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.
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.
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.
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.
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...
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.
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...
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…
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.
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.
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…
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…
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).
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 ...
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.
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.
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.
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...
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...
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 ...
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.
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…
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…
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…
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…
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.
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.
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.
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.
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).
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.
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.
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.
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.
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...
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.
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.
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.
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%).
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.
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.
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.
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
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.
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.
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.
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.
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
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.
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.
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.
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.
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.
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.
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.
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
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.
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.
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.
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…
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…
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…
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…
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.
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 ...
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.
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.
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.
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 ...
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.
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.
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.
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.
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…
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…
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.
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.
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.
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.
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.
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.
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.
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.
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).
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...
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...
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.
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…
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.
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 ...
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.
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...
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.
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.
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.
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...
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...
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...
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.
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...
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.
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…
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.
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
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.
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.
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.
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.)
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.)
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.
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.
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.
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.
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
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 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.
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.
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.
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.
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 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.
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.
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.
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.
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.
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.
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.
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.
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)).
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.
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.
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
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.
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.
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.
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...
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.
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.
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.
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.
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.
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.
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.
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
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.
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.
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.
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...
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...
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.
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
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.
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.
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.
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.
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.
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.
Kinetic modelling of coupled transport across biological membranes.
Korla, Kalyani; Mitra, Chanchal K
2014-04-01
In this report, we have modelled a secondary active co-transporter (symport and antiport), based on the classical kinetics model. Michaelis-Menten model of enzyme kinetics for a single substrate, single intermediate enzyme catalyzed reaction was proposed more than a hundred years ago. However, no single model for the kinetics of co-transport of molecules across a membrane is available in the literature We have made several simplifying assumptions and have followed the basic Michaelis-Menten approach. The results have been simulated using GNU Octave. The results will be useful in general kinetic simulations and modelling.
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.
The kinetics of denitrification in permeable sediments
Evrard, Victor; Glud, Ronnie N.; Cook, Perran L. M.
2013-01-01
on sediments taken from six shallow coastal sites in Port Phillip Bay, Victoria, Australia. The results showed that denitrification commenced rapidly (within 30 min) after the onset of anoxia and the kinetics could be well described by Michaelis-Menten kinetics with half saturation constants (apparent K...
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.
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.
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...
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
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.
Vosika, Z.; Mitić, V. V.; Vasić, A.; Lazović, G.; Matija, L.; Kocić, Lj. M.
2017-03-01
In this paper, Caputo based Michaelis-Menten kinetic model based on Time Scale Calculus (TSC) is proposed. The main reason for its consideration is a study of tumor cells population growth dynamics. In the particular case discrete-continuous time kinetics, Michaelis-Menten model is numerically treated, using a new algorithm proposed by authors, called multistep generalized difference transformation method (MSGDETM). In addition numerical simulations are performed and is shown that it represents the upgrade of the multi-step variant of generalized differential transformation method (MSGDTM). A possible conditions for its further development are discussed and possible experimental verification is described.
Maggi, F.M.; Riley, W.J.
2009-06-01
The theoretical formulation of biological kinetic reactions in isotopic applications often assume first-order or Michaelis-Menten-Monod kinetics under the quasi-steady-state assumption to simplify the system kinetics. However, isotopic e ects have the same order of magnitude as the potential error introduced by these simpli cations. Both formulations lead to a constant fractionation factor which may yield incorrect estimations of the isotopic effect and a misleading interpretation of the isotopic signature of a reaction. We have analyzed the isotopic signature of denitri cation in biogeochemical soil systems by Menyailo and Hungate [2006], where high {sup 15}N{sub 2}O enrichment during N{sub 2}O production and inverse isotope fractionation during N{sub 2}O consumption could not be explained with first-order kinetics and the Rayleigh equation, or with the quasi-steady-state Michaelis-Menten-Monod kinetics. When the quasi-steady-state assumption was relaxed, transient Michaelis-Menten-Monod kinetics accurately reproduced the observations and aided in interpretation of experimental isotopic signatures. These results may imply a substantial revision in using the Rayleigh equation for interpretation of isotopic signatures and in modeling biological kinetic isotope fractionation with first-order kinetics or quasi-steady-state Michaelis-Menten-Monod kinetics.
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.
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...
Baesjou, PJ; Driessen, WL; Challa, G; Reedijk, J
1999-01-01
The kinetics of the copper/N-methylimidazole catalysed oxidative coupling reaction with the C-O coupled dimer of 2,6-dimethylphenol (DMP or monomer), viz. 4-(2',6'-dimethylphenoxy)-2,6-dimethylphenol (dimer), as the substrate have been studied. The reaction was found to obey Michaelis-Menten
Marcus, Leanne; Plumeri, Julia; Baker, Gary M.; Miller, Jon S.
2013-01-01
A previously published classroom teaching method for helping students visualize and understand Michaelis-Menten kinetics (19) was used as an anticipatory set with high school and middle school science teachers in an Illinois Math and Science Partnership Program. As part of the activity, the teachers were asked to collect data by replicating the…
A Century of Enzyme Kinetic Analysis, 1913 to 2013
Johnson, Kenneth A.
2013-01-01
This review traces the history and logical progression of methods for quantitative analysis of enzyme kinetics from the 1913 Michaelis and Menten paper to the application of modern computational methods today. Following a brief review of methods for fitting steady state kinetic data, modern methods are highlighted for fitting full progress curve kinetics based upon numerical integration of rate equations, including a re-analysis of the original Michaelis-Menten full time course kinetic data. ...
Baesjou, PJ; Driessen, WL; Challa, G; Reedijk, J
1998-01-01
The influence of varying concentrations and ratios of phenol, base and copper on the copper/N-methylimidazole catalysed oxidative coupling of 2,6-dimethylphenol (DMP) has been studied. The reaction obeys simple Michaelis-Menten kinetics with respect to the phenol. The amount of DPQ formed during the
Baesjou, PJ; Driessen, WL; Challa, G; Reedijk, J
1998-01-01
The influence of varying concentrations and ratios of phenol, base and copper on the copper/N-methylimidazole catalysed oxidative coupling of 2,6-dimethylphenol (DMP) has been studied. The reaction obeys simple Michaelis-Menten kinetics with respect to the phenol. The amount of DPQ formed during the
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.
Emergence of Dynamic Cooperativity in the Stochastic Kinetics of Fluctuating Enzymes
Kumar, Ashutosh; Nandi, Mintu; Dua, Arti
2016-01-01
Dynamic cooperativity in monomeric enzymes is characterized in terms of a non-Michaelis-Menten kinetic behaviour. The latter is believed to be associated with mechanisms that include multiple reaction pathways due to enzymatic conformational fluctuations. Recent advances in single-molecule fluorescence spectroscopy have provided new fundamental insights on the possible mechanisms underlying reactions catalyzed by fluctuating enzymes. Here, we present a bottom-up approach to understand enzyme turnover kinetics at physiologically relevant mesoscopic concentrations informed by mechanisms extracted from single-molecule stochastic trajectories. The stochastic approach, presented here, shows the emergence of dynamic cooperativity in terms of a slowing down of the Michaelis-Menten (MM) kinetics resulting in negative cooperativity. For fewer enzymes, dynamic cooperativity emerges due to the combined effects of enzymatic conformational fluctuations and molecular discreteness. The increase in the number of enzymes, how...
