero para altas concentraciones del mismo y una cinética de primer orden para bajas concentraciones de materia orgánica, es decir, durante los últimos días de fermentación.
Se aplica el modelo de Michaelis-Menten de eliminación de sustrato para la obtención de los parámetros cinéticos q_{máx} y K_{s} que rigen este proceso.
Depuración aerobia de las aguas de condensación del proceso de concentración térmica del alpechín
Borja Padilla, R.
1991-12-01
Full Text Available A study of aerobic treatment in batch regime of condensed water from thermal concentration process of olive mill wastewater was carried out.
An 80% of wastewater organic substances was removal after the third day of fermentation.
The substrate removal rate follows a zero-order kinetic for high concentrations, and a first-order kinetic for low organic matter concentration, during the last days of fermentation.
The kinetic parameters (q_{max} and K_{s} were obtain by Michaelis- Menten model.
Se ha efectuado un estudio del proceso de depuración aerobia, en régimen discontinuo, de los condensados resultantes del proceso de concentración térmica del alpechín.
Se comprueba que el 80% de la materia orgánica presente en este agua se elimina a partir del tercer día de fermentación.
La velocidad de eliminación de sustrato sigue una cinética de orden cero para altas concentraciones del mismo y una cinética de primer orden para bajas concentraciones de materia orgánica, es decir, durante los últimos días de fermentación.
Se aplica el modelo de Michaelis-Menten de eliminación de sustrato para la obtención de los parámetros cinéticos q_{max} y K_{s} que rigen este proceso.
Holzapfel, K.; Mueller, S.A.; Seidl, C.; Schwaiger, M.; Senekowitsch-Schmidtke, R. [Dept. of Nuclear Medicine, Technical Univ. of Munich (Germany); Grosu, A.L. [Dept. of Radiation Oncology, Technical Univ. of Munich (Germany)
2008-06-15
Background and purpose: choline positron emission tomography (PET) can help to optimize radiation treatment strategy of prostate cancer. Therefore, the aim of this study was to elucidate the effects of ionizing radiation on the choline uptake in an androgen-dependent (LNCaP) and an androgen-independent (PC3) prostate cancer cell line. Material and methods: uptake of [methyl-{sup 3}H]choline chloride was investigated between 4 and 96 h after irradiation with 6 Gy. Dose dependence of choline uptake was examined following irradiation with 2-12 Gy, and cell survival was analyzed via the clonogenic assay. Michaelis-Menten kinetics was determined 24 h (PC3) and 48 h (LNCaP) after irradiation with 6 Gy. Results: PC3 cells showed a significant transitory increase of [methyl-{sup 3}H]choline uptake with a maximum at 24 h after irradiation. In LNCaP cells irradiation induced a significant decrease with a minimum at 48 h. Changes in choline uptake in both cell lines were almost dose-independent up to 12 Gy. Following irradiation with 6 Gy, transport capacity (v{sub max}) increased and Michaelis-Menten constant (K{sub M}) decreased in PC3 cells, while in LNCaP cells the two parameters behaved vice versa. Conclusion: changes in choline uptake following irradiation might be due to metabolic changes associated with initiation of processes that finally cause cell death. Thus, changes in tumor choline uptake monitored by PET after radiotherapy might not exclusively reflect therapeutic success but also altered tracer uptake as a consequence of irradiation. (orig.)
TCE degradation in a methanotrophic attached-film bioreactor
Fennell, D.; Nelson, Y.M.; Underhill, S.E.; White, T.E.; Jewell, W.J. (Cornell Univ., Ithaca, NY (United States). Dept. of Agricultural and Biological Engineering)
1993-09-20
Trichloroethene was degraded in expanded-bed bioreactors operated with mixed-culture methanotrophic attached films. Biomass concentrations of 8 to 75 g volatile solids (VS) per liter static bed (L[sub sb]) were observed. Batch TCE degradation rates at 35C followed the Michaelis-Menten model, and a maximum TCE degradation rate (q[sub max]) of 10.6 mg TCE/gVS [center dot] day and a half velocity coefficient (K[sub s]) of 2.8 mg TCE/L were predicted. Continuous-flow kinetics also followed the Michaelis-Menten model, but other parameters may be limiting, such as dissolved copper and dissolved methane-q[sub max] and K[sub s] were 2.9 mg TCE/gVS [center dot] day and 1.5 mg TCE/L, respectively, at low copper concentrations (0.003 to 0.006 mg Cu/L). The maximum rates decreased substantially with small increases in dissolved copper. Methane consumption during continuous-flow operation varied from 23 to 1,200 g CH[sub 4]/g TCE degraded. Increasing the influent dissolved methane concentration from 0.01 mg/L to 5.4 mg/L reduced the TCE degradation rate by nearly an order of magnitude at 21C. Exposure of biofilms to 1.4 mg/L tetrachloroethene (PCE) at 35C resulted in the loss of methane utilization ability. Tests with methanotrophs grown on granular activated carbon indicated that lower effluent TCE concentrations could be obtained. The low efficiencies of TCE removal and low degradation rates obtained at 35C suggest that additional improvements will be necessary to make methanotrophic TCE treatment attractive.
Faridi, A; Murawska, D; Golian, A; Mottaghitalab, M; Gitoee, A; Lopez, S; France, J
2014-04-01
In this study, 2 alternative growth functions, the Lomolino and the extreme value function (EVF), are introduced and their ability to predict body, carcass, and breast weight in ducks evaluated. A comparative study was carried out of these equations with standard growth functions: Gompertz, exponential, Richards, and generalized Michaelis-Menten. Goodness of fit of the functions was evaluated using R(2), mean square error, Akaike information criterion, and Bayesian information criterion, whereas bias factor, accuracy factor, Durbin-Watson statistic, and number of runs of sign were the criteria used for analysis of residuals. Results showed that predictive performance of all functions was acceptable, though the Richards and exponential equations failed to converge in a few cases for both male and female ducks. Based on goodness-of-fit statistics, the Richards, Gompertz, and EVF were the best equations whereas the worst fits to the data were obtained with the exponential. Analysis of residuals indicated that, for the different traits investigated, the least biased and the most accurate equations were the Gompertz, EVF, Richards, and generalized Michaelis-Menten, whereas the exponential was the most biased and least accurate. Based on the Durbin-Watson statistic, all models generally behaved well and only the exponential showed evidence of autocorrelation for all 3 traits investigated. Results showed that with all functions, estimated final weights of males were higher than females for the body, carcass, and breast weight profiles. The alternative functions introduced here have desirable advantages including flexibility and a low number of parameters. However, because this is probably the first study to apply these functions to predict growth patterns in poultry or other animals, further analysis of these new models is suggested.
张利平; 谢晶
2012-01-01
货架期预测模型可以用来预测蔬菜的货架期.文章通过数学模型讨论蔬菜相关品质,如Vc降解、叶绿素损失、颜色以及质构的变化；介绍不同研究中使用的Arrhenius模型及相关参数或方程,比如Q10、Weibull方程,Michaelis-Menten方程和不同级数的动力学方程,还介绍各个预测模型的局限性.经典的Arrhenius模型结合动力学方程形式有待改进,而Arrhenius方程结合Weibull模型和Michaelis- Menten 方程则有望在新鲜蔬菜货架期中广为应用.%Shelf life prediction model can be used to predict the storage time of certain vegetable. This article discusses relevant qualities of vegetable, such as vitamin C degradation, chlorophyll loss, color and texture changes via mathematical models; Arrhemus model applied in different reaserches is introduced with related parameters or equations, such as Q10,, Weibull mode], Michaehs-Menten equation and kinetic model with different orders used in various studies, while limitations of each prediction models are also investigated. Classical forms of Arrhenius equation combined with kinetic models need to be improved, while models combined with Weibull model and Michaelis-Menten equation were promising used widely in predicting shelf life of fresh vegetables.
M Iyan Sofyan
2004-12-01
Full Text Available The objectives of this research were: 1 to determine aeration rate and substrate concentration of pure cellulose to produce maximum glucose by Trichoderma reesei QM 9414 at 30 oC, and agitation 150 rpm; 2 to study the kinetics of pure cellulose fermentation by Trichoderma reesei QM 9414 to glucose and its implication upon fermentation of the lignin free rice straw. The experiment was arranged in factorial randomized complete design in three times replication. Treatments consisted of three levels of aeration (1,00 vvm; 1,5 vvm; 2,0 vvm and three levels of substrate concentration (0,75 ; 1,00 ; 1,25 % w/v. The results showed that at the exponential phase the average specific growth of Trichoderma reesei QM 9414 was 0,05374 hour-1, the maximum glucose product concentration of pure cellulose was 0.1644 gL-1,and the oxygen transfer was 0,0328 mg L-1 hour-1. According to t-test, the kinetics of pure cellulose fermentation model just the same as the lignin free rice straw fermentation.The enzymes produced by Trichoderma reesei QM 9414 in pure cellulose fermentation media followed the Michaelis-Menten model. The enzyme kinetic parameters were the maximum growth rate was 37x10-3 hour-1 and Michaelis-Menten constant was Ã‚Â½ maximum μ =17,5x10-3 hour-1. The volumetric oxygen transfer (KLa using rice straw was 0,0337 mg.hour-1. The value of KLa could be used for conversion from bioreactor at laboratory scale to commercial scale design.
丁效东; 张士荣
2015-01-01
To learn nitrogen absorption characteristics of plant under salt stress, the NO3--N absorption ability of barley (Hordeum vulgare L.) cultivar ‘Jian 4’ pretreated with NaCl and NO3--N were investigated using culture solution. The pretreatment concentrations of NaCl were 1 mmol×L-1(CK) and 120 mmol×L-1, those of NO3--N were 1 mmol (NO3--N)×L-1 and 10 mmol (NO3--N)×L-1. Barley growth and NO3--N absorption were measured and the kinetics of NO3--N absorption of high- affinity transport system and low-affinity transport system of barley were investigated. The results showed that the uptake of NO3--N of barley pretreated with different concentrations of NaCl and NO3--N was in accordance with Michelis-Menten equation. Also the uptake kinetics parametersVmax andKm were enhanced with increasing pretreatment concentration of NO3--N. For high-affinity system, the uptake of NO3--N of barley was in accordance with Michaelis-Menten equation for all the pretreatments. Under 1 mmol(NO3--N)×L-1 pretreatment, compared with 1 mmol×L-1 NaCl treatment, 120 mmol×L-1 NaCl pretreatment significantly increased barley uptake rate of NO3--N; while under 10 mmol(NO3--N)×L-1, no significant difference in the rate of uptake of NO3--N was observed between 1 mmol×L-1 NaCl and 120 mmol×L-1 NaCl treatments. This indicated that in low nitrogen environment, NaCl restrained uptake of NO3--N of high-affinity system. For low-affinity systems, the uptake rate of NO3--N of barley was in accordance with Michaelis-Menten equation for all pretreatments. Under 1 mmol(NO3--N)×L-1 pretreatment, compared with 1 mmol×L-1 NaCl treatment, 120 mmol×L-1 NaCl treatment significantly increased the rate of uptake of NO3--N. With 10 mmol×L-1 NO3--N pretreatment, the uptake rate of NO3--N under 120 mmol×L-1 NaCl was lower than that of under 1 mmol×L-1 NaCl pretreatment. This showed that under low nitrogen environment, salt stress improved root uptake of NO3--N in low-affinity system. However, under
Kale, Mehmet; Aşçi, Alper; Bayrak, Coşkun; Açikada, Caner
2009-11-01
The purpose of this study was to investigate the relationships among jumping performances and speed parameters during maximum speed phase in sprinters. Twenty-one men sprinters volunteered to participate at the beginning of the preparation training phase. All tests-including 100-m sprint running, squat jump (SJ), countermovement jump (CMJ), drop jump (DJ), 60-second repetitive jump (RJ), standing long jump (SLJ), standing triple jump (STJ), standing quintuple jump (SQJ), and standing 10-stride jump (STENJ)-were done on switching mats. Flight (FT) and contact times (CT) during the vertical jump tests and 10-m split times during 100-m sprint running were measured by a 2-channel precision timing system (PTS) connected to the mats. The trace marking method was used for measuring the stride length (SL) through 60 m in 100-m sprint running. Stride frequency (SF), maximum velocity (Vmax), jump height for all vertical jumps, and lower-body power in DJ and RJ were calculated. Statistical analysis showed that the highest significant correlation was found between Vmax and DJ height (r = 0.69; p sprint running and SJ (r = 0.39; p sprint running than the other vertical and horizontal jump tests at the beginning of the preparation training phase.
The CYP2B6*6 allele significantly alters the N-demethylation of ketamine enantiomers in vitro.
Li, Yibai; Coller, Janet K; Hutchinson, Mark R; Klein, Kathrin; Zanger, Ulrich M; Stanley, Nathan J; Abell, Andrew D; Somogyi, Andrew A
2013-06-01
Ketamine is primarily metabolized to norketamine by hepatic CYP2B6 and CYP3A4-mediated N-demethylation. However, the relative contribution from each enzyme remains controversial. The CYP2B6*6 allele is associated with reduced enzyme expression and activity that may lead to interindividual variability in ketamine metabolism. We examined the N-demethylation of individual ketamine enantiomers using human liver microsomes (HLMs) genotyped for the CYP2B6*6 allele, insect cell-expressed recombinant CYP2B6 and CYP3A4 enzymes, and COS-1 cell-expressed recombinant CYP2B6.1 and CYP2B6.6 protein variant. Effects of CYP-selective inhibitors on norketamine formation were also determined in HLMs. The two-enzyme Michaelis-Menten model best fitted the HLM kinetic data. The Michaelis-Menten constants (K(m)) for the high-affinity enzyme and the low-affinity enzyme were similar to those for the expressed CYP2B6 and CYP3A4, respectively. The intrinsic clearance for both ketamine enantiomers by the high-affinity enzyme in HLMs with CYP2B6*1/*1 genotype were at least 2-fold and 6-fold higher, respectively, than those for CYP2B6*1/*6 genotype and CYP2B6*6/*6 genotype. The V(max) and K(m) values for CYP2B6.1 were approximately 160 and 70% of those for CYP2B6.6, respectively. N,N'N'-triethylenethiophosphoramide (thioTEPA) (CYP2B6 inhibitor, 25 μM) and the monoclonal antibody against CYP2B6 but not troleandomycin (CYP3A4 inhibitor, 25 μM) or the monoclonal antibody against CYP3A4 inhibited ketamine N-demethylation at clinically relevant concentrations. The degree of inhibition was significantly reduced in HLMs with the CYP2B6*6 allele (gene-dose P < 0.05). These results indicate a major role of CYP2B6 in ketamine N-demethylation in vitro and a significant impact of the CYP2B6*6 allele on enzyme-ketamine binding and catalytic activity.
Efecto de la sacarosa en la producción de celulosa por Gluconacetobacter xylinus en cultivo estático
Rubén Jaramillo L.
2012-08-01
Full Text Available Objetivo. Determinar el efecto de sacarosa en la productividad de BC por Gluconacetobacter xylinus IFO 13693 en condición estática. Materiales y métodos. La síntesis de celulosa bacteriana (BC por Gluconacetobacter xylinus se llevo a cabo en un cultivo estático discontinuo a temperatura ambiente, en presencia de sacarosa como la principal fuente de carbono a concentraciones iniciales de 0.8 a 7.6 % (p/v. Las concentraciones remanentes de BC, sacarosa, glucosa y fructosa se determinaron cada semana. Para la cinética de la hidrólisis de la sacarosa y formación de celulosa y el coeficiente de rendimiento del producto se utilizo el software Microcal Origin 6.0®. Resultados. En la cuarta semana los valores de BC se encontraron entre 32.5 a 39.5 g/L para las diferentes concentraciones de sacarosa. La cinética para la hidrólisis de sacarosa se ajusta al modelo de Michaelis-Menten, con una Vmax de 0.0002 mol L-1 h-1 y Km de 0.018 M. La producción de BC se ajusta al modelo propuesto por Marx-Figini y Pion, con un valor de la pendiente (kc, entre 0.0018 y 0.0024 h-1 para las diferentes concentraciones iniciales de sacarosa. Los coeficientes de rendimiento tienen valores de 0.8 a 2.4 g de BC producida/g de sacarosa consumida. Conclusiones. La hidrólisis de sacarosa, el consumo de glucosa y fructosa se refleja en la síntesis de celulosa. La hidrólisis de sacarosa y la producción de BC se ajustan a los modelos de Michaelis-Menten y al propuesto por Marx-Figini y Pion, respectivamente. Finalmente, el rendimiento depende de la concentración de sacarosa.