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...
Stone, Andrew N; Mackenzie, Peter I; Galetin, Aleksandra; Houston, J Brian; Miners, John O
2003-09-01
Morphine elimination involves UDP-glucuronosyltransferase (UGT) catalyzed conjugation with glucuronic acid to form morphine 3- and 6-glucuronides (M3G and M6G, respectively). It has been proposed that UGT2B7 is the major enzyme involved in these reactions, but there is evidence to suggest that other isoforms also catalyze morphine glucuronidation in man. Thus, we have characterized the selectivity and kinetics of M3G and M6G formation by recombinant human UGTs. UGT 1A1, 1A3, 1A6, 1A8, 1A9, 1A10, and 2B7 all catalyzed M3G formation, but only UGT2B7 formed M6G. The kinetics of M3G formation by the UGT1A family isoforms was consistent with a single enzyme Michaelis-Menten model, with apparent Km values ranging from 2.6 to 37.4 mM. In contrast, M3G and M6G formation by UGT2B7 exhibited atypical kinetics. The atypical kinetics may be described by a model with high- and low-affinity Km values (0.42 and 8.3 mM for M3G, and 0.97 and 7.4 mM for M6G) from fitting to a biphasic Michaelis-Menten model. However, a multisite model with an interaction between two identical binding sites in a negative cooperative manner provides a more realistic approach to modeling these data. According to this model, the respective binding affinities (Ks) for M3G and M6G were 1.76 and 1.41 mM, respectively. These data suggest that M6G formation may be used as a selective probe for UGT2B7 activity, and morphine glucuronidation by UGT2B7 appears to involve the simultaneous binding of two substrate molecules, highlighting the need for careful analysis of morphine glucuronidation kinetics in vitro.
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.
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.
Kinetic Measurements for Enzyme Immobilization.
Cooney, Michael J
2017-01-01
Enzyme kinetics is the study of the chemical reactions that are catalyzed by enzymes, with a focus on their reaction rates. The study of an enzyme's kinetics considers the various stages of activity, reveals the catalytic mechanism of this enzyme, correlates its value to assay conditions, and describes how a drug or a poison might inhibit the enzyme. Victor Henri initially reported that enzyme reactions were initiated by a bond between the enzyme and the substrate. By 1910, Michaelis and Menten were advancing their work by studying the kinetics of an enzyme saccharase which catalyzes the hydrolysis of sucrose into glucose and fructose. They published their analysis and ever since the Michaelis-Menten equation has been used as the standard to describe the kinetics of many enzymes. Unfortunately, soluble enzymes must generally be immobilized to be reused for long times in industrial reactors. In addition, other critical enzyme properties have to be improved like stability, activity, inhibition by reaction products, and selectivity towards nonnatural substrates. Immobilization is by far the chosen process to achieve these goals.Although the Michaelis-Menten approach has been regularly adapted to the analysis of immobilized enzyme activity, its applicability to the immobilized state is limited by the barriers the immobilization matrix places upon the measurement of compounds that are used to model enzyme kinetics. That being said, the estimated value of the Michaelis-Menten coefficients (e.g., V max, K M) can be used to evaluate effects of immobilization on enzyme activity in the immobilized state when applied in a controlled manner. In this review enzyme activity and kinetics are discussed in the context of the immobilized state, and a few novel protocols are presented that address some of the unique constraints imposed by the immobilization barrier.
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.
Innovative first order elimination kinetics working model for easy learning
Navin Budania
2016-06-01
Conclusions: First order elimination kinetics is easily understood with the help of above working model. More and more working models could be developed for teaching difficult topics. [Int J Basic Clin Pharmacol 2016; 5(3.000: 862-864
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
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.
A Century of Enzyme Kinetic Analysis, 1913 to 2013
Johnson, Kenneth A.
2013-01-01
This review traces the history and logical progression of methods for quantitative analysis of enzyme kinetics from the 1913 Michaelis and Menten paper to the application of modern computational methods today. Following a brief review of methods for fitting steady state kinetic data, modern methods are highlighted for fitting full progress curve kinetics based upon numerical integration of rate equations, including a re-analysis of the original Michaelis-Menten full time course kinetic data. Finally, several illustrations of modern transient state kinetic methods of analysis are shown which enable the elucidation of reactions occurring at the active sites of enzymes in order to relate structure and function. PMID:23850893
A century of enzyme kinetic analysis, 1913 to 2013.
Johnson, Kenneth A
2013-09-02
This review traces the history and logical progression of methods for quantitative analysis of enzyme kinetics from the 1913 Michaelis and Menten paper to the application of modern computational methods today. Following a brief review of methods for fitting steady state kinetic data, modern methods are highlighted for fitting full progress curve kinetics based upon numerical integration of rate equations, including a re-analysis of the original Michaelis-Menten full time course kinetic data. Finally, several illustrations of modern transient state kinetic methods of analysis are shown which enable the elucidation of reactions occurring at the active sites of enzymes in order to relate structure and function.
Salivary paracetamol elimination kinetics during the menstrual cycle.
Somaja, L; Thangam, J
1987-01-01
Studies were done to examine the influence of the menstrual cycle on the elimination kinetics of paracetamol. Salivary concentrations of paracetamol were determined after oral administration of 1 g of paracetamol on day 3, 10, 14, 20 and 25 of the menstrual cycle in normal healthy women volunteers with regular menstrual cycles. There was no significant difference in elimination half-life (t 1/2) or metabolic clearance rate (CL) between the various days of the menstrual cycle. The result sugge...
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.
A kinetic model for the penicillin biosynthetic pathway in
Nielsen, Jens; Jørgensen, Henrik
1996-01-01
A kinetic model for the first two steps in the penicillin biosynthetic pathway, i.e. the ACV synthetase (ACVS) and the isopenicillin N synthetase (IPNS) is proposed. The model is based on Michaelis-Menten type kinetics with non-competitive inhibition of the ACVS by ACV, and competitive inhibition...... of the IPNS by glutathione. The model predicted flux through the pathway corresponds well with the measured rate of penicillin biosynthesis. From the kinetic model the elasticity coefficients and the flux control coefficients are calculated throughout a fed-batch cultivation, and it is found...
Avalos Ramirez, Antonio; Bénard, Sandrine; Giroir-Fendler, Anne; Jones, J Peter; Heitz, Michèle
2008-11-25
The kinetics of microbial growth and the biodegradation of methanol and toluene in (a) biofilters (BFs), and (b) biotrickling filters (BTFs), packed with inert materials, has been studied and analyzed. The specific growth rate, mu, for the treatment of methanol was 0.037h(-1) for a wide range of operating conditions. In the BF, mu was found to be a function of the methanol and toluene concentrations in the biofilm. In the BF used for treating methanol, mu was found to be affected by (1) the nitrogen concentration present in the nutrient solution, and (2) the kind of packing material employed. The kinetics of the methanol and toluene biodegradations were also analyzed using "mixed order" models. A Michaelis-Menten model type provided a good fit for the elimination capacity (EC) of the BTF treating methanol, while a Haldane model type provided a good fit to the EC of the BF treating methanol and toluene. The carbon dioxide production rate was related to the packed bed temperature and the content of the volatile solids within the biofilm. For the BF, the ratio of temperature/carbon dioxide production rate (PCO(2)) was 0.024 degrees C per unit of PCO(2), and for the BTF it was 0.15 degrees C per unit of PCO(2).
Santos, E.G. [Universidade Federal de Campina Grande, PB (Brazil). Programa de Recursos Humanos da ANP, PRH-25]. E-mail: elbagomes@uol.com.br; Alsina, O.L.S.; Silva, F.L.H. [Universidade Federal de Campina Grande, PB (Brazil). Centro de Ciencias e Tecnologia. Dept. de Engenharia Quimica]. E-mail: odelsia@deq.ufpb.br; flhs@deq.ufpb.br
2003-07-01
During the petroleum exploration and production processes, a great amount of water is produced together with the oil and the natural gas. This water needs an appropriate treatment before been discarded or reuse, due to a their great amount of organic pollutants content. Several separation processes are used in order to improve the effluent quality. In this way, the research of new adsorbent materials that present a low industrial cost has great importance. In this paper, adsorption experiments of organic pollutants using as adsorbent, the corn-cob, the powder wood and the coconut mesocarp, were accomplished. The organic effluent used in this work was simulated by a dispersion of gas in water and the experimental data were obtained through experiments in an agitated reactor. The kinetic curve was been adjusted for Michaelis-Menten equation and equilibrium isotherm modeling with Langmuir isotherm. Both model fitted well the experimental data. The obtained results show the viability of the use of the biomass as adsorbents for organic pollutants, once, with appropriate amounts of the gas/biomass, it was possible to eliminate, practically, the whole pollutant. (author)
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.
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.
Kinetics and specificity of paternal mitochondrial elimination in Caenorhabditis elegans
Wang, Yang; Zhang, Yi; Chen, Lianwan; Liang, Qian; Yin, Xiao-Ming; Miao, Long; Kang, Byung-Ho; Xue, Ding
2016-01-01
In most eukaryotes, mitochondria are inherited maternally. The autophagy process is critical for paternal mitochondrial elimination (PME) in Caenorhabditis elegans, but how paternal mitochondria, but not maternal mitochondria, are selectively targeted for degradation is poorly understood. Here we report that mitochondrial dynamics have a profound effect on PME. A defect in fission of paternal mitochondria delays PME, whereas a defect in fusion of paternal mitochondria accelerates PME. Surprisingly, a defect in maternal mitochondrial fusion delays PME, which is reversed by a fission defect in maternal mitochondria or by increasing maternal mitochondrial membrane potential using oligomycin. Electron microscopy and tomography analyses reveal that a proportion of maternal mitochondria are compromised when they fail to fuse normally, leading to their competition for the autophagy machinery with damaged paternal mitochondria and delayed PME. Our study indicates that mitochondrial dynamics play a critical role in regulating both the kinetics and the specificity of PME. PMID:27581092
Kinetics and specificity of paternal mitochondrial elimination in Caenorhabditis elegans.
Wang, Yang; Zhang, Yi; Chen, Lianwan; Liang, Qian; Yin, Xiao-Ming; Miao, Long; Kang, Byung-Ho; Xue, Ding
2016-09-01
In most eukaryotes, mitochondria are inherited maternally. The autophagy process is critical for paternal mitochondrial elimination (PME) in Caenorhabditis elegans, but how paternal mitochondria, but not maternal mitochondria, are selectively targeted for degradation is poorly understood. Here we report that mitochondrial dynamics have a profound effect on PME. A defect in fission of paternal mitochondria delays PME, whereas a defect in fusion of paternal mitochondria accelerates PME. Surprisingly, a defect in maternal mitochondrial fusion delays PME, which is reversed by a fission defect in maternal mitochondria or by increasing maternal mitochondrial membrane potential using oligomycin. Electron microscopy and tomography analyses reveal that a proportion of maternal mitochondria are compromised when they fail to fuse normally, leading to their competition for the autophagy machinery with damaged paternal mitochondria and delayed PME. Our study indicates that mitochondrial dynamics play a critical role in regulating both the kinetics and the specificity of PME.
Modeling uptake kinetics of cadmium by field-grown lettuce
Chen Weiping [Department of Environmental Sciences, University of California, 900 University Avenue, Riverside, CA 92521 (United States)], E-mail: chenweip@yahoo.com.cn; Li Lianqing [Institute of Resources, Ecosystem and Environment of Agriculture, Nanjing Agricultural University, Nanjing 210095 (China); Chang, Andrew C.; Wu Laosheng [Department of Environmental Sciences, University of California, 900 University Avenue, Riverside, CA 92521 (United States); Kwon, Soon-Ik [Agricultural Environmental and Ecology Division, National Institute of Agricultural Science and Technology, Suwon 441-707 (Korea, Republic of); Bottoms, Rick [Desert Research and Extension Center, 1004 East Holton Road, El Centro, CA 92243 (United States)
2008-03-15
Cadmium uptake by field grown Romaine lettuce treated with P-fertilizers of different Cd levels was investigated over an entire growing season. Results indicated that the rate of Cd uptake at a given time of the season can be satisfactorily described by the Michaelis-Menten kinetics, that is, plant uptake increases as the Cd concentration in soil solution increases, and it gradually approaches a saturation level. However, the rate constant of the Michaelis-Menten kinetics changes over the growing season. Under a given soil Cd level, the cadmium content in plant tissue decreases exponentially with time. To account for the dynamic nature of Cd uptake, a kinetic model integrating the time factor was developed to simulate Cd plant uptake over the growing season: C{sub Plant} = C{sub Solution} . PUF{sub max} . exp[-b . t], where C{sub Plant} and C{sub Solution} refer to the Cd content in plant tissue and soil solution, respectively, PUF{sub max} and b are kinetic constants. - A kinetic model was developed to evaluate the uptake of Cd under field conditions.
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
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.
Sivuk, V F; Rusina, I M; Luchko, T A; Makarchikov, A F
2008-01-01
Soluble nucleoside triphosphatase differing in its properties from all known proteins with NTPase activity was partially purified from bovine kidneys. The enzyme has pH optimum of 7.5, molecular mass of 60 kDa, as estimated by gel chromatography, and shows an absolute dependence on divalent metal ions. NTPase obeyed Michaelis-Menten kinetics in the range of substrate concentration tested from 45 to 440 microM; the apparent Km for inosine-5'-triphosphate was calculated to be 23.3 microM. The enzyme was found to possess a broad substrate specificity, being capable of hydrolyzing various nucleoside-5'-tri- as well as diphosphates.
Lipase-catalyzed ethanolysis of fish oils: multi-response kinetics.