Biphasic kinetic behavior of E. coli WrbA, an FMN-dependent NAD(PH:quinone oxidoreductase.
Iryna Kishko
Full Text Available The E. coli protein WrbA is an FMN-dependent NAD(PH:quinone oxidoreductase that has been implicated in oxidative defense. Three subunits of the tetrameric enzyme contribute to each of four identical, cavernous active sites that appear to accommodate NAD(PH or various quinones, but not simultaneously, suggesting an obligate tetramer with a ping-pong mechanism in which NAD departs before oxidized quinone binds. The present work was undertaken to evaluate these suggestions and to characterize the kinetic behavior of WrbA. Steady-state kinetics results reveal that WrbA conforms to a ping-pong mechanism with respect to the constancy of the apparent Vmax to Km ratio with substrate concentration. However, the competitive/non-competitive patterns of product inhibition, though consistent with the general class of bi-substrate reactions, do not exclude a minor contribution from additional forms of the enzyme. NMR results support the presence of additional enzyme forms. Docking and energy calculations find that electron-transfer-competent binding sites for NADH and benzoquinone present severe steric overlap, consistent with the ping-pong mechanism. Unexpectedly, plots of initial velocity as a function of either NADH or benzoquinone concentration present one or two Michaelis-Menten phases depending on the temperature at which the enzyme is held prior to assay. The effect of temperature is reversible, suggesting an intramolecular conformational process. WrbA shares these and other details of its kinetic behavior with mammalian DT-diaphorase, an FAD-dependent NAD(PH:quinone oxidoreductase. An extensive literature review reveals several other enzymes with two-plateau kinetic plots, but in no case has a molecular explanation been elucidated. Preliminary sedimentation velocity analysis of WrbA indicates a large shift in size of the multimer with temperature, suggesting that subunit assembly coupled to substrate binding may underlie the two-plateau behavior. An
Mehrabadi, Mohammad; Bandani, Ali R; Saadati, Fatemeh
2010-01-01
The effect of triticale α-amylases inhibitors on starch hydrolysis catalyzed by the Sunn pest, Eurygaster integriceps Puton (Hemiptera: Scutelleridae) midgut amylases was examined. Biochemical studgawies showed that inhibitors from Triticale (a hybrid of wheat and rye) had inhibitiory effects on E. integriceps α-amylases. The effects of the triticale α-amylase inhibitor (T-αAI) on α-amylase of E. integriceps showed a dose dependent manner of inhibition, e.g. less inhibition of enzyme activity (around 10%) with a lower dose (0.25 mg protein) and high inhibition of enzyme activity (around 80%) when a high dose of inhibitor was used (1.5 mg protein). The enzyme kinetic studies using Michaelis-Menten and Lineweaver-Burk equations showed the K(m) remained constant (0.58%) but the maximum velocity (V(max)) decreased in the presence of a crude extract of Triticale inhibitors, indicating mixed inhibition. The temperature giving 50% inactivation of enzyme (T(50)) during a 30-min incubation at pH 7.0 was 73° C. The maximum inhibitory activity was achieved at 35° C and pH 5.0. Gel assays showed the meaningful inhibition of E. integriceps α-amylases by various concentrations of Triticale inhibitors. Based on the data presented in this study, it could be said that the T-αAI has good inhibitory activity on E. integriceps gut α-amylase.
Tam, Tsz Kin; Chen, Baowei; Lei, Chenghong; Liu, Jun
2012-08-01
NAD/NADH is a coenzyme found in all living cells, carrying electrons from one reaction to another. We report on characterizations of in situ regeneration of NADH via lipoamide dehydrogenase (LD)-catalyzed electron transfer reaction to regenerate NADH using UV-vis spectroelectrochemistry. The Michaelis-Menten constant (Km) and maximum velocity (Vmax) of NADH regeneration were measured as 0.80 {+-} 0.15 mM and 1.91 {+-} 0.09 {micro}M s-1 in a 1-mm thin-layer spectroelectrochemical cell using gold gauze as the working electrode at the applied potential -0.75 V (vs. Ag/AgCl). The electrocatalytic reduction of the NAD system was further coupled with the enzymatic conversion of pyruvate to lactate by lactate dehydrogenase to examine the coenzymatic activity of the regenerated NADH. Although the reproducible electrocatalytic reduction of NAD into NADH is known to be difficult compared to the electrocatalytic oxidation of NADH, our spectroelectrochemical results indicate that the in situ regeneration of NADH via LD-catalyzed electron transfer reaction is fast and sustainable and can be potentially applied to many NAD/NADH-dependent enzyme systems.
treA Codifies for a Trehalase with Involvement in Xanthomonas citri subsp. citri Pathogenicity
Alexandrino, André Vessoni; Goto, Leandro Seiji; Novo-Mansur, Maria Teresa Marques
2016-01-01
Citrus canker, caused by the bacterium Xanthomonas citri subsp. citri (Xcc), is a severe disease of citrus. Xcc presents broad spectrum of citrus hosts including economically important species whereas X. fuscans subsp. aurantifolii–type C (XauC) causes a milder disease and only infects Citrus aurantifolia. Trehalase catalyzes hydrolysis of the disaccharide trehalose, a sugar that has been reported to be related to Xcc pathogenicity. We expressed the recombinant gene product and assessed Xcc trehalase structural and kinetics data. The recombinant protein presented 42.7% of secondary structures in α-helix and 13% in β-sheets, no quaternary structure in solution, and Michaelis-Menten constant (KM) of 0.077 mM and Vmax 55.308 μMol glucose.min-1.mg protein-1 for trehalose. A Xcc mutant strain (XccΔtreA) was produced by gene deletion from Xcc genome. Enzymatic activity of trehalase was determined in Xcc, XauC and XccΔtreA cellular lysates, showing the highest values for XauC in in vitro infective condition and no activity for XccΔtreA. Finally, leaves of Citrus aurantifolia infected with XccΔtreA showed much more drenching and necrosis than those infected by wild type Xcc. We concluded that trehalase contributes to alleviate bacterial virulence and that inability for trehalose hydrolysis may promote higher Xcc infectivity. PMID:27611974
treA Codifies for a Trehalase with Involvement in Xanthomonas citri subsp. citri Pathogenicity.
Alexandrino, André Vessoni; Goto, Leandro Seiji; Novo-Mansur, Maria Teresa Marques
2016-01-01
Citrus canker, caused by the bacterium Xanthomonas citri subsp. citri (Xcc), is a severe disease of citrus. Xcc presents broad spectrum of citrus hosts including economically important species whereas X. fuscans subsp. aurantifolii-type C (XauC) causes a milder disease and only infects Citrus aurantifolia. Trehalase catalyzes hydrolysis of the disaccharide trehalose, a sugar that has been reported to be related to Xcc pathogenicity. We expressed the recombinant gene product and assessed Xcc trehalase structural and kinetics data. The recombinant protein presented 42.7% of secondary structures in α-helix and 13% in β-sheets, no quaternary structure in solution, and Michaelis-Menten constant (KM) of 0.077 mM and Vmax 55.308 μMol glucose.min-1.mg protein-1 for trehalose. A Xcc mutant strain (XccΔtreA) was produced by gene deletion from Xcc genome. Enzymatic activity of trehalase was determined in Xcc, XauC and XccΔtreA cellular lysates, showing the highest values for XauC in in vitro infective condition and no activity for XccΔtreA. Finally, leaves of Citrus aurantifolia infected with XccΔtreA showed much more drenching and necrosis than those infected by wild type Xcc. We concluded that trehalase contributes to alleviate bacterial virulence and that inability for trehalose hydrolysis may promote higher Xcc infectivity.
Zheng, Lisa; Khemlani, Adrina; Lorenz, Natalie; Loh, Jacelyn M S; Langley, Ries J; Proft, Thomas
2015-12-25
Streptococcus pyogenes is an important human pathogen that causes a wide range of diseases. Using bioinformatics analysis of the complete S. pyogenes strain SF370 genome, we have identified a novel S. pyogenes virulence factor, which we termed streptococcal 5'-nucleotidase A (S5nA). A recombinant form of S5nA hydrolyzed AMP and ADP, but not ATP, to generate the immunomodulatory molecule adenosine. Michaelis-Menten kinetics revealed a Km of 169 μm and a Vmax of 7550 nmol/mg/min for the substrate AMP. Furthermore, recombinant S5nA acted synergistically with S. pyogenes nuclease A to generate macrophage-toxic deoxyadenosine from DNA. The enzyme showed optimal activity between pH 5 and pH 6.5 and between 37 and 47 °C. Like other 5'-nucleotidases, S5nA requires divalent cations and was active in the presence of Mg(2+), Ca(2+), or Mn(2+). However, Zn(2+) inhibited the enzymatic activity. Structural modeling combined with mutational analysis revealed a highly conserved catalytic dyad as well as conserved substrate and cation-binding sites. Recombinant S5nA significantly increased the survival of the non-pathogenic bacterium Lactococcus lactis during a human whole blood killing assay in a dose-dependent manner, suggesting a role as an S. pyogenes virulence factor. In conclusion, we have identified a novel S. pyogenes enzyme with 5'-nucleotidase activity and immune evasion properties.
Valenzuela-Chavira, Ignacio; Contreras-Vergara, Carmen A; Arvizu-Flores, Aldo A; Serrano-Posada, Hugo; Lopez-Zavala, Alonso A; García-Orozco, Karina D; Hernandez-Paredes, Javier; Rudiño-Piñera, Enrique; Stojanoff, Vivian; Sotelo-Mundo, Rogerio R; Islas-Osuna, Maria A
2017-04-01
We studied a mango glutathione S-transferase (GST) (Mangifera indica) bound to glutathione (GSH) and S-hexyl glutathione (GSX). This GST Tau class (MiGSTU) had a molecular mass of 25.5 kDa. MiGSTU Michaelis-Menten kinetic constants were determined for their substrates obtaining a Km, Vmax and kcat for CDNB of 0.792 mM, 80.58 mM min(-1) and 68.49 s(-1) respectively and 0.693 mM, 105.32 mM min(-1) and 89.57 s(-1), for reduced GSH respectively. MiGSTU had a micromolar affinity towards GSH (5.2 μM) or GSX (7.8 μM). The crystal structure of the MiGSTU in apo or bound to GSH or GSX generated a model that explains the thermodynamic signatures of binding and showed the importance of enthalpic-entropic compensation in ligand binding to Tau-class GST enzymes. Copyright © 2017 Elsevier B.V. and Société Française de Biochimie et Biologie Moléculaire (SFBBM). All rights reserved.
Jiang, Jun Fang; Qiao, Juan; Mu, Xiao Yu; Moon, Myeong Hee; Qi, Li
2017-04-01
In this work, a unique D-amino acid oxidase reactor for enhanced enzymolysis efficiency is presented. A kind of magnetic polymer matrices, composed of iron oxide nanoparticles and porous polymer membrane (poly styrene-co-maleic anhydride), was prepared. With covalent bonding D-Amino acid oxidase on the surface of the matrices and characterization of scanning electron microscope and vibrating sample magnetometer, it demonstrated that the membrane enzyme reactor was successfully constructed. The enzymolysis efficiency of the enzyme reactor was evaluated and the apparent Michaelis-Menten constants of D-Amino acid oxidase were determined (Km was 1.10mM, Vmax was 23.8mMmin(-1)) by a chiral ligand exchange capillary electrophoresis protocol with methionine as the substrate. The results indicated that the enzyme reactor could exhibit good stability and excellent reusability. Importantly, because the enzyme and the substrate could be confined into the pores of the matrices, the enzyme reactor displayed the improved enzymolysis efficiency due to the confinement effect. Further, the prepared enzyme reactor was applied for D-Amino acid oxidase inhibitors screening. It has displayed that the proposed protocol could pave a new way for fabrication of novel porous polymer membrane based enzyme reactors to screen enzyme inhibitors.
Efficient hydrolysis of tuna oil by a surfactant-coated lipase in a two-phase system.
Ko, Wen-Ching; Wang, Hsiu-Ju; Hwang, Jyh-Sheng; Hsieh, Chang-Wei
2006-03-08
A surfactant-coated lipase (SCL) prepared by mixing Candida rugosa lipase with emulsifier in ethanol was used to hydrolyze tuna oil in a two-phase aqueous-organic system. Both enzyme (SCL) and substrate (tuna oil) were soluble in the organic phase, and the hydrolysis could occur with water molecules from the aqueous phase. This hydrolysis could promptly proceed compared to that catalyzed by native lipases which only occurred at the interface between the two phases. Michaelis-Menten kinetics in the two-phase reactions showed that the K(m) value of the SCL was half that of the native lipase, while the maximum velocity (V(max)) was 11.5 times higher. The hydrolysis method resulted in enrichment of n-3 polyunsaturated fatty acid (n-3 PUFA) content in glyceride mixtures from 26.4% to 49.8% and DHA from 19.1% to 38.9%. The SCL acted as an efficient hydrolytic catalyst for tuna oil.
Jahir Khan, Mohammad; Qayyum, Shariq; Alam, Fahad; Husain, Qayyum
2011-11-01
Proteins adsorbed on nanoparticles (NPs) are being used in biotechnology, biosensors and drug delivery. However, understanding the effect of NPs on the structure of proteins is still in a nascent state. In the present paper tin oxide (SnO2) NPs were synthesized by the reaction of SnCl4·5H2O in methanol via the sol-gel method and characterized by x-ray diffraction (XRD), Fourier transform infrared spectroscopy (FT-IR) and transmission electron microscopy (TEM). The binding of these SnO2-NPs with α-amylase was investigated by using UV-vis, fluorescence and circular dichroism (CD) spectroscopic techniques. A strong quenching of tryptophan fluorescence intensity in α-amylase was observed due to formation of a ground state complex with SnO2-NPs. Far-UV CD spectra showed that the secondary structure of α-amylase was changed in the presence of NPs. The Michaelis-Menten constant (Km), was found to be 26.96 and 28.45 mg ml - 1, while Vmax was 4.173 and 3.116 mg ml - 1 min - 1 for free and NP-bound enzyme, respectively.
Dubey, Nidhi C; Tripathi, Bijay P; Stamm, Manfred; Ionov, Leonid
2014-07-14
The flexibility in tuning the structure and charge properties of PNIPAm microgels during their synthesis makes them a suitable choice for various biological applications. Two-step free radical polymerization, a common method employed for synthesis of core-shell microgel has been well adopted to obtain cationic poly(N-isopropylacrylamide-aminoethyl methacrylate) (PNIPAm-AEMA) shell and PNIPAm core. Scanning electron microscopy (SEM), dynamic light scattering (DLS), zeta potential, and ninhydrin assay suggests nearly monodispersed particles of cationic nature. Amino groups on the microgel provides suitable attachment point for covalent immobilization of acetyl coenzyme A synthetase (Acs) via 1-ethyl-3-(3-N,N- dimethylaminopropyl) carbodiimide (EDC) chemistry. On immobilization, 61.55% of initial activity of Acs has been retained, while Michaelis-Menten kinetics of the immobilized Acs indicates identical K(m) (Michaelis constant) but decrease in the V(max) (maximum substrate conversion rate) compared to free enzyme. Immobilized Acs shows an improvement in activity at wide temperature and pH range and also demonstrates good thermal, storage, and operational stability. The Acs-microgel bioconjugate has been successfully reused for four consecutive operation cycles with more than 50% initial activity.
Esawy, Mona A; Gamal, Amira A; Kamel, Zeinat; Ismail, Abdel-Mohsen S; Abdel-Fattah, Ahmed F
2013-02-15
The Aspergillus niger NRC1ami pectinase was evaluated according to its hydrolysis efficiency of dry untreated orange peels (UOP), HCl-treated orange peels and NaOH-treated orange peels (HOP and NOP). Pectinase was entrapped in polyvinyl alcohol (PVA) sponge and the optimum pH and temperature of the free and immobilized enzymes were shifted from 4, 40 °C to 6, 50 °C respectively. The study of pH stability of free and immobilized pectinase showed that the immobilization process protected the enzyme strongly from severe alkaline pHs. The immobilization process improved the enzyme thermal stability to great instant. The unique feature of the immobilization process is its ability to solve the orange juice haze problem completely. Immobilized enzyme was reused 12 times in orange juice clarification with 9% activity loss from the original activity. Maximum reaction rate (V(max)) and Michaelis-Menten constant (K(m)) of the partially purified form were significantly changed after immobilization.