Torres, Carlos F; Moeljadi, Marlina; Hill, Charles G
2003-08-05
The kinetics of the lipase-catalyzed (Pseudomonas cepacia) ethanolysis of fish oil has been studied in a batch reactor using menhaden oil, tuna oil, and acylglycerol mixtures derived from menhaden oil. Multi-response models derived from a generalized Michaelis-Menten mechanism were developed to describe the rates of formation of ethyl esters of the primary fatty acids present in the precursor oil. A first-order model for deactivation of the lipase was fit simultaneously to one of the data sets.
Biochemical kinetics in changing volumes.
Pawłowski, Piotr H; Zielenkiewicz, Piotr
2004-01-01
The need of taking into account the change of compartment volume when developing chemical kinetics analysis inside the living cell is discussed. Literature models of a single enzymatic Michaelis-Menten process, glycolytic oscillations, and mitotic cyclin oscillations were tested with appropriate theoretical extension in the direction of volume modification allowance. Linear and exponential type of volume increase regimes were compared. Due to the above, in a growing cell damping of the amplitude, phase shift, and time pattern deformation of the metabolic rhythms considered were detected, depending on the volume change character. The performed computer simulations allow us to conclude that evolution of the cell volume can be an essential factor of the chemical kinetics in a growing cell. The phenomenon of additional metabolite oscillations caused by the periodic cell growth and division was theoretically predicted and mathematically described. Also, the hypothesis of the periodized state in the growing cell as the generalization of the steady-state was formulated.
Emergence of dynamic cooperativity in the stochastic kinetics of fluctuating enzymes.
Kumar, Ashutosh; Chatterjee, Sambarta; Nandi, Mintu; Dua, Arti
2016-08-28
Dynamic co-operativity in monomeric enzymes is characterized in terms of a non-Michaelis-Menten kinetic behaviour. The latter is believed to be associated with mechanisms that include multiple reaction pathways due to enzymatic conformational fluctuations. Recent advances in single-molecule fluorescence spectroscopy have provided new fundamental insights on the possible mechanisms underlying reactions catalyzed by fluctuating enzymes. Here, we present a bottom-up approach to understand enzyme turnover kinetics at physiologically relevant mesoscopic concentrations informed by mechanisms extracted from single-molecule stochastic trajectories. The stochastic approach, presented here, shows the emergence of dynamic co-operativity in terms of a slowing down of the Michaelis-Menten (MM) kinetics resulting in negative co-operativity. For fewer enzymes, dynamic co-operativity emerges due to the combined effects of enzymatic conformational fluctuations and molecular discreteness. The increase in the number of enzymes, however, suppresses the effect of enzymatic conformational fluctuations such that dynamic co-operativity emerges solely due to the discrete changes in the number of reacting species. These results confirm that the turnover kinetics of fluctuating enzyme based on the parallel-pathway MM mechanism switches over to the single-pathway MM mechanism with the increase in the number of enzymes. For large enzyme numbers, convergence to the exact MM equation occurs in the limit of very high substrate concentration as the stochastic kinetics approaches the deterministic behaviour.
Emergence of dynamic cooperativity in the stochastic kinetics of fluctuating enzymes
Kumar, Ashutosh; Chatterjee, Sambarta; Nandi, Mintu; Dua, Arti
2016-08-01
Dynamic co-operativity in monomeric enzymes is characterized in terms of a non-Michaelis-Menten kinetic behaviour. The latter is believed to be associated with mechanisms that include multiple reaction pathways due to enzymatic conformational fluctuations. Recent advances in single-molecule fluorescence spectroscopy have provided new fundamental insights on the possible mechanisms underlying reactions catalyzed by fluctuating enzymes. Here, we present a bottom-up approach to understand enzyme turnover kinetics at physiologically relevant mesoscopic concentrations informed by mechanisms extracted from single-molecule stochastic trajectories. The stochastic approach, presented here, shows the emergence of dynamic co-operativity in terms of a slowing down of the Michaelis-Menten (MM) kinetics resulting in negative co-operativity. For fewer enzymes, dynamic co-operativity emerges due to the combined effects of enzymatic conformational fluctuations and molecular discreteness. The increase in the number of enzymes, however, suppresses the effect of enzymatic conformational fluctuations such that dynamic co-operativity emerges solely due to the discrete changes in the number of reacting species. These results confirm that the turnover kinetics of fluctuating enzyme based on the parallel-pathway MM mechanism switches over to the single-pathway MM mechanism with the increase in the number of enzymes. For large enzyme numbers, convergence to the exact MM equation occurs in the limit of very high substrate concentration as the stochastic kinetics approaches the deterministic 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.
Ordens não inteiras em cinética química Non-integer orders in chemical kinetics
André P. Oliveira
2010-01-01
Full Text Available Starting from zero-, first-, and second-order integrated laws for chemical kinetics, some cases are shown which produce fractional orders. Taking the Michaelis-Menten mechanism as a first example, it is shown that substrate order can go from 1 to zero, depending on relative concentration of enzyme and substrate. Using other examples which show fractional orders higher than one and even negative (inhibition, it is shown that the presence of an equilibrium before or parallel to the rate determining step can be the reason for fractional orders, which is an indication of a more complex mechanism.
Transport Reversal during Heteroexchange: A Kinetic Study
V. Makarov
2013-01-01
Full Text Available It is known that secondary transporters, which utilize transmembrane ionic gradients to drive their substrates up a concentration gradient, can reverse the uptake and instead release their substrates. Unfortunately, the Michaelis-Menten kinetic scheme, which is popular in transporter studies, does not include transporter reversal, and it completely neglects the possibility of equilibrium between the substrate concentrations on both sides of the membrane. We have developed a complex two-substrate kinetic model that includes transport reversal. This model allows us to construct analytical formulas allowing the calculation of a “heteroexchange” and “transacceleration” using standard Michaelis coefficients for respective substrates. This approach can help to understand how glial and other cells accumulate substrates without synthesis and are able to release such substrates and gliotransmitters.
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 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.
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.
QE+QSS for Derivation of Kinetic Equations and Stiffness Removing
Gorban, A N
2010-01-01
We present the general formalism of the Quasiequilibrium approximation (QE) with the proof of the persistence of entropy production in the QE approximation. We demonstrate, how to apply this formalism to chemical kinetics and describe the difference between QE and Quasi--Steady--State (QSS) approximations. The celebrated QSS "Michaelis--Menten" kinetics is, as a matter of fact, the "Briggs-Haldane" kinetics. Michaelis and Menten used the QE assumption that all intermediate complexes are in fast equilibrium with free substrates and enzyme. Similar approach was developed by Stuekelberg (1952) for the Boltzmann kinetics. Following them, we combine the QE (fast equilibria) and the QSS (small amounts) approaches and study the general kinetics with fast intermediates present in small amount. We prove the representation of the rate of an elementary reaction as a product of the Boltzmann factor (purely thermodynamic) and the kinetic factor, and found the basic relations between kinetic factors. In the practice of mod...
Michaëlis--Menten kinetics of phenazone elimination in the perfused pig liver
Andreasen, B; Tonnesen, K; Rabol, A;
1977-01-01
followed saturation kinetics (concentrations 0.1-12 mmol x 1(-1) and the maximal elimination rate (Vmax) was on average 102 mumol x min-1 x kg-1 liver and the Michaëlis-constant (Km) of 2.6 mmol x 1(-1). Estimates of Vmax and Km for the microsomal phenazone hydroxylase activity measured in liver biopsies......The purpose of the present study was to define the elimination kinetics of phenazone (NFN) in the isolated perfused pig liver. In five experiments phenazone was administered as constant infusion to obtain steady-state periods over a wide range of concentrations. The elimination of phenazone...... found to be considerably lower than in the perfused liver. The hepatic elimination of phenazone during perfusion of pig liver at phenazone concentrations corresponding to human therapeutic doses follows first-order kinetics....
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.
Modelling atypical CYP3A4 kinetics: principles and pragmatism.
Houston, J Brian; Galetin, Aleksandra
2005-01-15
The Michaelis-Menten model, and the existence of a single active site for the interaction of substrate with drug metabolizing enzyme, adequately describes a substantial number of in vitro metabolite kinetic data sets for both clearance and inhibition determination. However, in an increasing number of cases (involving most notably, but not exclusively, CYP3A4), atypical kinetic features are observed, e.g., auto- and heteroactivation; partial, cooperative, and substrate inhibition; concentration-dependent effector responses (activation/inhibition); limited substrate substitution and inhibitory reciprocity necessitating sub-group classification. The phenomena listed above cannot be readily interpreted using single active site models and the literature indicates that three types of approaches have been adopted. First the 'nai ve' approach of using the Michaelis-Menten model regardless of the kinetic behaviour, second the 'empirical' approach (e.g., employing the Hill or uncompetitive inhibition equations to model homotropic phenomena of sigmoidicity and substrate inhibition, respectively) and finally, the 'mechanistic' approach. The later includes multisite kinetic models derived using the same rapid equilibrium/steady-state assumptions as the single-site model. These models indicate that 2 or 3 binding sites exist for a given CYP3A4 substrate and/or effector. Multisite kinetic models share common features, depending on the substrate kinetics and the nature of the effector response observed in vitro, which allow a generic model to be proposed. Thus although more complex than the other two approaches, they show more utility and can be comprehensively applied in relatively simple versions that can be readily generated from generic model. Multisite kinetic features, observed in isolated hepatocytes as well as in microsomes from hepatic tissue and heterologous expression systems, may be evident in substrate depletion-time profiles as well as in metabolite formation rates
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.
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.
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.
Multiple alternative substrate kinetics.
Anderson, Vernon E
2015-11-01
The specificity of enzymes for their respective substrates has been a focal point of enzyme kinetics since the initial characterization of metabolic chemistry. Various processes to quantify an enzyme's specificity using kinetics have been utilized over the decades. Fersht's definition of the ratio kcat/Km for two different substrates as the "specificity constant" (ref [7]), based on the premise that the important specificity existed when the substrates were competing in the same reaction, has become a consensus standard for enzymes obeying Michaelis-Menten kinetics. The expansion of the theory for the determination of the relative specificity constants for a very large number of competing substrates, e.g. those present in a combinatorial library, in a single reaction mixture has been developed in this contribution. The ratio of kcat/Km for isotopologs has also become a standard in mechanistic enzymology where kinetic isotope effects have been measured by the development of internal competition experiments with extreme precision. This contribution extends the theory of kinetic isotope effects to internal competition between three isotopologs present at non-tracer concentrations in the same reaction mix. This article is part of a special issue titled: Enzyme Transition States from Theory and Experiment.
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.
Spectral Quasi-Equilibrium Manifold for Chemical Kinetics.
Kooshkbaghi, Mahdi; Frouzakis, Christos E; Boulouchos, Konstantinos; Karlin, Iliya V
2016-05-26
The Spectral Quasi-Equilibrium Manifold (SQEM) method is a model reduction technique for chemical kinetics based on entropy maximization under constraints built by the slowest eigenvectors at equilibrium. The method is revisited here and discussed and validated through the Michaelis-Menten kinetic scheme, and the quality of the reduction is related to the temporal evolution and the gap between eigenvalues. SQEM is then applied to detailed reaction mechanisms for the homogeneous combustion of hydrogen, syngas, and methane mixtures with air in adiabatic constant pressure reactors. The system states computed using SQEM are compared with those obtained by direct integration of the detailed mechanism, and good agreement between the reduced and the detailed descriptions is demonstrated. The SQEM reduced model of hydrogen/air combustion is also compared with another similar technique, the Rate-Controlled Constrained-Equilibrium (RCCE). For the same number of representative variables, SQEM is found to provide a more accurate description.
Variable elimination in chemical reaction networks with mass-action kinetics
Feliu, Elisenda; Wiuf, C.
2012-01-01
We consider chemical reaction networks taken with mass-action kinetics. The steady states of such a system are solutions to a system of polynomial equations. Even for small systems the task of finding the solutions is daunting. We develop an algebraic framework and procedure for linear elimination...
Kinetics and mechanism of the oxidation of formic and oxalic acids by quinolinium fluorochromate
Madhu Khurana; Pradeep K Sharma; Kalyan K Banerji
2000-04-01
Kinetics and mechanism of oxidation of formic and oxalic acids by quinolinium fluorochromate (QFC) have been studied in dimethylsulphoxide. The main product of oxidation is carbon dioxide. The reaction is first-order with respect to QFC. Michaelis-Menten type of kinetics were observed with respect to the reductants. The reaction is acid-catalysed and the acid dependence has the form: obs = + [H+]. The oxidation of -deuterioformic acid exhibits a substantial primary kinetic isotope effect (H/D = 6.01 at 303 K). The reaction has been studied in nineteen different organic solvents and the solvent effect has been analysed using Taft’s and Swain’s multiparametric equations. The temperature dependence of the kinetic isotope effect indicates the presence of a symmetrical cyclic transition state in the rate-determining step. Suitable mechanisms have been proposed
The kinetics of β-elimination of cystine and the formation of lanthionine in gliadin.
Lagrain, Bert; De Vleeschouwer, Kristel; Rombouts, Ine; Brijs, Kristof; Hendrickx, Marc E; Delcour, Jan A
2010-10-13
When gliadin, a mixture of wheat storage proteins containing only intramolecular disulfide (SS) bonds, is heated at high temperatures and preferably at alkaline pH, the SS bonds are cleaved by β-elimination reactions leading to decreased cystine levels and the generation of dehydroalanine (DHA) and free sulfhydryl (SH) groups. DHA and the free SH group of cysteine can further react to form the irreversible cross-link lanthionine (LAN). The kinetics of this reaction were studied by heating model systems containing gliadin at different pH values (pH 6.0, 8.0 and 11.0) at temperatures up to 120 °C. Multiresponse modeling was applied to simultaneously describe the course of the reaction partners, intermediates and products. The estimated kinetic parameters indicate that the reaction rate constant for the elimination reaction increases with temperature and pH. Moreover, the predominant reaction consuming the intermediary DHA is the cross-link with cysteine to form LAN following second-order reaction kinetics. The corresponding reaction rate constant is less dependent on temperature and pH. Use of the proposed kinetic model to estimate reaction product concentrations in cereal-based foods allowed us to conclude that the β-elimination reaction may be less important during, e.g., bread making, but may well contribute to gluten network formation during the production of soft wheat products. It may also well be relevant in the production of bioplastics made from gluten.