Some properties of the intestinal proteases of the rabbitfish, Siganus canaliculatus (Park).
Sabapathy, U; Teo, L H
1995-06-01
Some properties of the intestinal proteases of the rabbitfish were examined. At 25°C, both trypsin and chymotrypsin showed pH optima of 8.0. Leucine aminopeptidase, however, displayed maximum activity in the pH range, 7.0-9.0. Leucine aminopeptidase had the highest optimum temperature (60°C), and chymotrypsin, the lowest (30°C). The optimum temperature of trypsin was 55°C. The activation energy, Ea, was found to be 8.24 for trypsin and 8.50 kcal mol(-1) for chymotrypsin. The Ea for leucine aminopeptidase was 6.29 kcal mol(-1) above 40°C and 1.73 kcal mol(-1) below 40°C. Substrate concentration-velocity plots showed that all three enzymes followed Michaelis-Menten kinetics; the Km and Vmax were estimated for the three enzymes. The effects of various protease inhibitors on enzyme activity were also examined and confirmed the protease classes to which each enzyme belonged. The three proteases examined have similar properties to proteases in other fishes.
Kamble, Ashwini L; Banoth, Linga; Meena, Vachan Singh; Singh, Amit; Chisti, Yusuf; Banerjee, U C
2013-08-01
The intracellular cobalt-type nitrile hydratase was purified from the bacterium Rhodococcuserythropolis. The pure enzyme consisted of two subunits of 29 and 30 kDa. The molecular weight of the native enzyme was estimated to be 65 kDa. At 25 °C the enzyme had a half-life of 25 h. The Michaelis-Menten constants Km and vmax for the enzyme were 0.624 mM and 5.12 μmol/min/mg, respectively, using 3-cyanopyridine as the substrate. The enzyme-containing freely-suspended bacterial cells and the cells immobilized within alginate beads were evaluated for converting the various nitriles to amides. In a packed bed reactor, alginate beads (2 % alginate; 3 mm bead diameter) containing 200 mg/mL of cells, achieved a conversion of >90 % for benzonitrile and 4-cyanopyridine in 38 h (25 °C, pH 7.0) at a feed substrate concentration of 100 mM. The beads could be reused for up to six reaction cycles.
Nadar, Shamraja S; Rathod, Virendra K
2017-02-01
The self-assembled glucoamylase metal-organic framework (glucoamylase-MOF) was synthesized by facile one-step method within 20min by simply mixing aqueous solution of 2-methylimidazole (160mM), glucoamylase (5mg/mL) and zinc acetate (40mM) at room temperature (28±2°C). The prepared glucoamylase-MOF was characterized by using FT-IR, confocal scanning laser microscopy, XRD and SEM. The robustness and thermal stability of glucoamylase embedded MOF was evaluated in terms of half-life (in the range of 60-80°C) which showed 6 folds increment as against free form. Further, in Michaelis-Menten kinetics studies, glucoamylase entrapped MOF exhibited higher Km value and lower Vmax value as compared to native enzyme. Moreover, the immobilized glucoamylase exhibited up to 57% of residual activity after six consecutive cycles of reuse, whereas it retained 91% of residual activity till 25days of storage. Finally, the conformational changes occurred after the encapsulation of glucoamylase in the interior of MOF, which was analyzed by using FT-IR data analysis tools.
Homaei, Ahmad
2017-02-01
Biotechnology of enzyme has gained popularity due to the growing need for novel environmental technologies and the development of innovative mass-production. The work describes the original application of biosensors based on Penaeus merguiensis alkaline phosphatase (PM ALP) immobilized on gold nanorods (GNRs) to heavy metal determination. Penaeus merguiensis alkaline phosphatase (PM ALP) was immobilized on gold nanorods (GNRs) by ionic exchange and hydrophobic interactions. The optimum pH and temperature for maximum enzyme activity for the immobilized PM ALP are identified to be 11.0 and 60°C, respectively, for the hydrolysis of para-Nitrophenylphosphate (p-NPP). The kinetic studies confirm the Michaelis-Menten behavior and suggests overall slightly decrease in the performance of the immobilized enzyme with reference to the free enzyme. Km and Vmax values were 0.32µm and 54µm. min(-1) for free and 0.39µm and 48µmmin(-1) for immobilized enzymes, respectively. Similarly, the thermal stability, storage stability and stability at extreme pH of the enzyme is found to increase after the immobilization. The inhibitory effect heavy metal ions was studied on free and immobilized PM ALP. The bi-enzymatic biosensor were tested to study the influence of heavy metal ions and pesticides on the corresponding enzyme. The obtained high stability and lower decrease in catalytic efficiency suggested the great potential and feasibility of immobilized PM ALP nanobiocatalyst in efficient and apply the biosensor in total toxic metal content determination.
Jornil, Jakob; Jensen, Klaus Gjervig; Larsen, Frank
2010-01-01
the importance of the identified paroxetine-metabolizing P450 isoforms for human metabolism, taking mechanism-based inhibition into account. The amount of active hepatic CYP2D6 and CYP3A4 (not inactivated by mechanism-based inhibition) was also estimated by Simcyp. For extensive and poor metabolizers of CYP2D6......We identify here for the first time the low-affinity cytochrome P450 (P450) isoforms that metabolize paroxetine, using cDNA-expressed human P450s measuring substrate depletion and paroxetine-catechol (product) formation by liquid chromatography-tandem mass spectrometry. CYP1A2, CYP2C19, CYP2D6, CYP......3A4, and CYP3A5 were identified as paroxetine-catechol-forming P450 isoforms, and CYP2C19 and CYP2D6 were identified as metabolizing P450 isoforms by substrate depletion. Michaelis-Menten constants K(m) and V(max) were determined by product formation and substrate depletion. Using selective...
The 3-ureidopropionase of Caenorhabditis elegans, an enzyme involved in pyrimidine degradation.
Janowitz, Tim; Ajonina, Irene; Perbandt, Markus; Woltersdorf, Christian; Hertel, Patrick; Liebau, Eva; Gigengack, Ulrike
2010-10-01
Pyrimidines are important metabolites in all cells. Levels of cellular pyrimidines are controlled by multiple mechanisms, with one of these comprising the reductive degradation pathway. In the model invertebrate Caenorhabditis elegans, two of the three enzymes of reductive pyrimidine degradation have previously been characterized. The enzyme catalysing the final step of pyrimidine breakdown, 3-ureidopropionase (β-alanine synthase), had only been identified based on homology. We therefore cloned and functionally expressed the 3-ureidopropionase of C. elegans as hexahistidine fusion protein. The purified recombinant enzyme readily converted the two pyrimidine degradation products: 3-ureidopropionate and 2-methyl-3-ureidopropionate. The enzyme showed a broad pH optimum between pH 7.0 and 8.0. Activity was highest at approximately 40 °C, although the half-life of activity was only 65 s at that temperature. The enzyme showed clear Michaelis-Menten kinetics, with a K(m) of 147 ± 26 μM and a V(max) of 1.1 ± 0.1 U·mg protein(-1). The quaternary structure of the recombinant enzyme was shown to correspond to a dodecamer by 'blue native' gel electrophoresis and gel filtration. The organ specific and subcellular localization of the enzyme was determined using a translational fusion to green fluorescent protein and high expression was observed in striated muscle cells. With the characterization of the 3-ureidopropionase, the reductive pyrimidine degradation pathway in C. elegans has been functionally characterized.
Hexagonal tungsten oxide nanoflowers as enzymatic mimetics and electrocatalysts
Park, Chan Yeong; Seo, Ji Min; Jo, Hongil; Park, Juhyun; Ok, Kang Min; Park, Tae Jung
2017-01-01
Tungsten oxide (WOx) has been widely studied for versatile applications based on its photocatalytic, intrinsic catalytic, and electrocatalytic properties. Among the several nanostructures, we focused on the flower-like structures to increase the catalytic efficiency on the interface with both increased substrate interaction capacities due to their large surface area and efficient electron transportation. Therefore, improved WOx nanoflowers (WONFs) with large surface areas were developed through a simple hydrothermal method using sodium tungstate and hydrogen chloride solution at low temperature, without any additional surfactant, capping agent, or reducing agent. Structural determination and electrochemical analyses revealed that the WONFs have hexagonal Na0.17WO3.085·0.17H2O structure and exhibit peroxidase-like activity, turning from colorless to blue by catalyzing the oxidation of a peroxidase substrate, such as 3,3′,5,5′-tetramethylbenzidine, in the presence of H2O2. Additionally, a WONF-modified glassy carbon electrode was adopted to monitor the electrocatalytic reduction of H2O2. To verify the catalytic efficiency enhancement by the unique shape and structure of the WONFs, they were compared with calcinated WONFs, cesium WOx nanoparticles, and other peroxidase-like nanomaterials. The results indicated that the WONFs showed a low Michaelis-Menten constant (km), high maximal reaction velocity (vmax), and large surface area. PMID:28128306
Nikola Milašinović
2014-01-01
Full Text Available This study reports the synthesis of polymeric matrices based on N-isopropylacrylamide and itaconic acid and its application for immobilization of lipase from Candida rugosa. The lipase was immobilized by entrapment method. Free and immobilized lipase activities, pH and temperature optima, and storage stability were investigated. The optimum temperature for free and entrapped lipase was found to be 40 and 45°C, while the optimum pH was observed at pH 7 and 8, respectively. Both hydrolytic activity in an aqueous medium and esterolytic activity in an organic medium have been evaluated. Maximum reaction rate (Vmax and Michaelis-Menten constants (Km were also determined for immobilized lipase. Storage stability of lipase was increased as a result of immobilization process. Furthermore, the operational stability and reusability of the immobilized lipase in esterification reaction have been studied, and it was observed that after 10 cycles, the residual activity for entrapped lipase was as high as 50%, implying that the developed hydrogel and immobilized system could provide a promising solution for the flavor ester synthesis at the industrial scale.
Kinetics of Papain: An Introductory Biochemistry Laboratory Experiment
Cornely, Kathleen; Crespo, Eric; Earley, Michael; Kloter, Rachel; Levesque, Aime; Pickering, Mary
1999-05-01
Enzyme kinetics experiments are popular in the undergraduate laboratory. These experiments have pedagogic value because they reinforce the concepts of Michaelis-Menten kinetics covered in the lecture portion of the course and give students the experience of calculating kinetic constants from data they themselves have generated. In this experiment, we investigate the kinetics of the thiol protease papain. The source of the papain is commercially available papaya latex. A specific substrate, Na-benzoyl-arginine-p-nitroanilide (BAPNA), is used, which takes advantage of the fact that papain interacts with a phenylalanine residue two amino acids away from the peptide bond cleaved. Upon hydrolysis by papain, a bright yellow product is released, p-nitroaniline. This allows the reaction to be monitored spectrophotometrically by measuring the rate of formation of the p-nitroaniline product as a function of the increase in absorbance of the solution at the lmax of p-nitroaniline (400 nm) over time at various substrate concentrations. These data are used to plot a Lineweaver-Burk plot from which the vmax and KM are obtained. If time permits, students carry out additional investigations in which e of p-nitroaniline is measured, the enzyme solution protein concentration is measured, the enzyme purity is evaluated by SDS-PAGE, and a pH-rate profile is constructed from experimental data.
Sen, A; Kirikbakan, A
2004-09-01
In this study, feral leaping mullet (Liza saliens) liver cytosolic glutathione S-transferases (GSTs) were investigated and characterized using 1-chloro-2,4-dinitrobenzene (CDNB) and ethacrynic acid (EA) as substrates. The average GST activities towards CDNB and EA were found to be 1365 +/- 41 and 140 +/- 20 nmol/min per mg protein, respectively. The effects of cytosolic protein amount and temperature ranging from 4 to 70 degrees C on enzyme activities were examined. While both activities towards CDNB and EA showed similar dependence on protein amount, temperature optima were found as 37 and 42 degrees C, respectively. In addition, the effects of pH on GST-CDNB and -EA activities were studied and different pH activity profiles were observed. For both substrates, GST activities were found to obey Michaelis-Menten kinetics with apparent V(max) and K(m) values of 1661 nmol/min per mg protein and 0.24 mM and 157 nmol/min per mg protein and 0.056 mM for CDNB and EA, respectively. Distribution of GST in Liza saliens tissues was investigated and compared with other fish species. Very high GST activities were measured in tissues from Liza saliens such as liver, kidney, testis, proximal intestine, and gills. Moreover, our results suggested that GST activities from Liza saliens would be a valuable biomarker for aquatic pollution.
Narumi, Katsuya; Kobayashi, Masaki; Kondo, Ayuko; Furugen, Ayako; Yamada, Takehiro; Takahashi, Natsuko; Iseki, Ken
2016-11-01
Loxoprofen, a propionate non-steroidal anti-inflammatory drug (NSAID), is used widely in East Asian countries. However, little is known about the transport mechanisms contributing to its intestinal absorption. The objectives of this study were to characterize the intestinal transport of loxoprofen using the human intestinal Caco-2 cell model. The transport of loxoprofen was investigated in cellular uptake studies. The uptake of loxoprofen into Caco-2 cells was pH- and concentration-dependent, and was described by a Michaelis-Menten equation with passive diffusion (Km : 4.8 mm, Vmax : 142 nmol/mg protein/30 s, and Kd : 2.2 μl/mg protein/30 s). Moreover, the uptake of loxoprofen was inhibited by a typical monocarboxylate transporter (MCT) inhibitor as well as by various monocarboxylates. The uptake of [(14) C] l-lactic acid, a typical MCT substrate, in Caco-2 cells was saturable with relatively high affinity for MCT. Because loxoprofen inhibited the uptake of [(14) C] l-lactic acid in a noncompetitive manner, it was unlikely that loxoprofen uptake was mediated by high-affinity MCT(s). Our results suggest that transport of loxoprofen in Caco-2 cells is, at least in part, mediated by a proton-dependent transport system. Copyright © 2016 John Wiley & Sons, Ltd.
Tanvir, Shazia; Thuróczy, György; Selmaoui, Brahim; Silva Pires Antonietti, Viviane; Sonnet, Pascal; Arnaud-Cormos, Delia; Lévêque, Philippe; Pulvin, Sylviane; de Seze, René
2016-10-01
Cell phones increase exposure to radiofrequency (RF) electromagnetic fields (EMFs). Whether EMFs exert specific effects on biological systems remains debatable. This study investigated the effect of cell phone exposure on the structure and function of human NADPH-cytochrome P450 reductase (CPR). CPR plays a key role in the electron transfer to cytochrome P450, which takes part in a wide range of oxidative metabolic reactions in various organisms from microbes to humans. Human CPR was exposed for 60min to 1966-MHz RF inside a transverse electromagnetic cell (TEM-cell) placed in an incubator. The specific absorption rate (SAR) was 5W·kg(-1). Conformation changes have been detected through fluorescent spectroscopy of flavin and tryptophan residues, and investigated through circular dichroism, dynamic light scattering and microelectrophoresis. These showed that CPR was narrowed. By using cytochrome C reductase activity to assess the electron flux through the CPR, the Michaelis Menten constant (Km) and the maximum initial velocity (Vmax) decreased by 22% as compared with controls. This change was due to small changes in the tertiary and secondary structures of the protein at 37°C. The relevance of these findings to an actual RF exposure scenario demands further biochemical and in-vivo confirmation.
Foster, Alexander; Barnes, Nicole; Speight, Robert; Keane, Mark A
2013-10-01
The catalytic action of putrescine specific amine oxidases acting in tandem with 4-aminobutyraldehyde dehydrogenase is explored as a degradative pathway in Rhodococcus opacus. By limiting the nitrogen source, increased catalytic activity was induced leading to a coordinated response in the oxidative deamination of putrescine to 4-aminobutyraldehyde and subsequent dehydrogenation to 4-aminobutyrate. Isolating the dehydrogenase by ion exchange chromatography and gel filtration revealed that the enzyme acts principally on linear aliphatic aldehydes possessing an amino moiety. Michaelis-Menten kinetic analysis delivered a Michaelis constant (K(M)=0.014 mM) and maximum rate (Vmax=11.2 μmol/min/mg) for the conversion of 4-aminobutyraldehyde to 4-aminobutyrate. The dehydrogenase identified by MALDI-TOF mass spectrometric analysis (E value=0.031, 23% coverage) belongs to a functionally related genomic cluster that includes the amine oxidase, suggesting their association in a directed cell response. Key regulatory, stress and transport encoding genes have been identified, along with candidate dehydrogenases and transaminases for the further conversion of 4-aminobutyrate to succinate. Genomic analysis has revealed highly similar metabolic gene clustering among members of Actinobacteria, providing insight into putrescine degradation notably among Micrococcaceae, Rhodococci and Corynebacterium by a pathway that was previously uncharacterised in bacteria.