The Kinetics of Enzyme Mixtures
Simon Brown
2014-03-01
Full Text Available Even purified enzyme preparations are often heterogeneous. For example, preparations of aspartate aminotransferase or cytochrome oxidase can consist of several different forms of the enzyme. For this reason we consider how different the kinetics of the reactions catalysed by a mixture of forms of an enzyme must be to provide some indication of the characteristics of the species present. Based on the standard Michaelis-Menten model, we show that if the Michaelis constants (Km of two isoforms differ by a factor of at least 20 the steady-state kinetics can be used to characterise the mixture. However, even if heterogeneity is reflected in the kinetic data, the proportions of the different forms of the enzyme cannot be estimated from the kinetic data alone. Consequently, the heterogeneity of enzyme preparations is rarely reflected in measurements of their steady-state kinetics unless the species present have significantly different kinetic properties. This has two implications: (1 it is difficult, but not impossible, to detect molecular heterogeneity using kinetic data and (2 even when it is possible, a considerable quantity of high quality data is required.
Kinetics and mechanism of the oxidation of some diols by benzyltrimethylammonium tribromide
Garima Goswami; Seema Kothari; Kalyan K Banerji
2001-02-01
The kinetics of oxidation of five vicinal and four non-vicinal diols, and two of their monoethers by benzyltrimethylammonium tribromide (BTMAB) have been studied in 3:7 (/) acetic acid-water mixture. The vicinal diols yield the carbonyl compounds arising out of the glycol bond fission while the other diols give the hydroxycarbonyl compounds. The reaction is first-order with respect to BTMAB. Michaelis-Menten type kinetics is observed with respect to diol. Addition of benzyltrimethylammonium chloride does not affect the rate. Tribromide ion is postulated to be the reactive oxidizing species. Oxidation of [1,1,2,2-2H4] ethanediol shows the absence of a kinetic isotope effect. The reaction exhibits substantial solvent isotope effect. A mechanism involving a glycol-bond fission has been proposed for the oxidation of the vicinal diols. The other diols are oxidized by a hydride ion transfer to the oxidant, as are the monohydric alcohols.
Aon, Miguel Antonio; O'Rourke, Brian; Cortassa, Sonia
2004-01-01
In this work, we highlight the links between fractals and scaling in cells and explore the kinetic consequences for biochemical reactions operating in fractal media. Based on the proposal that the cytoskeletal architecture is organized as a percolation lattice, with clusters emerging as fractal forms, the analysis of kinetics in percolation clusters is especially emphasized. A key consequence of this spatiotemporal cytoplasmic organization is that enzyme reactions following Michaelis-Menten or allosteric type kinetics exhibit higher rates in fractal media (for short times and at lower substrate concentrations) at the percolation threshold than in Euclidean media. As a result, considerably faster and higher amplification of enzymatic activity is obtained. Finally, we describe some of the properties bestowed by cytoskeletal organization and dynamics on metabolic networks.
Catalytic and Inhibitory Kinetic Behavior of Horseradish Peroxidase on the Electrode Surface
Titi Wang
2012-10-01
Full Text Available Enzymatic biosensors are often used to detect trace levels of some specific substance. An alternative methodology is applied for enzymatic assays, in which the electrocatalytic kinetic behavior of enzymes is monitored by measuring the faradaic current for a variety of substrate and inhibitor concentrations. Here we examine a steady-state and pre-steady-state reduction of H2O2 on the horseradish peroxidase electrode. The results indicate the substrate-concentration dependence of the steady-state current strictly obeys Michaelis-Menten kinetics rules; in other cases there is ambiguity, whereby he inhibitor-concentration dependence of the steady-state current has a discontinuity under moderate concentration conditions. For pre-steady-state phases, both catalysis and inhibition show an abrupt change of the output current. These anomalous phenomena are universal and there might be an underlying biochemical or electrochemical rationale.
Kinetics and mechanism of oxidation of aliphatic alcohols by tetrabutylammonium tribromide
Manju Baghmar; Pradeep K Sharma
2001-04-01
Oxidation of nine primary aliphatic alcohols by tetrabutylammonium tribromide (TBATB) in aqueous acetic acid leads to the formation of the corresponding aldehydes. The reaction is first order with respect to TBATB. Michaelis-Menten type kinetics is observed with respect to alcohols. The reaction failed to induce the polymerization of acrylonitrile. Tetrabutylammonium chloride has no effect on the reaction rate. The proposed reactive oxidizing species is the tribromide ion. The oxidation of [1,1-2H2]ethanol exhibits a substantial kinetic isotope effect. The effect of solvent composition indicates that the rate increases with increase in the polarity of the solvent. The reaction is susceptible to both polar and steric effects of substituents. A mechanism involving transfer of a hydride ion in the ratedetermining step has been proposed.
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.
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.
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.
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.
Jonathan B. Ford
2013-01-01
Full Text Available Primary ethanol metabolism occurs through alcohol dehydrogenase, but minor metabolic pathways such as the P450 enzymes CYP2E1 and CYP1A2 and the enzyme catalase exist. These enzymes have distinct developmental stages. Elimination kinetics of ethanol in the infant is limited. We report the elimination kinetics of ethanol in a 5-week-old African-American male who had a serum ethanol level of 270 mg/dL on admission. A previously healthy 5-week-old African-American male was brought to the ED with a decreased level of consciousness. His initial blood ethanol level was 270 mg/dL. Serial blood ethanol levels were obtained. The elimination rate of ethanol was calculated to be in a range from 17.1 to 21.2 mg/dL/hr and appeared to follow zero-order elimination kinetics with a R2=0.9787. Elimination kinetics for ethanol in the young infant has been reported in only four previously published reports. After reviewing these reports, there appears to be variability in the elimination rates of ethanol in infants. Very young infants may not eliminate ethanol as quickly as previously described. Given that there are different stages of enzyme development in children, caution should be used when generalizing the elimination kinetics in young infants and children.
Complex kinetics of fluctuating enzymes: phase diagram characterization of a minimal kinetic scheme.