Fratebianchi, Dante; Cavello, Ivana Alejandra; Cavalitto, Sebastián Fernando
2017-01-01
An endo-polygalacturonase secreted by Aspergillus sojae was characterized after being purified to homogeneity from submerged cultures with orange peel as the sole carbon source by gel filtration and ion-exchange chromatographies. According to SDS-PAGE and analytical isoelectric focusing analyses, the enzyme presents a molecular weight of 47 kDa and pI value of 4.2. This enzyme exhibits considerable stability under highly acidic to neutral conditions (pH 1.5-6.5) and presents a half-life of 2 h at 50°C. Besides its activity towards pectin and polygalacturonic acid, the enzyme displays pectin-releasing activity, acting best in a pH range of 3.3-5.0. Thin-layer chromatographic analysis revealed that tri-galacturonate is the main enzymatic end product of polygalacturonic acid hydrolysis, indicating that it is an endo-polygalacturonase. The enzyme exhibits Michaelis-Menten kinetics, with KM and VMAX values of 0.134 mg/mL and 9.6 µmol/mg/min, respectively, and remained stable and active in the presence of SO2, ethanol, and various cations assayed except Hg2+. © 2017 S. Karger AG, Basel.
Hexagonal tungsten oxide nanoflowers as enzymatic mimetics and electrocatalysts
Park, Chan Yeong; Seo, Ji Min; Jo, Hongil; Park, Juhyun; Ok, Kang Min; Park, Tae Jung
2017-01-01
Tungsten oxide (WOx) has been widely studied for versatile applications based on its photocatalytic, intrinsic catalytic, and electrocatalytic properties. Among the several nanostructures, we focused on the flower-like structures to increase the catalytic efficiency on the interface with both increased substrate interaction capacities due to their large surface area and efficient electron transportation. Therefore, improved WOx nanoflowers (WONFs) with large surface areas were developed through a simple hydrothermal method using sodium tungstate and hydrogen chloride solution at low temperature, without any additional surfactant, capping agent, or reducing agent. Structural determination and electrochemical analyses revealed that the WONFs have hexagonal Na0.17WO3.085·0.17H2O structure and exhibit peroxidase-like activity, turning from colorless to blue by catalyzing the oxidation of a peroxidase substrate, such as 3,3‧,5,5‧-tetramethylbenzidine, in the presence of H2O2. Additionally, a WONF-modified glassy carbon electrode was adopted to monitor the electrocatalytic reduction of H2O2. To verify the catalytic efficiency enhancement by the unique shape and structure of the WONFs, they were compared with calcinated WONFs, cesium WOx nanoparticles, and other peroxidase-like nanomaterials. The results indicated that the WONFs showed a low Michaelis-Menten constant (km), high maximal reaction velocity (vmax), and large surface area.
Fabrício M. Gomes
2006-07-01
Full Text Available Microbial lipase from Candida rugosa was immobilized by covalent binding on wood cellulignin (Eucaliptus grandis chemically modified with carbonyldiimidazole. The immobilized system was fully evaluated in aqueous (olive oil hydrolysis and organic (ester synthesis media. A comparative study between free and immobilized lipase was carried out in terms of pH, temperature and thermal stability. A higher pH value (8.0 was found optimal for the immobilized lipase. The optimal reaction temperature shifted from 37 °C for the free lipase to 45 °C for the immobilized lipase. The pattern of heat stability indicated that the immobilization process tends to stabilize the enzyme. Kinetics tests at 37 °C following the hydrolysis of olive oil obeyed the Michaelis-Menten rate equation. Values for Km = 924.9 mM and Vmax = 198.3 U/mg were lower than for free lipase, suggesting that the affinity towards the substrate changed and the activity of the immobilized lipase decreased during the course of immobilization. The immobilized derivative was also tested in the ester synthesis from several alcohols and carboxylic acids.
Butylbenzyl phthalate hydrolysis in liver microsomes of humans, monkeys, dogs, rats and mice.
Takahara, Yuka; Kinashi, Yu; Takahara, Yuusuke; Hichiya, Hiroyuki; Okada, Kenji; Murata, Mikio; Shigeyama, Masato; Hanioka, Nobumitsu
2014-01-01
Butylbenzyl phthalate (BBzP) is used as a plasticizer to import flexibility to polyvinylchloride plastics. In this study, hydrolysis of BBzP to monobutyl phthalate (MBP) and monobenzyl phthalate (MBzP) in liver microsomes of humans, monkeys, dogs, rats and mice was examined. The kinetics for MBP formation by human, dog and mouse liver microsomes followed the Michaelis-Menten model, whereas the kinetics by monkey and rat liver microsomes fitted the Hill model. The kinetics for MBzP formation fitted the Hill model for all liver microsomes. The Vmax and in vitro clearance (CLint or CLmax) ratios of MBP/MBzP formation varied among animal species, although the Km for MBP and MBzP formation in each liver microsomes were generally comparable. The hydrolysis of BBzP to monoester phthalates in mammalian liver microsomes could be classified into two types: MBzP>MBP type for humans and dogs, and MBP>MBzP type for monkeys, rats and mice. These findings suggest that the formation profile of MBzP and MBP from BBzP by liver microsomes differs extensively among animal species.
Novel grafted agar disks for the covalent immobilization of β-D-galactosidase.
Wahba, Marwa I; Hassan, Mohamed E
2015-12-01
Novel grafted agar disks were prepared for the covalent immobilization of β-D-galactosidase (β-gal). The agar disks were activated through reacting with ethylenediamine or different molecular weights of Polyethyleneimine (PEI), followed by glutaraldehyde (GA). The modification of the agar gel and the binding of the enzyme were verified by Fourier Transform Infrared (FTIR) and elemental analysis. Moreover, the agar's activation process was optimized, and the amount of immobilized enzyme increased 3.44 folds, from 38.1 to 131.2 U/g gel, during the course of the optimization process. The immobilization of β-gal onto the activated agar disks caused its optimum temperature to increase from 45°C to 45-55°C. The optimum pH of the enzyme was also shifted towards the acidic side (3.6-4.6) after its immobilization. Additionally, the Michaelis-Menten constant (Km ) increased for the immobilized β-gal as compared to its free counterpart whereas the maximum reaction rate (Vmax ) decreased. The immobilized enzyme was also shown to retain 92.99% of its initial activity after being used for 15 consecutive times.
Fernández-Fernández, María; Moldes, Diego; Domínguez, Alberto; Sanromán, M Ángeles; Tavares, Ana Paula M; Rodríguez, Oscar; Macedo, Eugénia A
2014-01-01
The use of ionic liquids (ILs) as reaction media for enzymatic reactions has increased their potential because they can improve enzyme activity and stability. Kinetic and stability properties of immobilized commercial laccase from Myceliophthora thermophila in the water-soluble IL 1-ethyl-3-methylimidazolium ethylsulfate ([emim][EtSO4 ]) have been studied and compared with free laccase. Laccase immobilization was carried out by covalent binding on glyoxyl-agarose beads. The immobilization yield was 100%, and the activity was totally recovered. The Michaelis-Menten model fitted well to the kinetic data of enzymatic oxidation of a model substrate in the presence of the IL [emim][EtSO4 ]. When concentration of the IL was augmented, the values of Vmax for free and immobilized laccases showed an increase and slight decrease, respectively. The laccase-glyoxyl-agarose derivative improved the laccase stability in comparison with the free laccase regarding the enzymatic inactivation in [emim][EtSO4 ]. The stability of both free and immobilized laccase was slightly affected by small amounts of IL (<50%). A high concentration of the IL (75%) produced a large inactivation of free laccase. However, immobilization prevented deactivation beyond 50%. Free and immobilized laccase showed a first-order thermal inactivation profile between 55 and 70°C in the presence of the IL [emim][EtSO4 ]. Finally, thermal stability was scarcely affected by the presence of the IL.
Mahn, Andrea; Angulo, Alejandro; Cabañas, Fernanda
2014-12-03
Myrosinase (β-thioglucosidase glucohydrolase, EC 3.2.1.147) from broccoli (Brassica oleracea var. italica) was purified by ammonium sulfate precipitation followed by concanavalin A affinity chromatography, with an intermediate dialysis step, resulting in 88% recovery and 1318-fold purification. These are the highest values reported for the purification of any myrosinase. The subunits of broccoli myrosinase have a molecular mass of 50-55 kDa. The native molecular mass of myrosinase was 157 kDa, and accordingly, it is composed of three subunits. The maximum activity was observed at 40 °C and at pH below 5.0. Kinetic assays demonstrated that broccoli myrosinase is subjected to substrate (sinigrin) inhibition. The Michaelis-Menten model, considering substrate inhibition, gave Vmax equal to 0.246 μmol min(-1), Km equal to 0.086 mM, and K(I) equal to 0.368 mM. This is the first study about purification and characterization of broccoli myrosinase.
Enzymatic mechanisms of soil-carbon response to temperature on Mt. Kilimanjaro
Blagodatskaya, Evgenia; Blagodatskiy, Sergey; Kuzyakov, Yakov
2016-04-01
Short-term acceleration of soil organic matter (SOM) decomposition by increasing temperature contradicts the acclimation observed in long-term studies. We used the unique altitudinal gradient (from colline tropical zone to subalpine zone) on Mt. Kilimanjaro to demonstrate the mechanisms of short- and long-term acclimation of extra- and intracellular enzymes that decompose polymers (cellulose, chitin, phytate) and oxidize monomers (14C-glucose). Basing on Michaelis-Menten kinetics we determined the enzymes affinity to substrate (Km) and mineralization potential of heterotrophic microorganisms (Vmax) 1) for three hydrolytic enzymes: β-1,4-glucosidase, N-acetyl- β -D-glucosaminidase and phosphatase by the application of fluorogenically labeled substrates and 2) for mineralization of 14C-labeled glucose by substrate-dependent respiratory response. Here we show that the amount of available substrate is responsible for temperature sensitivity of hydrolysis of polymers in soil, whereas monomers oxidation to CO2 does not depend on substrate amount and is mainly temperature governed. We also found that substrate affinity of enzymes (which is usually decreases with the temperature) differently responded to warming for the process of depolymerisation versus monomers oxidation. We suggest the mechanism to temperature acclimation based on different temperature sensitivity of enzymes kinetics for hydrolysis of polymers and for monomers oxidation
Platelet serotonin content and uptake in spontaneously hypertensive rats
Guicheney, P.; Legros, M.; Marcel, D.; Kamal, L.; Meyer, P.
1985-02-18
Platelet serotonin (5-HT) content and uptake were studied in male SHR and WKY at various ages. Blood was withdrawn from the carotid artery under anesthesia and 5-HT levels determined from platelet rich plasma (PRP) using a HPLC technique coupled with an electrochemical detection method. Platelet 5-HT uptake was studied by incubating PRP at 37/sup 0/C for 10 sec with increasing concentrations of /sup 3/H-5HT. Lineweaver-Burk plots of /sup 3/H-5HT uptake were linear suggesting simple Michaelis-Menten uptake kinetics. The SHR had more platelets than age-matched controls and consequently a higher blood circulating pool of 5-HT. Nevertheless, the 5-HT platelet levels were similar to those of their age-matched rats. The 5 week-old SHR and WKY had greater numbers of platelets and higher 5-HT platelet levels than the older rats of both strains. The affinity constants (Km) and the maximal velocities (Vmax) of platelet 5-HT uptake did not differ significantly between the 12 week- and the 6 month-old SHR and WKY. These data suggest that the SHR do not show the same impairment in platelet 5-HT metabolism as observed in essential hypertension in man.
Lee, Won-Heong; Jin, Yong-Su
2017-03-10
Although simultaneous saccharification and fermentation (SSF) of cellulosic biomass can offer efficient hydrolysis of cellulose through alleviating feed-back inhibition of cellulases by glucose, supplementation of β-glucosidase is necessary because most fermenting microorganisms cannot utilize cellobiose. Previously, we observed that SSF of cellulose by an engineered Saccharomyces cerevisiae expressing a cellobiose transporter (CDT-1) and an intracellular β-glucosidase (GH1-1) without β-glucosidase could not be performed as efficiently as the traditional SSF with extracellular β-glucosidase. However, we improved the ethanol production from SSF of cellulose by employing a further engineered S. cerevisiae expressing a mutant cellobiose transporter [CDT-1 (F213L) exhibiting higher VMAX than CDT-1] and GH1-1 in this study. Furthermore, limitation of cellobiose formation by reducing the amounts of cellulases mixture in SSF could lead the further engineered strain to produce ethanol considerably better than the parental strain with β-glucosidase. Probably, better production of ethanol by the further engineered strain seemed to be due to a higher affinity to cellobiose, which might be attributed to not only 2-times lower Monod constant (KS) for cellobiose than KS of the parental strain for glucose but also 5-times lower KS than Michaelis-Menten constant (KM) of the extracellular β-glucosidase for glucose. Our results suggest that modification of the cellobiose transporter in the engineered yeast to transport lower level of cellobiose enables a more efficient SSF for producing ethanol from cellulose.
Enhancement by cytidine of membrane phospholipid synthesis
G-Coviella, I. L.; Wurtman, R. J.
1992-01-01
Cytidine, as cytidine 5'-diphosphate choline, is a major precursor in the synthesis of phosphatidylcholine in cell membranes. In the present study, we examined the relationships between extracellular levels of cytidine, the conversion of [14C]choline to [14C]phosphatidylcholine, and the net syntheses of phosphatidylcholine and phosphatidylethanolamine by PC12 cells. The rate at which cytidine (as [3H]cytidine) was incorporated into the PC12 cells followed normal Michaelis-Menten kinetics (Km = 5 microM; Vmax = 12 x 10(-3) mmol/mg of protein/min) when the cytidine concentrations in the medium were below 50 microM; at higher concentrations, intracellular [3H]cytidine nucleotide levels increased linearly. Once inside the cell, cytidine was converted mainly into cytidine triphosphate. In pulse-chase experiments, addition of cytidine to the medium caused a time- and dose-dependent increase (by up to 30%) in the incorporation of [14C]choline into membrane [14C]-phosphatidylcholine. When the PC12 cells were supplemented with both cytidine and choline for 14 h, small but significant elevations (p less than 0.05) were observed in their absolute contents of membrane phosphatidylcholine, phosphatidylethanolamine, and phosphatidylserine, all increasing by 10-15% relative to their levels in cells incubated with choline alone. Exogenous cytidine, acting via cytidine triphosphate, can thus affect the synthesis and levels of cell membrane phospholipids.
Purification and Characterization of PRL Protein Tyrosine Phosphatases
LI Zhao-fa; WANG Yan; LI Qing-shan; ZHAO Zhi-zhuang Joe; FU Xue-qi; LI Yu-lin; LI Yi-lei
2005-01-01
PRLs constitute a subfamily of protein tyrosine phosphatases(PTPs). In the present paper are reported the molecular cloning, expression, purification, and characterization of all the three members of the PRL enzymes in human and the only PRL in C.elegans. These enzymes were expressed as glutathione S-transferase(GST) fusion proteins in DE3pLysS E.coli cells, and the recombinant fusion proteins were purified on glutathione-Sepharose affinity columns. Having been cleaved with thrombin, GST-free enzymes were further purified on an S-100 Sepharose gel filtration column. The purified proteins show single polypeptide bands on SDS-polyacrylamide gel electrophoresis. With para-nitrophenyl phosphate(p-NPP) as a substrate, PRLs exhibit classical Michaelis-Menten kinetics with Vmax values two orders of magnitude smaller than those of classic PTPs. The responses of PRLs to ionic strength, metal ions and phosphatase inhibitors are similar to those of other characterized PTPs, but their optimal pH values are different. These data thus reveal distinct common biochemical properties of PRL subfamily PTPs as well.
Zhuowei Cheng; Pengfei Sun; Yifeng Jiang; Lili Zhang; Jianmeng Chen
2012-01-01
Biodegradation has become a popular alternative remediation technology for its economic and ecological advantages.An aerobic bacterium (strain ZW) capable of degrading α-pinene was isolated from a biofilter by a selective enrichment.Based on the 16S rRNA gene analysis and physiochemical properties,this strain was identified as Pseudomonas veronii.Under the optimized condition achieved by the response surface methodology (RSM),as well as pH 6.82,temperature 26.3°C and NaCl concentration 1.36％,almost 100％α-pinene could be removed within 45 hr.Enzymatic biodegradation by the crude intracellular enzyme could be described well by the Michaelis-Menten model in which the maximum degradation rate Vmax and the half-saturation constant Km were calculated to be 0.431 mmol/(L.min) and 0.169 mmol/L,respectively.Activity assay of catechol suggested that the strain ZW possessed a catechol1,2-dioxygenase and could decompose benzene-ring through ortho ring cleavage.Based on the identified intermediates by GC/MS,a new metabolic pathway was proposed,in which the final metabolites were some simpler organic and inorganic compounds.The present work demonstrated that the strain ZW would have a great application prospect for the remediation of α-pinene-contaminated environment.
Amyloglucosidase enzymatic reactivity inside lipid vesicles
Kim Jin-Woo
2007-10-01
Full Text Available Abstract Efficient functioning of enzymes inside liposomes would open new avenues for applications in biocatalysis and bioanalytical tools. In this study, the entrapment of amyloglucosidase (AMG (EC 3.2.1.3 from Aspergillus niger into dipalmitoylphosphatidylcholine (DPPC multilamellar vesicles (MLVs and large unilamellar vesicles (LUVs was investigated. Negative-stain, freeze-fracture, and cryo-transmission electron microscopy images verified vesicle formation in the presence of AMG. Vesicles with entrapped AMG were isolated from the solution by centrifugation, and vesicle lamellarity was identified using fluorescence laser confocal microscopy. The kinetics of starch hydrolysis by AMG was modeled for two different systems, free enzyme in aqueous solution and entrapped enzyme within vesicles in aqueous suspension. For the free enzyme system, intrinsic kinetics were described by a Michaelis-Menten kinetic model with product inhibition. The kinetic constants, Vmax and Km, were determined by initial velocity measurements, and Ki was obtained by fitting the model to experimental data of glucose concentration-time curves. Predicted concentration-time curves using these kinetic constants were in good agreement with experimental measurements. In the case of the vesicles, the time-dependence of product (glucose formation was experimentally determined and simulated by considering the kinetic behavior of the enzyme and the permeation of substrate into the vesicle. Experimental results demonstrated that entrapped enzymes were much more stable than free enyzme. The entrapped enzyme could be recycled with retention of 60% activity after 3 cycles. These methodologies can be useful in evaluating other liposomal catalysis operations.
Quantifying the relative contributions of different solute carriers to aggregate substrate transport
Taslimifar, Mehdi; Oparija, Lalita; Verrey, Francois; Kurtcuoglu, Vartan; Olgac, Ufuk; Makrides, Victoria
2017-01-01
Determining the contributions of different transporter species to overall cellular transport is fundamental for understanding the physiological regulation of solutes. We calculated the relative activities of Solute Carrier (SLC) transporters using the Michaelis-Menten equation and global fitting to estimate the normalized maximum transport rate for each transporter (Vmax). Data input were the normalized measured uptake of the essential neutral amino acid (AA) L-leucine (Leu) from concentration-dependence assays performed using Xenopus laevis oocytes. Our methodology was verified by calculating Leu and L-phenylalanine (Phe) data in the presence of competitive substrates and/or inhibitors. Among 9 potentially expressed endogenous X. laevis oocyte Leu transporter species, activities of only the uniporters SLC43A2/LAT4 (and/or SLC43A1/LAT3) and the sodium symporter SLC6A19/B0AT1 were required to account for total uptake. Furthermore, Leu and Phe uptake by heterologously expressed human SLC6A14/ATB0,+ and SLC43A2/LAT4 was accurately calculated. This versatile systems biology approach is useful for analyses where the kinetics of each active protein species can be represented by the Hill equation. Furthermore, its applicable even in the absence of protein expression data. It could potentially be applied, for example, to quantify drug transporter activities in target cells to improve specificity. PMID:28091567
Turpeinen, Miia; Hofmann, Ute; Klein, Kathrin; Mürdter, Thomas; Schwab, Matthias; Zanger, Ulrich M
2009-05-01
Nabumetone, a widely used nonsteroidal anti-inflammatory drug, requires biotransformation into 6-methoxy-2-naphthylacetic acid (6-MNA), a close structural analog to naproxen, to achieve its analgesic and anti-inflammatory effects. Despite its wide use, the enzymes involved in metabolism have not been identified. In the present study, several in vitro approaches were used to identify the cytochrome P450 (P450) enzyme(s) responsible for 6-MNA formation. In human liver microsomes (HLMs) 6-MNA formation displayed monophasic Michaelis-Menten kinetics with apparent K(m) and V(max) values (mean +/- S.D.) of 75.1 +/- 15.3 microM and 1304 +/- 226 pmol/min/mg protein, respectively, and formation rate of 6-MNA varied approximately 5.5-fold (179-983 pmol/min/mg protein). 6-MNA activity correlated strongly with both CYP1A2-mediated phenacetin O-deethylation activity and CYP1A2 protein content (r = 0.85 and 0.74, respectively; p nabumetone, 6-MNA, is predominantly catalyzed by CYP1A2 in HLMs with only minor contribution of other P450s.
Characterization of glucose uptake by cultured rat podocytes.
Lewko, Barbara; Bryl, Ewa; Witkowski, Jacek M; Latawiec, Elzbieta; Gołos, Magdalena; Endlich, Nicole; Hähnel, Brunhilde; Koksch, Claudia; Angielski, Stefan; Kriz, Wilhelm; Stepinski, Jan
2005-01-01
The nonmetabolizable glucose analogue [(3)H]-2-deoxy-D-glucose ((3)H-2DG) was used to study glucose transport in cultured rat podocytes. Intracellular accumulation of (3)H-2DG was linear up to 20 min and was inhibited by cytochalasin B (80% inhibition) and by phlorizin (20% inhibition). Pretreatment with insulin stimulated the (3)H-2DG uptake 1.5-fold. A Hill analysis of the rate of glucose transport yielded a V(max) value of approximately 10 mM and S(0.5)of 7.8 mM. The value h = 1.0 for a Hill coefficient confirmed that glucose uptake exhibited a Michaelis-Menten kinetics. Transporters GLUT2 and GLUT4 were expressed in over 90% podocytes. Of the GLUT2- and GLUT4-expressing cells, approximately one-fourth expressed the membrane-bound fraction. We conclude that cultured rat podocytes possess a differentiated glucose transport system consisting chiefly of facilitative GLUT2 and GLUT4 transporters. It seems likely that a sodium-dependent glucose cotransporter may also be present in these cells.
Yafuso, Jannai T; Negi, Vishal Singh; Bingham, Jon-Paul; Borthakur, Dulal
2014-07-01
In plants, the final step of cysteine formation is catalyzed by O-acetylserine (thiol) lyase (OAS-TL). The purpose of this study was to isolate and characterize an OAS-TL from the tree legume Leucaena leucocephala (leucaena). Leucaena contains a toxic, nonprotein amino acid, mimosine, which is also formed by an OAS-TL, and characterization of this enzyme is essential for developing a mimosine-free leucaena for its use as a protein-rich fodder. The cDNA for a cytosolic leucaena OAS-TL isoform was obtained through interspecies suppression subtractive hybridization. A 40-kDa recombinant protein was purified from Escherichia coli and used in enzyme activity assays where it was found to synthesize only cysteine. The enzyme followed Michaelis-Menten kinetics, and the Km was calculated to be 1,850±414 μM sulfide and the Vmax was 200.6±19.92 μM cysteine min(-1). The N-terminal affinity His-tag was cleaved from the recombinant OAS-TL to eliminate its possible interference in binding with the substrate, 3-hydroxy-4-pyridone, for mimosine formation. The His-tag-cleaved OAS-TL was again observed to catalyze the formation of cysteine but not mimosine. Thus, the cytosolic OAS-TL from leucaena used in this study is specific for only cysteine synthesis and is different from previously reported OAS-TLs that also function as β-substituted alanine synthases.
Industrial waste based compost as a source of novel cellulolytic strains and enzymes.
Amore, Antonella; Pepe, Olimpia; Ventorino, Valeria; Birolo, Leila; Giangrande, Chiara; Faraco, Vincenza
2013-02-01
Ninety bacteria isolated from raw composting materials were screened for their cellulolytic activity on solid medium containing carboxymethylcellulose. The bacteria producing the highest cellulolytic activity levels were identified by 16S rRNA sequencing as Bacillus licheniformis strain 1, Bacillus subtilis subsp. subtilis strain B7B, Bacillus subtilis subsp. spizizenii strain 6, and Bacillus amyloliquefaciens strain B31C. Cellulase activity production by the most productive strain B. amyloliquefaciens B31C was optimized in liquid culture varying the carbon source. Comparison of growth curves of B. amyloliquefaciens B31C at temperatures from 28 to 47 °C indicated its thermotolerant nature. Moreover, analysis of time courses of cellulase activity production in this thermal range showed that increase of temperature from 28 to 37 °C causes an increase of cellulase activity levels. Investigating the enzymes responsible for cellulase activity produced by B. amyloliquefaciens B31C by proteomic analyses, an endoglucanase was identified. It was shown that the purified enzyme catalyzes carboxymethylcellulose's hydrolysis following Michaelis-Menten kinetics with a K(M) of 9.95 mg ml(-1) and a v(max) of 284 μM min(-1) . It shows a retention of 90% of its activity for at least 144 h of incubation at 40 °C and exhibits a range of optimum temperatures from 50 to 70 °C.
Lactoperoxidase catalyzes in vitro activation of acrylonitrile to cyanide.
Nasralla, Sherry N; Ghoneim, Asser I; Khalifa, Amani E; Gad, Mohamed Z; Abdel-Naim, Ashraf B
2009-12-15
Acrylonitrile (ACN) is a widely used industrial chemical. Although it is a well reported animal carcinogen, its current designation to humans is "possibly carcinogenic". The present study aimed at investigating the ability of LPO enzyme system to oxidize ACN to cyanide (CN(-)) in vitro. Detection of CN(-) served as a marker for the possible generation of free radical intermediates implicated in ACN induced toxicity in the activation process. Optimum conditions for the oxidation of ACN to CN(-) were characterized with respect to pH, temperature and time of incubation as well as ACN, LPO and H(2)O(2) concentrations in incubation mixtures. Maximum reaction velocity (V(max)) and Michaelis-Menten constant (K(m)) were assessed. Addition of nitrite (NO(2)(-)) salts to the reaction mixtures significantly enhanced the rate of the reaction. Free radical scavengers (quercetin and trolox C), LPO enzyme inhibitor (resorcinol) and competitors for LPO binding (sodium azide and indomethacin) were found to reduce the rate of CN(-) production. Inclusion of the sulfhydryl compounds glutathione (GSH), NAC (N-acetylcysteine), D-penicillamine or L-cysteine enhanced the rate of ACN oxidation. The present results demonstrate the ability of LPO enzyme system to oxidize ACN to CN(-) and provide insight for the elucidation of ACN chronic toxicity.
Acetylcholinesterase immobilized onto PEI-coated silica nanoparticles.
Tumturk, Hayrettin; Yüksekdag, Hazer
2016-01-01
Polyethyleneimine (PEI) coated-silica nanoparticles were prepared by the Stöber method. The formation and the structure of the nanoparticles were characterized by ATR-FT-IR spectroscopy and transmission electron microscopy (TEM). TEM images of the silica and PEI-coated nanoparticles revealed that they were well dispersed and that there was no agglomeration. The acetylcholineesterase enzyme was immobilized onto these nanoparticles. The effects of pH and temperature on the storage stability of the free and immobilized enzyme were investigated. The optimum pHs for free and immobilized enzymes were determined as 7.0 and 8.0, respectively. The optimum temperatures for free and immobilized enzymes were found to be 30.0 and 35.0°C, respectively. The maximum reaction rate (Vmax) and the Michaelis-Menten constant (Km) were investigated for the free and immobilized enzyme. The storage stability of acetylcholinesterase was increased when immobilized onto the novel PEI-coated silica nanoparticles. The reuse numbers of immobilized enzyme were also studied. These hybrid nanoparticles are desirable as carriers for biomedical applications.
Dadshahi, Zahra; Homaei, Ahmad; Zeinali, Farrokhzad; Sajedi, Reza H; Khajeh, Khosro
2016-07-01
A novel thermostable protease was purified from Penaeus vannamei from Persian Gulf to homogeneity level using ammonium sulfate precipitation and anion-exchange chromatography. The purified protease showed a single band on native and SDS-PAGE with a molecular weight of 24kDa on SDS-PAGE. The enzyme showed the broad highest catalytic activity for hydrolysis of the substrate with maximal activity at pH 7 and 80°C. Activity of the enzyme was inhibited by Hg(2+), Zn(2+) Co(2+) and Cu(2+), while protease activity was increased in the presence of Fe(2+) and Mn(2+) by factors of 173% and 102%, respectively. Enzyme shows a broad substrate specificity and hydrolyzes both natural and synthetic substrates. Based on the Michaelis-Menten plots, the Km with casein as substrate was 16.8μM and Vmax was 82.6μM/min. The enzyme, derived from L. vannamei, possesses unique characteristics and could be used in various industrial and biotechnological applications.
Kumar, Devendra; Ashfaque, Mohd; Muthukumar, M; Singh, Munna; Garg, Neelima
2012-01-01
Mango peel, a solid mango processing waste, comprises 15-20% of total fruit weight. This, being a rich source of lignocelluloses, was used as substrate for carboxymethyl cellulase (CMCase) production using Paenibacillus polymyxa. Maximum CMCase production (7.814 U mg(-1)) was observed in a medium containing 7% mango peel (w/v) with 1.5% ammonium sulphate (w/v) at 37 degrees C and pH 5.5. Purification to an extent of 28.24 fold was achieved by affinity column chromatography. Bands corresponding to 26.5 and 34.0 kDa molecular sizes were observed on 12% denaturing Sodium dodecyl sulphate-polyacrylamide gel electrophoresis (SDS-PAGE) while of 72 kDa on 10% non-denaturing Native-PAGE, proving its heteromeric multienzyme nature. The enzyme was stable over a range of 20-60 degrees C and pH of 4.0-7.5. Michaelis-Menten equation constant (Km and Vmax) values of purified CMCase were 8.73 mg ml(-1) and 17.805 mM ml(-1) min(-1), respectively.
Merchant, Mark; Mead, Stephanie; McAdon, Charles; McFatter, Justin; Wasilewski, Joe
2010-07-01
Serum from the American crocodile was assayed for dipeptidyl peptidase IV (DPP4) activity. We measured the DPP4-mediated hydrolysis of Ala-Pro-AFC. The generation of AFC was dependent on the titer of serum, with significant DPP4 activity (0.20 + or - 0.03 nmol product formed) measured using only 2 microL of crocodile serum, with maximum activity measured using 500 microL of serum. The hydrolysis of substrate was inhibited in a concentration-dependent manner by diprotin A, a specific inhibitor of DPP4 activity, indicating that this activity was due to the presence of DPP4. The crocodile serum DPP4 exhibited classical Michaelis-Menten kinetics, with K(m) and V(max) extrapolated, by double-reciprocal plot, to be 14.7 + or - 1.3 microM and 75.5 + or - 4.3 nmol/min, respectively. Crocodile DPP4 catalyzed the hydrolysis of Ala-Pro-AFC rapidly, with substantial activity measured within 5 min of the addition of substrate. After an initial rapid increase in activity, near maximal activity (7.43 + or - 0.24 nmol product formed) measured at 180 min. Crocodile serum DPP4 activity was temperature-dependent, with steadily increased activity from 5 to 40 degrees C.
Mukai, M; Tanaka, S; Yamamoto, K; Murata, M; Okada, K; Isobe, T; Shigeyama, M; Hichiya, H; Hanioka, N
2014-11-01
Propofol (2,6-diisopropylphenol) is intravenously administered for anesthetic induction and maintenance, and is rapidly metabolized into its glucuronide, mainly by UDP-glucuronosyltransferase 1A9 (UGT1A9). In this study, propofol glucuronidation by liver microsomes (HLM), intestinal microsomes (HIM) and kidney microsomes (HKM) of humans were examined. The expression of UGT1A9 protein in HLM, HIM and HKM was analyzed by immunoblotting. The staining band intensities for UGT1A9 of HIM and HKM were 12% and 119% those of HLM, respectively. The kinetics of propofol glucuronidation by HLM and HKM exhibited substrate inhibition, whereas the kinetics by HIM followed the Michaelis-Menten model. The K(m), V(max) and CL(int) values of HLM were 41.8 μM, 5.21 nmol/min/mg protein and 126 μl/min/mg protein, respectively. The K(m) value of HIM was significantly higher (6.7-fold) than that of HLM, and the V(max) and CL(int) values were significantly lower (56% and 8.3%, respectively) than those of HLM. The K(m) value of HKM was comparable to that of HLM, and the V(max) and CL(int) values were significantly higher (2.1- and 3.7-fold, respectively) than those of HLM, respectively. These findings suggest that UGT1A9 expressed in the kidney as well as in the liver plays an important role in propofol glucuronidation. The information gained in this study should contribute to an appropriate use of drugs metabolized by UGT1A9.