Min, Wei; Jiang, Liang; Xie, X Sunney
2010-05-03
Enzyme molecules are dynamic entities with stochastic fluctuation in both protein conformation and enzymatic activity. However, such a notion of fluctuating enzymes, best characterized by recent single-molecule experiments, was not considered in the classic Michaelis-Menten (MM) kinetic scheme. Here we incorporate the fluctuation concept into the reversible MM scheme, and solve analytically all the possible kinetics (i.e., substrate concentration dependent enzymatic velocity) for a minimal model of fluctuating enzymes. Such a minimal model is found to display a variety of distinct kinetic behaviors (phases) in addition to the classic MM kinetics; excess substrate inhibition, sigmoidal kinetics, and concave biphasic kinetics. We find that all these kinetic phases are interrelated and unified under the framework of fluctuating enzymes and can be adequately described by a phase diagram that consists of two master parameters. Functionally, substrate inhibition, sigmoidal kinetics, and convex biphasic phases exhibit positive cooperativity, whereas concave biphasic phases display negative cooperativity. Remarkably, all these complex kinetics are produced by fluctuating enzymes with single substrate binding site, but the two conformations are, therefore, fundamentally different from the classic MWC and KNF models that require multiple subunit or binding sites. This model also suggests that, for a given enzyme/substrate pair, the non-MM behaviors could undergo transitions among different kinetic phases induced by varying product concentrations, owing to the fundamental Haldane symmetry in the reversible MM scheme.
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.
Acetylene in breath: background levels and real-time elimination kinetics after smoking.
Metsälä, M; Schmidt, F M; Skyttä, M; Vaittinen, O; Halonen, L
2010-12-01
We have measured the acetylene concentration in the exhaled breath of 40 volunteers (31 non-smokers, nine smokers) using near-infrared cavity ring-down spectroscopy. The acetylene levels were found to be the same as in ambient air for non-smokers, whereas elevated levels were observed for smokers. Real-time measurements with sub-second time resolution have been applied to measure the elimination kinetics of acetylene in breath after exposure to tobacco smoke. Three exponential time constants can be distinguished from the data and these can be used to define the residence times for different compartments, according to the multi-compartment model of the human body.
Gómez-Uribe, Carlos A; Verghese, George C; Tzafriri, Abraham R
2008-12-28
Widely different time scales are common in systems of chemical reactions and can be exploited to obtain reduced models applicable to the time scales of interest. These reduced models enable more efficient computation and simplify analysis. A classic example is the irreversible enzymatic reaction, for which separation of time scales in a deterministic mass action kinetics model results in approximate rate laws for the slow dynamics, such as that of Michaelis-Menten. Recently, several methods have been developed for separation of slow and fast time scales in chemical master equation (CME) descriptions of stochastic chemical kinetics, yielding separate reduced CMEs for the slow variables and the fast variables. The paper begins by systematizing the preliminary step of identifying slow and fast variables in a chemical system from a specification of the slow and fast reactions in the system. The authors then present an enhanced time-scale-separation method that can extend the validity and improve the accuracy of existing methods by better accounting for slow reactions when equilibrating the fast subsystem. The resulting method is particularly accurate in systems such as enzymatic and protein interaction networks, where the rates of the slow reactions that modify the slow variables are not a function of the slow variables. The authors apply their methodology to the case of an irreversible enzymatic reaction and show that the resulting improvements in accuracy and validity are analogous to those obtained in the deterministic case by using the total quasi-steady-state approximation rather than the classical Michaelis-Menten. The other main contribution of this paper is to show how mass fluctuation kinetics models, which give approximate evolution equations for the means, variances, and covariances of the concentrations in a chemical system, can feed into time-scale-separation methods at a variety of stages.
Tavares, Ana P M; Rodríguez, Oscar; Fernández-Fernández, María; Domínguez, Alberto; Moldes, Diego; Sanromán, María A; Macedo, Eugénia A
2013-03-01
Laccase was immobilized on modified silica carrier. The immobilization conditions, pH and enzyme concentration were optimized. Operational stability of 10 reaction cycles showed that immobilized laccase in buffer was stable, presenting an activity loss 80% was obtained in ionic liquid (IL) solution. Activity of immobilized laccase was maintained when incubated in IL. After 7days of incubation, immobilized laccase lost 30-50% of its initial activity. Immobilization also improved thermal stability of laccase in the presence of IL. Enzyme kinetics was modelled with Michaelis-Menten model. The Km value for free laccase increases significantly with the IL concentration. Slight differences were found in Vm for free enzyme. Unusual kinetic behaviour was obtained for immobilized laccase in IL: Both Vm and Km increased with IL concentration, resulting in increased catalytic efficiency of the immobilized enzyme in presence of IL.
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
Raghvendra Shukla; Pradeep K Sharma; Kalyan K Banerji
2004-03-01
The oxidation of eleven amino acids by tetrabutylammonium tribromide (TBATB) in aqueous acetic acid results in the formation of the corresponding carbonyl compounds and ammonia. The reaction is first order with respect to TBATB. Michaelis-Menten type kinetics is observed with some of the amino acids while others exhibit second-order dependence. It failed to induce polymerization of acrylonitrile. The effect of solvent composition indicate that the rate of reaction increases with increase in the polarity of the medium. Addition of tetrabutylammonium chloride has no effect on the rate of oxidation. Addition of bromide ion causes decrease in the oxidation rate but only to a limiting value. The reaction is susceptible to both polar and steric effects of the substituents. A suitable mechanism has been proposed.
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.
Kinetic and molecular analyses reveal isoprene degradation potential of Methylobacterium sp.
Srivastva, Navnita; Vishwakarma, P; Bhardwaj, Y; Singh, A; Manjunath, K; Dubey, Suresh K
2017-10-01
Efforts were made to isolate and characterize bacteria capable of growing on methane and organic compounds, and to achieve the simultaneous degradation of more than one pollutant. Among the methanotrophs, species of Methylobacterium was able to catabolize a variety of hydrocarbons, including the branched-chain alkenes. Therefore, laboratory incubations experiments were carried out in batch mode to assess the potential of Methylobacterium sp. PV1 for degrading isoprene, the low-molecular-weight alkene, the most abundant non-methane volatile hydrocarbon present in the environment. Methylobacterium sp. PV1, isolated from paddy field soil, was characterized by pmoA and 16S rRNA gene sequencing and FAME analysis, and used for isoprene degradation. The kinetics of biodegradation is studied using the Michaelis-Menten model. The optimum degradation (80%) with maximum average relative degradation rate was observed at 150ppm isoprene. The degradation products were also analyzed using FTIR. Copyright © 2017 Elsevier Ltd. All rights reserved.
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
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
Elimination of the Translational Kinetic Energy Contamination in pre-Born-Oppenheimer Calculations
Simmen, Benjamin; Reiher, Markus
2012-01-01
In this paper we present a simple strategy for the elimination of the translational kinetic energy contamination of the total energy in pre-Born--Oppenheimer calculations carried out in laboratory-fixed Cartesian coordinates (LFCCs). The simple expressions for the coordinates and the operators are thus preserved throughout the calculations, while the mathematical form and the parametrisation of the basis functions are chosen so that the translational and rotational invariances are respected. The basis functions are constructed using explicitly correlated Gaussian functions (ECGs) and the global vector representation. First, we observe that it is not possible to parametrise the ECGs so that the system is at rest in LFCCs and at the same time the basis functions are square-integrable with a non-vanishing norm. Then, we work out a practical strategy to circumvent this problem by making use of the properties of the linear transformation between the LFCCs and translationally invariant and center-of-mass Cartesian ...