Poet, T S; Wu, H; Kousba, A A; Timchalk, C
2003-04-01
Chlorpyrifos (CPF) and diazinon (DZN) are thionophosphorus organophosphate (OP) insecticides; their toxicity is mediated through CYP metabolism to CPF-oxon and DZN-oxon, respectively. Conversely, CYPs also detoxify these OPs to trichloropyridinol (TCP) and 2-isopropyl-4-methyl-6-hydroxypyrimidine (IMHP), respectively. In addition, A-esterase (PON1) metabolism of CPF- and DZN-oxon also forms TCP and IMHP. This study evaluated the role intestinal and hepatic metabolism may play in both the activation and detoxification of CPF and DZN in Sprague-Dawley rats. Similar CYP- and PON1-mediated metabolic profiles were demonstrated in microsomes from liver or isolated intestinal enterocytes. The metabolic efficiency was estimated by calculating the psuedo-1st order rate constant from the metabolic constants by dividing Vmax/Km. In enterocyte microsomes, the CYP metabolic efficiency for metabolism to the oxon metabolites was approximately 28-fold greater for CPF than DZN. Compared on a per nmol P450 basis, the Vmax for CPF in enterocytes was approximately 2-3 times higher than in liver microsomes for the production of CPF-oxon and TCP. The Michaelis-Menten rate constant (Km) for the metabolism of CPF to CPF-oxon was comparable in liver and enterocyte microsomes; however, the enterocyte Km for TCP production was higher (indicating a lower affinity). The smaller volume of intestine, lower amount of CYP, and higher Km for TCP in the enterocyte microsomes, resulted in a lower catalytic efficiency (2 and 62 times) than in liver for oxon and TCP. PON1-mediated metabolism of CPF- and DZN-oxon was also demonstrated in liver and enterocyte microsomes. Although PON1 affinity for the substrates was comparable in hepatic and enterocytic microsomes, the Vmax were 48- to 275-fold higher, in the liver. These results suggest that intestinal metabolism may impact the metabolism of CPF and DZN, especially following low-dose oral exposures.
Muhammad Shahbaz Akhtar; Yoko Oki; Tadashi Adachi
2009-01-01
related to P influx: maximal transport rate (V_(max)), the Michaelis-Menten constant (K_m), and the external concentration when net uptake is zero (C_(min)) were tested in experiment 4. Lower K_m and C_(min) values were better indicative of the P-uptake ability of the class-Ⅰ cultivars, evidencing their adaptability to P-starved environmental cues. In experiment 5, class-Ⅰ cultivars exuded two- to threefold more carboxylates than class-Ⅱ cultivars under the P-stress environment. The amount and types of carboxylates exuded from the roots of P-starved plants differed from those of plants grown under P-sufficient conditions. Nevertheless, the exudation rate of both class-Ⅰ and class-Ⅱ cultivars decreased with time, and the highest exudation rate was found after the first 4 h of carboxylates collection. Higher P uptake by class-Ⅰ cultivars was significantly related to the drop in root medium pH, which can be ascribed to H~+-efflux from the roots supplied with sparingly soluble rock-P and Ca_3(PO_4)_2. These classical rescue strategies provided the basis of P-solubilization and acquisition from sparingly soluble P-sources by Brassica cultivars to thrive in a typically stressful environment.
Ibsen, Lars Bo; Liingaard, M.
2006-12-15
A lumped-parameter model represents the frequency dependent soil-structure interaction of a massless foundation placed on or embedded into an unbounded soil domain. In this technical report the steps of establishing a lumped-parameter model are presented. Following sections are included in this report: Static and dynamic formulation, Simple lumped-parameter models and Advanced lumped-parameter models. (au)
Redefining solubility parameters: the partial solvation parameters.
Panayiotou, Costas
2012-03-21
The present work reconsiders a classical and universally accepted concept of physical chemistry, the solubility parameter. Based on the insight derived from modern quantum chemical calculations, a new definition of solubility parameter is proposed, which overcomes some of the inherent restrictions of the original definition and expands its range of applications. The original single solubility parameter is replaced by four partial solvation parameters reflecting the dispersion, the polar, the acidic and the basic character of the chemical compounds as expressed either in their pure state or in mixtures. Simple rules are adopted for the definition and calculation of these four parameters and their values are tabulated for a variety of common substances. In contrast, however, to the well known Hansen solubility parameters, their design and evaluation does not rely exclusively on the basic rule of "similarity matching" for solubility but it makes also use of the other basic rule of compatibility, namely, the rule of "complementarity matching". This complementarity matching becomes particularly operational with the sound definition of the acidic and basic components of the solvation parameter based on the third σ-moments of the screening charge distributions of the quantum mechanics-based COSMO-RS theory. The new definitions are made in a simple and straightforward manner, thus, preserving the strength and appeal of solubility parameter stemming from its simplicity. The new predictive method has been applied to a variety of solubility data for systems of pharmaceuticals and polymers. The results from quantum mechanics calculations are critically compared with the results from Abraham's acid/base descriptors.
The effect of organic solvents on enzyme kinetic parameters of human CYP3A4 and CYP1A2 in vitro.
Rokitta, Dennis; Pfeiffer, Kay; Streich, Christina; Gerwin, Henrik; Fuhr, Uwe
2013-10-01
Abstract Enzyme kinetic parameters provide essential quantitative information about characterization of individual steps in drug metabolism. Such enzymes are located in a (partially) aqueous environment. For in vitro measurements potential lipophilic substrates regularly require organic solvents to achieve concentrations sufficient for access of the drug to the binding site of the enzyme. However, solvents may interact with the enzymes. In this study, we investigated the effects of methanol, ethanol, acetonitrile and dimethyl sulfoxide (1% to 4%) on the assessment of km, Vmax and Clint for the metabolism of midazolam via CYP3A4 to 1-hydroxymidazolam and the metabolism of caffeine to paraxanthine via CYP1A2 using expressed enzymes in vitro. The presence of acetonitrile proved the highest apparent Vmax value for paraxanthine formation but the lowest values for 1-hydroxymidazolam formation. The km value for midazolam showed no systematic effects of organic solvents, while for caffeine km was up to 8-fold lower for solvent free samples compared to solvent containing samples. The present example suggests that effects of solvents may considerably influence enzyme kinetic parameters beyond a mere change in apparent activity. These effects illustrate a difference for individual enzyme--substrate pairs, solvents, and solvent concentrations. What remains is the determination to which extent these effects compromise in vitro-in vivo extrapolations, and which solvents are most appropriate.
Kuby, S A; Roy, R N
1976-05-04
A systematic study has been made of the pH- and temperature-dependency of the steady-state kinetic parameters of the stabilized two-subunit enzyme species of glucose-6-phosphate dehydrogenase, in the absence of superimposed association-dissociation reactions. The Vmax(app) data obtained in several buffers between pH 5 and 10 and at 18-32 degrees C lead to the postulate that at least two sets of protonic equilibria may govern the catalysis (one near pH 5.7 AT 25 DEGREES C and another near pH 9.2); furthermore, two pathways for product formation (i.e., two Vmax's) appear to be required to explain the biphasic nature of the log Vmax(app) vs. pH curves, with Vmax(basic) greater than Vmax(acidic + neutral). Of the several buffers explored, either a uniform degree of interaction or a minimal degree of buffer species interaction could be assessed from the enthalpy changes associated with the derived values for ionization constants attributed to the protonic equilibria in the enzyme-substrates ternary complexes for the case of Tris-acetate-EDTA buffers, at constant ionic strength. With the selection of this buffer at 0.1 (T/2) and at 25 and 32 degrees C, a self-consistent kinetic mechanism has emerged which allows for the random binding of the two fully ionized substrates to the enzyme via two major pathways, and product formation by both E-A--B- and HE-A--B-. As before (Kuby et al. Arch. Biochem, Biophys. 165, 153-178, 1974), a quasi-equilibrium is presumed, with rate-limiting steps (k + 5 and k + 5') at the interconversion of the ternary complexes. Values for the two sets of protonic equilibria defined by this mechanism (viz., pKk, pKH2 for the first ionizations, and pKk', pKH' for the second) could then be estimated. From their numerical values (e.g., at 25 degrees C: pKK = 5.7 PKH2 = 5.2; and pKK' = 9.1, PKH' = 8.2) and from the values for delta H degrees ioniz (e.g., delta H degrees pKK APPROXIMATELY 5.1 KCAL/MOL; DELTA H degrees pKK' APPROXIMATELY 11 KCAL/MOL), A
Agbogbo Frank K
2010-03-01
Full Text Available Abstract Background Different mechanistic models have been used in the literature to describe the enzymatic hydrolysis of pretreated biomass. Although these different models have been applied to different substrates, most of these mechanistic models fit into two- and three-parameter mechanistic models. The purpose of this study is to compare the models and determine the activation energy and the enthalpy of adsorption of Trichoderma reesei enzymes on ammonia fibre explosion (AFEX-treated wheat straw. Experimental enzymatic hydrolysis data from AFEX-treated wheat straw were modelled with two- and three-parameter mechanistic models from the literature. In order to discriminate between the models, initial rate data at 49°C were subjected to statistical analysis (analysis of variance and scatter plots. Results For three-parameter models, the HCH-1 model best fitted the experimental data; for two-parameter models Michaelis-Menten (M-M best fitted the experimental data. All the three-parameter models fitted the data better than the two-parameter models. The best three models at 49°C (HCH-1, Huang and M-M were compared using initial rate data at three temperatures (35°, 42° and 49°C. The HCH-1 model provided the best fit based on the F values, the scatter plot and the residual sum of squares. Also, its kinetic parameters were linear in Arrhenius/van't Hoff's plots, unlike the other models. The activation energy (Ea is 47.6 kJ/mol and the enthalpy change of adsorption (ΔH is -118 kJ/mol for T. reesei enzymes on AFEX-treated wheat straw. Conclusion Among the two-parameter models, Michaelis-Menten model provided the best fit compared to models proposed by Humphrey and Wald. For the three-parameter models, HCH-1 provided the best fit because the model includes a fractional coverage parameter (ϕ which accounts for the number of reactive sites covered by the enzymes.
Hsyu, P H; Bowen, B; Tang-Liu, D
1994-07-01
The pharmacokinetics of AGN 190168, a novel synthetic retinoid, and its major metabolite, AGN 190299, in rat blood after intravenous administration was investigated. Approximately 4.4 mg kg-1 (high dose) or 0.49 mg kg-1 (low dose) of AGN 190168 was administered to rats via the femoral vein. Blood was collected from the femoral artery at various time points during an 8 h period. Blood concentrations of AGN 190168 and AGN 190299 were determined by a specific and sensitive high-pressure liquid chromatographic (HPLC) method. AGN 190168 was rapidly metabolized in rats. The only detectable drug-related species in the blood was AGN 190299. Therefore, only pharmacokinetics of AGN 190299 were calculated. Elimination of AGN 190299 appeared to be non-linear after administration of the high dose, and linear after administration of the low dose. The maximum elimination rate (Vmax) and the concentration at half of the Vmax (km), as estimated by a Michaelis-Menten one-compartment model, were 7.58 +/- 2.42 micrograms min-1 (mean +/- SD) and 6.10 +/- 1.58 micrograms mL-1, respectively. The value of the area under the blood concentration time curve (AUC) was 9.54 +/- 1.68 micrograms h mL-1 after administration of the high dose and 0.594 +/- 0.095 micrograms h mL-1 after administration of the low dose. The clearance value was 7.79 +/- 1.20 mL min-1 kg-1 after the high dose, statistically significantly different from that after the low dose (p AGN 190168 to AGN 190299, non-linear pharmacokinetics of AGN 190299 after the 4.4 mg kg-1 dose, and the lack of difference in disposition profiles between sexes after intravenous administration of AGN 190168 to rats.
Roles of quaternary structure and cysteine residues in the activity of human serine racemase
Wang Wei
2011-12-01
Full Text Available Abstract Background D-serine is an important coagonist at the NR1 subunit of the NMDA receptor class of glutamate receptors. It is chiefly synthesized in the CNS by serine racemase (SR. Regulation of SR activity is still poorly understood. As step toward developing reagents and methods for investigating SR in vitro, we analyzed structure-function relationships of a recombinant enzyme of human sequence. Results Michaelis-Menten kinetic analysis indicated a KM value of 14 mM and Vmax value of 3.66 μmol·mg-1·hr-1 when L-serine was used as a substrate for purified SR. Gel-filtration chromatography and protein cross-linking experiments revealed that dimer is the major oligomeric form of recombinant SR in aqueous solution, though the proportions of monomer, tetramer, and larger aggregates differed somewhat with the specific buffer used. These buffers also altered activity in a manner correlating with the relative abundance of dimer. Activity assays showed that the dimeric gel-filtration fraction held the highest activity. Chemical reduction with DTT increased the activity of SR by elevating Vmax; cystamine, a reagent that blocks sulfhydryl groups, abolished SR activity. Gel-filtration chromatography and western blot analysis indicated that DTT enhanced the recovery of noncovalent SR dimer. Conclusions These data suggest that SR is most active as a noncovalent dimer containing one or more free sulfhydryls in the enzyme's active center or a modulatory site. Buffer composition and reduction/oxidation status during preparation can dramatically impact interpretations of SR activity. These findings also highlight the possibility that SR is sensitive to oxidative stress in vivo.
Study on characteristics of polyphenol oxidase of Cucurbita pepo L.%西葫芦多酚氧化酶酶学特性研究
王国英; 董海洲; 王兆升; 刘传富
2012-01-01
The characteristics of polyphenol oxidase （PPO）of Cucurbita pepo L.and effect of various inhibitors to PPO were studied by spectrophotometer.The results showed that the optimum pH and temperature were 6.6 and 35℃. However,the PPQ was inactivated in 90℃ water for 5min.The kinetics of enzyme-catalyzed reaction of PPO was in accord with Michaelis-Menten equation,the Km, Vmax of kinetic equation were 0.0417mol/L,208.33U using catechol as substrate,respectively.Four kinds of inhibitors had different effects on PPO, and the order of PPO as NaHSO3〉 L-Cysteine 〉 ascorbic acid 〉 citric acid.%以邻苯二酚为底物，采用分光光度法对西葫芦多酚氧化酶（PPO）的酶学特性及不同抑制剂对多酚氧化酶活性的影响进行研究。结果表明，西葫芦多酚氧化酶最适pH为6．6，最适温度为35℃，90℃处理5rain可使该酶失活。多酚氧化酶催化的酶促褐变反应动力学符合米氏方程，动力学参数为Km=0．0417mol／L，Vmax=208．33U。四种抑制剂对PPO的抑制效果由强到弱依次为：亚硫酸氢钠〉L-半胱氨酸〉抗坏血酸〉柠檬酸。
Estimating Cosmological Parameter Covariance
Taylor, Andy
2014-01-01
We investigate the bias and error in estimates of the cosmological parameter covariance matrix, due to sampling or modelling the data covariance matrix, for likelihood width and peak scatter estimators. We show that these estimators do not coincide unless the data covariance is exactly known. For sampled data covariances, with Gaussian distributed data and parameters, the parameter covariance matrix estimated from the width of the likelihood has a Wishart distribution, from which we derive the mean and covariance. This mean is biased and we propose an unbiased estimator of the parameter covariance matrix. Comparing our analytic results to a numerical Wishart sampler of the data covariance matrix we find excellent agreement. An accurate ansatz for the mean parameter covariance for the peak scatter estimator is found, and we fit its covariance to our numerical analysis. The mean is again biased and we propose an unbiased estimator for the peak parameter covariance. For sampled data covariances the width estimat...
Lehmeier, C.; Ballantyne, F.; Billings, S. A.
2011-12-01
Soil microbes obtain resources from substrates exhibiting variation in structural complexity, carbon to nitrogen ratio (C:N), and energy requirements for decomposition. Theory of enzyme kinetics predicts that the activation energy required for substrate decomposition decreases with increasing temperature, and that the magnitude of the decrease increases with structural complexity of the substrate. However, the temperature sensitivity of important substrate-enzyme reactions at soil-relevant temperatures is largely unknown. Predicting soil organic matter (SOM) decay with rising temperature may be further complicated by changing microbial resource uptake due to 1) direct physiological responses to temperature shifts and 2) altered C and N availability imposed by changing patterns of enzymatic SOM decomposition. This could generate departures from expectations of the overall temperature response of SOM decay. Thus, quantification of both factors (changes in single reaction rates and in microbial community functioning) is important to understand the mechanisms governing soil-atmosphere CO2 fluxes with rising temperature. Here, we quantify the temperature sensitivity of substrate-enzyme pairings relevant to global soil biogeochemistry: (1) β-D-cellobioside (BC) and β-Glucosidase (BGase); (2) N-acetyl-β-D-glucosaminide (NAG) and β-N-Acetyl glucosaminidase (NAGase) and (3) 3,4-Dihydroxy-L-phenylalanine (L-Dopa) and peroxidase (representative of breakdown products of cellulose, chitin and lignin and associated enzymes, respectively). We assessed reaction rates of BC/BGase and NAG/NAGase with fluorophotometric techniques. Both pairings exhibited Michaelis-Menten-like kinetics. When neither enzyme nor substrate was limiting, maximum specific activity (Vmax) of BGase was 28 μmol h-1 unit -1 at 27 °C, approximately three orders of magnitude higher than NAGase (2.5 nmol h-1 unit-1 at 25 °C). Spectrophomometric measurements of L-Dopa degradation rates did not yield
Löppmann, Sebastian; Blagodatskaya, Evgenia; Kuzyakov, Yakov
2014-05-01
detritivore communities in the soil. The kinetics (Km and Vmax) of four extracellular hydrolytic enzymes responsible for C- and phosphorous-cycle (β-glucosidase, β-xylosidase, β-cellobiohydrolase and acid phosphatase), microbial biomass, basal respiration (BR) and substrate-induced respiration (SIR) were measured in rhizosphere, detritusphere and control from 0 - 10 and 10 - 20 cm. The metabolic quotient (qCO2) was calculated as specific indicator for efficiency of microbial substrate utilization. We observed clear differences in enzymes activities at low and high concentrations of substrate. At substrate saturation enzyme activity rates of were significantly higher in rooted plots compared to litter amended plots, whereas at lower concentration no treatment effect could be found. The BR, SIR and qCO2 values were significantly higher at 0 - 10 cm of the planted treatment compared to litter and control plots, revealing a significantly higher respiration at lower efficiency of microbial substrate utilization in the rhizosphere. The Michaelis-Menten constant (Km) decreased with depth, especially for β-glucosidase, acid phosphatase and β-xylosidase, indicating higher substrate affinity of microorganisms in deeper soil and therefore different enzyme systems functioning. The substrate affinity factor (Vmax/Km) increased 2-fold with depth for various enzymes, reflecting a switch of predominantly occurring microbial strategies. Vmax/Km ratio indicated relative domination of zymogenous microbial communities (r-strategists) in 0 - 10 cm depth as compared with 10 - 20 cm depth where the K-strategists dominated.
Ibsen, Lars Bo; Liingaard, Morten
A lumped-parameter model represents the frequency dependent soil-structure interaction of a massless foundation placed on or embedded into an unbounded soil domain. The lumped-parameter model development have been reported by (Wolf 1991b; Wolf 1991a; Wolf and Paronesso 1991; Wolf and Paronesso 19...
Saruwatari J
2014-04-01
Full Text Available Junji Saruwatari,1 Hiroo Nakashima,1 Shoko Tsuchimine,2 Miki Nishimura,1 Naoki Ogusu,1 Norio Yasui-Furukori21Division of Pharmacology and Therapeutics, Graduate School of Pharmaceutical Sciences, Kumamoto University, Kumamoto, Japan; 2Department of Neuropsychiatry, Graduate School of Medicine, Hirosaki University, Hirosaki, JapanAbstract: It has been suggested that the reduced function allele with reduced cytochrome P450 (CYP 2D6 activity, CYP2D6*10, is associated with the interindividual differences in the plasma paroxetine concentrations, but there is no data presently available regarding the influence of the CYP2D6*10 polymorphism on the pharmacokinetic parameters, eg, Michaelis–Menten constant (Km and maximum velocity (Vmax, in Asian populations. The present study investigated the effects of the CYP2D6 polymorphisms, including CYP2D6*10, on the pharmacokinetic parameters of paroxetine in Japanese patients with major depressive disorders. This retrospective study included 15 Japanese patients with major depressive disorders (four males and eleven females who were treated with paroxetine. The CYP2D6*2, CYP2D6*4, CYP2D6*5, CYP2D6*10, CYP2D6*18, CYP2D6*39, and CYP2D6*41 polymorphisms were evaluated. A total of 56 blood samples were collected from the patients. The Km and Vmax values of paroxetine were estimated for each patient. The allele frequencies of CYP2D6*2, CYP2D6*4, CYP2D6*5, CYP2D6*10, CYP2D6*18, CYP2D6*39, and CYP2D6*41 were 6.7%, 0%, 10.0%, 56.7%, 0%, 26.7%, and 0%, respectively. The mean values of Km and Vmax were 50.5±68.4 ng/mL and 50.6±18.8 mg/day, respectively. Both the Km and Vmax values were significantly smaller in CYP2D6*10 allele carriers than in the noncarriers (24.2±18.3 ng/mL versus 122.5±106.3 ng/mL, P=0.008; 44.2±16.1 mg/day versus 68.3±15.0 mg/day, P=0.022, respectively. This is the first study to demonstrate that the CYP2D6*10 polymorphism could affect the nonlinear pharmacokinetic parameter estimates of
Jens B. Hafke
2013-07-01
Full Text Available Apart from a few using cut aphid stylets, no attempts have been made thus far to measure in vivo sucrose-uptake properties of sieve elements. We investigated the kinetics of sucrose uptake by single sieve elements and phloem parenchyma cells in Vicia faba plants. To this end, microelectrodes were inserted into free-lying phloem cells in the main vein of the youngest fully-expanded leaf, half-way along the stem, in the transition zone between the autotrophic and heterotrophic part of the stem, and in the root axis. A top-to-bottom membrane potential gradient of sieve elements was observed along the stem (-130 mV to -110 mV, while the membrane potential of the phloem parenchyma cells was stable (approx. -100 mV. In roots, the membrane potential of sieve elements dropped abruptly to -55 mV. Bathing solutions having various sucrose concentrations were administered and sucrose/H+-induced depolarisations were recorded. Data analysis by nonlinear least-square data fittings as well as by linear Eadie-Hofstee (EH -transformations pointed at biphasic Michaelis-Menten kinetics (2 MM, EH: Km1 1.2-1.8 mM, Km2 6.6-9.0 mM of sucrose uptake by sieve elements. However, Akaike’s Information Criterion (AIC favoured single MM kinetics. Using single MM as the best-fitting model, Km values for sucrose uptake by sieve elements decreased along the plant axis from 1 to 7 mM. For phloem parenchyma cells, higher Km values (EH: Km1 10 mM, Km2 70 mM as compared to sieve elements were found. In preliminary patch-clamp experiments with sieve-element protoplasts, small sucrose-coupled proton currents (-0.1 to -0.3 pA/ pF were detected in the whole-cell mode. In conclusion (a Km values for sucrose uptake measured by electrophysiology are similar to those obtained with heterologous systems, (b electrophysiology provides a useful tool for in-situ determination of Km values, (c As yet, it remains unclear if one or two uptake systems are involved in sucrose uptake by sieve
Supersymmetry Parameter Analysis
Kalinowski, Jan
2002-01-01
Supersymmetric particles can be produced copiously at future colliders. From the high-precision data taken at e+e- linear colliders, TESLA in particular, and combined with results from LHC, and CLIC later, the low-energy parameters of the supersymmetric model can be determined. Evolving the parameters from the low-energy scale to the high-scale by means of renormalization group techniques the fundamental supersymmetry parameters at the high scale, GUT or Planck, can be reconstructed to reveal the origin of supersymmetry breaking.
Sannino, Francesco
2010-01-01
We propose a direct test of the existence of gauge duals for nonsupersymmetric asymptotically free gauge theories developing an infrared fixed point by computing the S-parameter in the electric and dual magnetic description. In particular we show that at the lower bound of the conformal window...... the magnetic S-parameter, i.e. the one determined via the dual magnetic gauge theory, assumes a simple expression in terms of the elementary magnetic degrees of freedom. The results further support our recent conjecture of the existence of a universal lower bound on the S parameter and indicates...
Threshold-dominated regulation hides genetic variation in gene expression networks
Plahte Erik
2007-12-01
Full Text Available Abstract Background In dynamical models with feedback and sigmoidal response functions, some or all variables have thresholds around which they regulate themselves or other variables. A mathematical analysis has shown that when the dose-response functions approach binary or on/off responses, any variable with an equilibrium value close to one of its thresholds is very robust to parameter perturbations of a homeostatic state. We denote this threshold robustness. To check the empirical relevance of this phenomenon with response function steepnesses ranging from a near on/off response down to Michaelis-Menten conditions, we have performed a simulation study to investigate the degree of threshold robustness in models for a three-gene system with one downstream gene, using several logical input gates, but excluding models with positive feedback to avoid multistationarity. Varying parameter values representing functional genetic variation, we have analysed the coefficient of variation (CV of the gene product concentrations in the stable state for the regulating genes in absolute terms and compared to the CV for the unregulating downstream gene. The sigmoidal or binary dose-response functions in these models can be considered as phenomenological models of the aggregated effects on protein or mRNA expression rates of all cellular reactions involved in gene expression. Results For all the models, threshold robustness increases with increasing response steepness. The CVs of the regulating genes are significantly smaller than for the unregulating gene, in particular for steep responses. The effect becomes less prominent as steepnesses approach Michaelis-Menten conditions. If the parameter perturbation shifts the equilibrium value too far away from threshold, the gene product is no longer an effective regulator and robustness is lost. Threshold robustness arises when a variable is an active regulator around its threshold, and this function is maintained by
Comparative kinetic analysis of two fungal β-glucosidases
Casanave Dominique
2010-02-01
Full Text Available Abstract Background The enzymatic hydrolysis of cellulose is still considered as one of the main limiting steps of the biological production of biofuels from lignocellulosic biomass. It is a complex multistep process, and various kinetic models have been proposed. The cellulase enzymatic cocktail secreted by Trichoderma reesei has been intensively investigated. β-glucosidases are one of a number of cellulolytic enzymes, and catalyze the last step releasing glucose from the inhibitory cellobiose. β-glucosidase (BGL1 is very poorly secreted by Trichoderma reesei strains, and complete hydrolysis of cellulose often requires supplementation with a commercial β-glucosidase preparation such as that from Aspergillus niger (Novozymes SP188. Surprisingly, kinetic modeling of β-glucosidases lacks reliable data, and the possible differences between native T. reesei and supplemented β-glucosidases are not taken into consideration, possibly because of the difficulty of purifying BGL1. Results A comparative kinetic analysis of β-glucosidase from Aspergillus niger and BGL1 from Trichoderma reesei, purified using a new and efficient fast protein liquid chromatography protocol, was performed. This purification is characterized by two major steps, including the adsorption of the major cellulases onto crystalline cellulose, and a final purification factor of 53. Quantitative analysis of the resulting β-glucosidase fraction from T. reesei showed it to be 95% pure. Kinetic parameters were determined using cellobiose and a chromogenic artificial substrate. A new method allowing easy and rapid determination of the kinetic parameters was also developed. β-Glucosidase SP188 (Km = 0.57 mM; Kp = 2.70 mM has a lower specific activity than BGL1 (Km = 0.38 mM; Kp = 3.25 mM and is also more sensitive to glucose inhibition. A Michaelis-Menten model integrating competitive inhibition by the product (glucose has been validated and is able to predict the
Non-steady state population kinetics of intravenous phenytoin.
Frame, B; Beal, S L
1998-08-01
This observational study explored the effects of demographics, sickness, and polypharmacy on the non-steady state population pharmacokinetics of intravenous phenytoin. One hundred fifteen patients were studied. Models were developed using the NONMEM program with hybrid first-order conditional estimation. A Michaelis-Menten model with delayed induction was preferred over a Michaelis-Menten model without induction, a Michaelis-Menten model with immediate induction, or a linear model with delayed induction. When the data were fit to a Michaelis-Menten model with delayed induction, the volume of distribution (Vd) was found to depend on weight and serum albumin. The Vd was estimated to be 0.95 l/kg, assuming an albumin level of 3 g/dl. The Michaelis-Menten constant (km) was estimated to be 7.9 mg/l. The baseline maximum metabolic rate was 580 mg/day for a 70-kg patient. The average time to onset of induction was 59.5 hours. If a fever developed after induction began, it increased the extent of induction. This model was evaluated retrospectively in 26 additional patients, yielding a mean prediction error of -0.4 mg/l (-3.0-2.2 mg/l) and a mean absolute prediction error of 4.7 mg/l (3.2-6.2 mg/l) based on two-level feedback. Given the large interindividual variances in maximum metabolic rate, phenytoin levels should be measured frequently.
Bridging Mechanistic and Phenomenological Models of Complex Biological Systems
Transtrum, Mark K.; Qiu, Peng
2016-01-01
The inherent complexity of biological systems gives rise to complicated mechanistic models with a large number of parameters. On the other hand, the collective behavior of these systems can often be characterized by a relatively small number of phenomenological parameters. We use the Manifold Boundary Approximation Method (MBAM) as a tool for deriving simple phenomenological models from complicated mechanistic models. The resulting models are not black boxes, but remain expressed in terms of the microscopic parameters. In this way, we explicitly connect the macroscopic and microscopic descriptions, characterize the equivalence class of distinct systems exhibiting the same range of collective behavior, and identify the combinations of components that function as tunable control knobs for the behavior. We demonstrate the procedure for adaptation behavior exhibited by the EGFR pathway. From a 48 parameter mechanistic model, the system can be effectively described by a single adaptation parameter τ characterizing the ratio of time scales for the initial response and recovery time of the system which can in turn be expressed as a combination of microscopic reaction rates, Michaelis-Menten constants, and biochemical concentrations. The situation is not unlike modeling in physics in which microscopically complex processes can often be renormalized into simple phenomenological models with only a few effective parameters. The proposed method additionally provides a mechanistic explanation for non-universal features of the behavior. PMID:27187545
Revisiting Cosmological parameter estimation
Prasad, Jayanti
2014-01-01
Constraining theoretical models with measuring the parameters of those from cosmic microwave background (CMB) anisotropy data is one of the most active areas in cosmology. WMAP, Planck and other recent experiments have shown that the six parameters standard $\\Lambda$CDM cosmological model still best fits the data. Bayesian methods based on Markov-Chain Monte Carlo (MCMC) sampling have been playing leading role in parameter estimation from CMB data. In one of the recent studies \\cite{2012PhRvD..85l3008P} we have shown that particle swarm optimization (PSO) which is a population based search procedure can also be effectively used to find the cosmological parameters which are best fit to the WMAP seven year data. In the present work we show that PSO not only can find the best-fit point, it can also sample the parameter space quite effectively, to the extent that we can use the same analysis pipeline to process PSO sampled points which is used to process the points sampled by Markov Chains, and get consistent res...
Parameter Estimation Through Ignorance
Du, Hailiang
2015-01-01
Dynamical modelling lies at the heart of our understanding of physical systems. Its role in science is deeper than mere operational forecasting, in that it allows us to evaluate the adequacy of the mathematical structure of our models. Despite the importance of model parameters, there is no general method of parameter estimation outside linear systems. A new relatively simple method of parameter estimation for nonlinear systems is presented, based on variations in the accuracy of probability forecasts. It is illustrated on the Logistic Map, the Henon Map and the 12-D Lorenz96 flow, and its ability to outperform linear least squares in these systems is explored at various noise levels and sampling rates. As expected, it is more effective when the forecast error distributions are non-Gaussian. The new method selects parameter values by minimizing a proper, local skill score for continuous probability forecasts as a function of the parameter values. This new approach is easier to implement in practice than alter...
Kitano, Ryuichiro; Motono, Ryuji; Nagai, Minoru
2016-12-01
It is often argued that the minimal supersymmetric standard model has O (100 ) free parameters, and the generic parameter region is already excluded by the null observation of the flavor and C P -violating processes as well as the constraints from the LHC experiments. This situation naturally leads us to consider the case where all the dangerous soft supersymmetry breaking terms, such as the scalar masses and scalar couplings, are absent, while only the unified gaugino mass term and the μ term are nonvanishing at the grand unification scale. We revisit this simple situation taking into account the observed Higgs boson mass, 125 GeV. Since the gaugino mass and the μ term are fixed in order to explain the Higgs boson and the Z boson masses, there is no free parameter left in this scenario. We find that there are three independent parameter sets that exist including ones which have not been discussed in the literature. We also find that the abundance of the dark matter can be explained by relic gravitinos which are nonthermally produced as decay products of the supersymmetry particles while satisfying constraints from big bang nucleosynthesis. We discuss the effects of the gravity mediation which generically gives a contribution to the soft terms of the order of the gravitino mass. It turns out that a newly found parameter set is preferable to explain the Higgs boson mass as well as the gravitino dark matter while satisfying the constraints from the electric dipole moments of the electron and the nucleon.
Fundamental stellar parameters
Wittkowski, M
2004-01-01
I present a discussion of fundamental stellar parameters and their observational determination in the context of interferometric measurements with current and future optical/infrared interferometric facilities. Stellar parameters and the importance of their determination for stellar physics are discussed. One of the primary uses of interferometry in the field of stellar physics is the measurement of the intensity profile across the stellar disk, both as a function of position angle and of wavelength. High-precision fundamental stellar parameters are also derived by characterizations of binary and multiple system using interferometric observations. This topic is discussed in detail elsewhere in these proceedings. Comparison of observed spectrally dispersed center-to-limb intensity variations with models of stellar atmospheres and stellar evolution may result in an improved understanding of key phenomena in stellar astrophysics such as the precise evolutionary effects on the main sequence, the evolution of meta...
Variations on tremor parameters
Boose, A.; Jentgens, Ch.; Spieker, S.; Dichgans, J.
1995-03-01
This paper describes our analysis procedure for long-term tremor EMG recordings, as well as three examples of applications. The description of the method focuses on how characteristics of the tremor (e.g. frequency, intensity, agonist-antagonist interaction) can be defined and calculated based on surface EMG data. The resulting quantitative characteristics are called ``tremor parameters.'' We discuss sinusoidally modulated, band-limited white noise as a model for pathological tremor-EMG, and show how the basic parameters can be extracted from this class of signals. The method is then applied to (1) estimate tremor severity in clinical studies, (2) quantify agonist-antagonist interaction, and (3) investigate the variations of the tremor parameters using simple methods from time-series analysis.
Optomechanical parameter estimation
Ang, Shan Zheng; Bowen, Warwick P; Tsang, Mankei
2013-01-01
We propose a statistical framework for the problem of parameter estimation from a noisy optomechanical system. The Cram\\'er-Rao lower bound on the estimation errors in the long-time limit is derived and compared with the errors of radiometer and expectation-maximization (EM) algorithms in the estimation of the force noise power. When applied to experimental data, the EM estimator is found to have the lowest error and follow the Cram\\'er-Rao bound most closely. With its ability to estimate most of the system parameters, the EM algorithm is envisioned to be useful for optomechanical sensing, atomic magnetometry, and classical or quantum system identification applications in general.
Fractal Self-Organization of Bacteria-Inspired Agents
Huang, Yufeng; Krumanocker, Ian; Coppens, Marc-Olivier
2012-06-01
We develop an agent-based model as a preliminary theoretical basis to guide the synthesis of a new class of materials with dynamic properties similar to bacterial colonies. Each agent in the model is representative of an individual bacterium capable of: the uptake of chemicals (nutrients), which are metabolized; active movement (part viscous, part diffusive), consuming metabolic energy; and cellular division, when agents have doubled in size. The agents grow in number and self-organize into fractal structures, depending on the rules that define the actions of the agents and the parameter values. The environment of the agents includes chemicals responsible for their growth and is described by a diffusion-reaction equation with Michaelis-Menten kinetics. These rules are modeled mathematically by a set of equations with five dimensionless groups that are functions of physical parameters. Simulations are performed for different parameter values. The resulting structures are characterized by their fractal scaling regime, box-counting and mass-radius dimensions, and lacunarity. Each parameter influences the overall structure in a unique way, generating a wide spectrum of structures. For certain combinations of parameter values, the model converges to a steady state, with a finite population of agents that no longer divide.
Generaux, Claudia N; Ainslie, Garrett R; Bridges, Arlene S; Ismail, Mohamed A; Boykin, David W; Tidwell, Richard R; Thakker, Dhiren R; Paine, Mary F
2013-02-01
DB868 [2,5-bis [5-(N-methoxyamidino)-2-pyridyl] furan], a prodrug of the diamidine DB829 [2,5-bis(5-amidino-2-pyridyl) furan], has demonstrated efficacy in murine models of human African trypanosomiasis. A cross-species evaluation of prodrug bioconversion to the active drug is required to predict the disposition of prodrug, metabolites, and active drug in humans. The phase I biotransformation of DB868 was elucidated using liver microsomes and sandwich-cultured hepatocytes from humans and rats. All systems produced four NADPH-dependent metabolites via O-demethylation (M1, M2) and N-dehydroxylation (M3, M4). Compartmental kinetic modeling of the DB868 metabolic pathway suggested an unusual N-demethoxylation reaction that was supported experimentally. A unienzyme Michaelis-Menten model described the kinetics of M1 formation by human liver microsomes (HLMs) (K(m), 11 μM; V(max), 340 pmol/min/mg), whereas a two-enzyme model described the kinetics of M1 formation by rat liver microsomes (RLMs) (K(m1), 0.5 μM; V(max1), 12 pmol/min/mg; K(m2), 27 μM; V(max2), 70 pmol/min/mg). Human recombinant CYP1A2, CYP3A4, and CYP4F2, rat recombinant Cyp1a2 and Cyp2d2, and rat purified Cyp4f1 catalyzed M1 formation. M2 formation by HLMs exhibited allosteric kinetics (S(50), 18 μM; V(max), 180 pmol/mg), whereas M2 formation by RLMs was negligible. Recombinant CYP1A2/Cyp1a2 catalyzed M2 formation. DB829 was detected in trace amounts in HLMs at the end of the 180-min incubation and was detected readily in sandwich-cultured hepatocytes from both species throughout the 24-h incubation. These studies demonstrated that DB868 biotransformation to DB829 is conserved between humans and rats. An improved understanding of species differences in the kinetics of DB829 formation would facilitate preclinical development of a promising antitrypanosomal prodrug.
Band parameters of phosphorene
Lew Yan Voon, L. C.; Wang, J.; Zhang, Y.;
2015-01-01
Phosphorene is a two-dimensional nanomaterial with a direct band-gap at the Brillouin zone center. In this paper, we present a recently derived effective-mass theory of the band structure in the presence of strain and electric field, based upon group theory. Band parameters for this theory...
Bentzen, J G; Forman, Julie Lyng; Pinborg, Anja;
2012-01-01
was observed between duration of hormonal-contraception use and ovarian reserve parameters. No dose-response relation was found between the dose of ethinyloestradiol and AMH or AFC. This study indicates that ovarian reserve markers are lower in women using sex steroids for contraception. Thus, AMH...
Response model parameter linking
Barrett, Michelle Derbenwick
2015-01-01
With a few exceptions, the problem of linking item response model parameters from different item calibrations has been conceptualized as an instance of the problem of equating observed scores on different test forms. This thesis argues, however, that the use of item response models does not require
Transport of L-carnitine in human corneal epithelial cells%左旋肉碱在人角膜缘上皮细胞的转运特性
李宝全; 毕建成; 安翠平; 李延峰; 许顺江
2015-01-01
Objective To investigate the characteristics of L-carnitine (LC)import into human corneal limbal epithelia (HCLE)cells,and to provide an experimental basis for further study of transport mechanism of LC in human ocular epithelium.Methods The transport of [3 H ]-L-carnitine was determined using the radio uptake assay and the apparent kinetic parameters of carnitine uptake by HCLE were estimated by nonlinear regression curve fitting according to the Michaelis-Menten equation.Results The uptake of LC into HCLE cells was saturable and time-dependent,and it also required the presence of Na+ in the external medium.An Eadie-Hofstee plot showed two distinct components:a high-and a low-affinity carnitine transport system in HCLE cells.The unlabelled LC and acetyl-L-carnitine competitively inhibited the uptake of [3 H]-L-carnitine by HCLE cells.Conclusion L-carnitine is transported into HCLE cells from tears by an active carrier mediated transport system and exerts its biological function.%目的：检测左旋肉碱（L-carnitine，LC）在人角膜缘上皮（human corneal limbal epithelia，HCLE）细胞的转运特性，为进一步阐明 HCLE细胞对 LC的转运机制提供实验依据。方法采用放射摄入实验检测 HCLE细胞对[3 H]-L-carnitine的转运功能，并利用米氏方程（Michaelis-Menten equation）分析计算其动力学参数。结果HCLE细胞对 LC的转运过程具有饱和性和时间依赖性，并且反应体系中需要 Na＋的存在。Eadie-Hofstee作图提示 HCLE细胞存在高亲和力和低亲合力2个肉碱转运系统。非标记 LC和乙酰化左旋肉碱可竞争性抑制[3 H]-L-carnitine的转运过程。结论 HCLE细胞可通过主动转运过程将泪液中的左旋肉碱摄入细胞内，发挥其生物学功能。
Caracterización y digestión anaerobia de las aguas de lavado del aceite de oliva virgen
Borja, R.
1993-04-01
Full Text Available A characterization and kinetic study of the anaerobic digestion of waters from washing of virgin olive oil were carried out. The experimental setup used consisted of a 1;litre thorough mixing bioreactor that was operated at 35 °C and loaded with sepiolite-immobilized biomass at a concentration of 10.8 g VSS/L. The bioreactor worked satisfactorily for a hydraulic retention time of 1.1 to 5.0 days and eliminated more than 92% of the initial COD in all instances.
Guiot's kinetic model was used to determine the macroenergetic parameters of the system, which was found to have a true yield coefficient for the biomass Y = 0.006 g VSS/g COD and a specific rate of substrate uptake for cell maintenance m = 0.072 g COD/g VSS ∙ day.
According to the experimental results obtained, the rate of substrate uptake, Rs (g COD/g VSS ∙ day, was correlated with the concentration of biodegradable substrate, Sb (g COD/L, through an equation of the Michaelis-Menten type.
Se ha efectuado la caracterización y un estudio cinético del proceso de digestión anaerobia de las aguas residuales obtenidas en el lavado del aceite de oliva virgen. El equipo experimental consta de un biorreactor de mezcla completa de 1 litro de volumen y opera a 35 °C con una concentración de biomasa de 10.8 g SSV/L inmovilizada sobre sepiolita. El biorreactor opera de modo satisfactorio en un rango de 5.0 a 1.1 días de tiempo de retención hidráulico, eliminando en todos los casos más del 92% de la DQO inicial.
Se comprueba el modelo cinético propuesto por Guiot y con el auxilio del mismo se determinan los parámetros macroenergéticos de este sistema: Y = 0.006 (g SSV/g DQO, coeficientes de rendimiento verdadero para la biomasa y m = 0.072 (g DQO/g SSV ∙ día, velocidad específica de consumo de sustrato para el mantenimiento celular.
Los datos experimentales obtenidos indican que la velocidad de consumo de sustrato Rs (g DQO/día ∙ g SSV se correlaciona con la
A.L.O. Ferreira
2000-12-01
Full Text Available This work presents a kinetic study of the side reactions of the ampicillin enzymatic synthesis, from phenylglycine methyl ester and 6-aminopenicillanic acid using penicillin G acylase immobilized on agarose. A Michaelis-Menten model with competitive inhibition was fitted to initial rates of ester and antibiotic hydrolysis, at pH 6.5 and 25ºC. Inherent kinetic parameters were estimated for low enzymatic loads, to assure that diffusional resistance was not important. It was observed that ampicillin inhibits the hydrolysis of PGME, but the inhibitory effect of the ester on ampicillin hydrolysis was almost negligible. The obtained parameters were: k cat1= 0.025 mM/UI min, Km1 = 155.4mM, K AE = 16.18mM, k cat2= 4.67x10-3 mM/UI min, Km2 = 11.47, K EA = 0.68 mM. Parameter values are in the range reported in the literature, except for Km1, which is much higher. The large confidence interval for this parameter denotes that the model presents low sensitivity with respect to it.
Cai, Shuangfei; Han, Qiusen; Qi, Cui; Lian, Zheng; Jia, Xinghang; Yang, Rong; Wang, Chen
2016-02-01
To extend the functionalities of two-dimensional graphene-like layered compounds as versatile materials, the modification of transition metal dichalcogenide nanosheets such as MoS2 with metal nanoparticles is of great and widespread interest. However, few studies are available on the preparation of bimetallic nanoparticles supported on MoS2. Herein, a facile and efficient method to synthesize MoS2-PtAg nanohybrids by decorating ultrathin MoS2 nanosheets with octahedral Pt74Ag26 alloy nanoparticles has been reported. The as-prepared MoS2-Pt74Ag26 nanohybrids were investigated as novel peroxidase mimics to catalyze the oxidation of classical peroxidase substrate 3,3',5,5'-tetramethylbenzidine (TMB) in the presence of H2O2, producing a blue colored reaction and exhibiting typical Michaelis-Menten kinetics. MoS2-Pt74Ag26 has a higher affinity for H2O2 than horseradish peroxidase (HRP) and a higher vmax value with TMB as the substrate than MoS2. The improved catalytic activity of hybrids for colorimetric reactions could be attributed to the synergistic effects of octahedral Pt74Ag26 nanoparticles and ultrathin MoS2 nanosheets as supports. Meanwhile, the generation of active oxygen species (&z.rad;OH) by H2O2 decomposition with MoS2-Pt74Ag26 was responsible for the oxidation of TMB. On the basis of these findings, a colorimetric method based on MoS2-Pt74Ag26 nanohybrids that is highly sensitive and selective was developed for glucose detection. Lower values of the limit of detection (LOD) were obtained, which is more sensitive than MoS2 nanosheets.To extend the functionalities of two-dimensional graphene-like layered compounds as versatile materials, the modification of transition metal dichalcogenide nanosheets such as MoS2 with metal nanoparticles is of great and widespread interest. However, few studies are available on the preparation of bimetallic nanoparticles supported on MoS2. Herein, a facile and efficient method to synthesize MoS2-PtAg nanohybrids by decorating
Distributed Parameter Modelling Applications
2011-01-01
Here the issue of distributed parameter models is addressed. Spatial variations as well as time are considered important. Several applications for both steady state and dynamic applications are given. These relate to the processing of oil shale, the granulation of industrial fertilizers and the d......Here the issue of distributed parameter models is addressed. Spatial variations as well as time are considered important. Several applications for both steady state and dynamic applications are given. These relate to the processing of oil shale, the granulation of industrial fertilizers...... sands processing. The fertilizer granulation model considers the dynamics of MAP-DAP (mono and diammonium phosphates) production within an industrial granulator, that involves complex crystallisation, chemical reaction and particle growth, captured through population balances. A final example considers...
Physical Parameter Eclipse Mapping
Vrielmann, S
2000-01-01
The tomographic method "Physical Parameter Eclipse Mapping" is a tool to reconstruct spatial distributions of physical parameters (like temperatures and surface densities) in accretion discs of cataclysmic variables. After summarizing the method, we apply it to multi-colour eclipse light curves of various dwarf novae and nova-likes like VZ Scl, IP Peg in outburst, UU Aqr, V2051 Oph and HT Cas in order to derive the temperatures (and surface densities) in the disc, the white dwarf temperature, the disc size, the effective temperatures and the viscosities. The results allows us to establish or refine a physical model for the accretion disc. Our maps of HT Cas and V2051 Oph, for example, indicate that the (quiescent) disc must be structured into a cool, optically thick inner disc sandwiched by hot, optically thin chromospheres. In addition, the disc of HT Cas must be patchy with a covering factor of about 40% caused by magnetic activity in the disc.
1999-01-01
We introduce a class of "inverse parametric optimization" problems, in which one is given both a parametric optimization problem and a desired optimal solution; the task is to determine parameter values that lead to the given solution. We describe algorithms for solving such problems for minimum spanning trees, shortest paths, and other "optimal subgraph" problems, and discuss applications in multicast routing, vehicle path planning, resource allocation, and board game programming.