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.
A. Adetoro
2011-10-01
Full Text Available The kinetics of the oxidation of Pyrocatechol violet (PCVH by nitrite ion (NO2- in aqueous acidic medium has been studied at 24±1ºC, I = 0.50 mol/dm3(NaCl, [H+] = 1.0×10-3 mol/dm3. The reaction is first order to [PCVH] and half order to [NO2-]. The redox reaction displayed a 1:1 stoichiometry and obeys the rate law: d[PCVH]/dt = (a + b[H+] [PCVH][NO2-]½. The second-order rate constant increases with increase in acid concentration and ionic strength. This system displayed positive salt effect while spectroscopic investigation and Michaelis-Menten plot showed evidence of intermediate complex formation in the course of the reaction. A plausible mechanism has been proposed for the reaction.
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.
Aslam, M.; Travis, R. L.; Huffaker, R. C.
1992-01-01
Nitrate and NO2- transport by roots of 8-day-old uninduced and induced intact barley (Hordeum vulgare L. var CM 72) seedlings were compared to kinetic patterns, reciprocal inhibition of the transport systems, and the effect of the inhibitor, p-hydroxymercuribenzoate. Net uptake of NO3- and NO2- was measured by following the depletion of the ions from the uptake solutions. The roots of uninduced seedlings possessed a low concentration, saturable, low Km, possibly a constitutive uptake system, and a linear system for both NO3- and NO2-. The low Km system followed Michaelis-Menten kinetics and approached saturation between 40 and 100 micromolar, whereas the linear system was detected between 100 and 500 micromolar. In roots of induced seedlings, rates for both NO3- and NO2- uptake followed Michaelis-Menten kinetics and approached saturation at about 200 micromolar. In induced roots, two kinetically identifiable transport systems were resolved for each anion. At the lower substrate concentrations, less than 10 micromolar, the apparent low Kms of NO3- and NO2- uptake were 7 and 9 micromolar, respectively, and were similar to those of the low Km system in uninduced roots. At substrate concentrations between 10 and 200 micromolar, the apparent high Km values of NO3- uptake ranged from 34 to 36 micromolar and of NO2- uptake ranged from 41 to 49 micromolar. A linear system was also found in induced seedlings at concentrations above 500 micromolar. Double reciprocal plots indicated that NO3- and NO2- inhibited the uptake of each other competitively in both uninduced and induced seedlings; however, Ki values showed that NO3- was a more effective inhibitor than NO2-. Nitrate and NO2- transport by both the low and high Km systems were greatly inhibited by p-hydroxymercuribenzoate, whereas the linear system was only slightly inhibited.
Enzyme kinetics of conjugating enzymes: PAPS sulfotransferase.
James, Margaret O
2014-01-01
The sulfotransferase (SULT) enzymes catalyze the formation of sulfate esters or sulfamates from substrates that contain hydroxy or amine groups, utilizing 3'-phosphoadenosyl-5'-phosphosulfate (PAPS) as the donor of the sulfonic group. The rate of product formation depends on the concentrations of PAPS and substrate as well as the sulfotransferase enzyme; thus, if PAPS is held constant while varying substrate concentration (or vice versa), the kinetic constants derived are apparent constants. When studied over a narrow range of substrate concentrations, classic Michaelis-Menten kinetics can be observed with many SULT enzymes and most substrates. Some SULT enzymes exhibit positive or negative cooperativity during conversion of substrate to product, and the kinetics fit the Hill plot. A characteristic feature of most sulfotransferase-catalyzed reactions is that, when studied over a wide range of substrate concentrations, the rate of product formation initially increases as substrate concentration increases, then decreases at high substrate concentrations, i.e., they exhibit substrate inhibition or partial substrate inhibition. This chapter gives an introduction to sulfotransferases, including a historical note, the nomenclature, a description of the function of SULTs with different types of substrates, presentation of examples of enzyme kinetics with SULTs, and a discussion of what is known about mechanisms of substrate inhibition in the sulfotransferases.
Liu, Qingqing; Peng, Hanyong; Lu, Xiufen; Zuidhof, Martin J.; Li, Xing-Fang; Le, X. Chris
2016-01-01
Background: Chicken meat has the highest per capita consumption among all meat types in North America. The practice of feeding 3-nitro-4-hydroxyphenylarsonic acid (Roxarsone, Rox) to chickens lasted for more than 60 years. However, the fate of Rox and arsenic metabolites remaining in chicken are poorly understood. Objectives: We aimed to determine the elimination of Rox and metabolites from chickens and quantify the remaining arsenic species in chicken meat, providing necessary information for meaningful exposure assessment. Methods: We have conducted a 35-day feeding experiment involving 1,600 chickens, of which half were control and the other half were fed a Rox-supplemented diet for the first 28 days and then a Rox-free diet for the final 7 days. We quantified the concentrations of individual arsenic species in the breast meat of 229 chickens. Results: Rox, arsenobetaine, arsenite, monomethylarsonic acid, dimethylarsinic acid, and a new arsenic metabolite, were detected in breast meat from chickens fed Rox. The concentrations of arsenic species, except arsenobetaine, were significantly higher in the Rox-fed than in the control chickens. The half-lives of elimination of these arsenic species were 0.4–1 day. Seven days after termination of Rox feeding, the concentrations of arsenite (3.1 μg/kg), Rox (0.4 μg/kg), and a new arsenic metabolite (0.8 μg/kg) were significantly higher in the Rox-fed chickens than in the control. Conclusion: Feeding of Rox to chickens increased the concentrations of five arsenic species in breast meat. Although most arsenic species were excreted rapidly when the feeding of Rox stopped, arsenic species remaining in the Rox-fed chickens were higher than the background levels. Citation: Liu Q, Peng H, Lu X, Zuidhof MJ, Li XF, Le XC. 2016. Arsenic species in chicken breast: temporal variations of metabolites, elimination kinetics, and residual concentrations. Environ Health Perspect 124:1174–1181; http://dx.doi.org/10.1289/ehp
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
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.
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.
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.
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.
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...
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 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...
Mihara, H; Kurihara, T; Yoshimura, T; Esaki, N
2000-04-01
We have purified three NifS homologs from Escherichia coli, CSD, CsdB, and IscS, that appear to be involved in iron-sulfur cluster formation and/or the biosynthesis of selenophosphate. All three homologs catalyze the elimination of Se and S from L-selenocysteine and L-cysteine, respectively, to form L-alanine. These pyridoxal 5'-phosphate enzymes were inactivated by abortive transamination, yielding pyruvate and a pyridoxamine 5'-phosphate form of the enzyme. The enzymes showed non-Michaelis-Menten behavior for L-selenocysteine and L-cysteine. When pyruvate was added, they showed Michaelis-Menten behavior for L-selenocysteine but not for L-cysteine. Pyruvate significantly enhanced the activity of CSD toward L-selenocysteine. Surprisingly, the enzyme activity toward L-cysteine was not increased as much by pyruvate, suggesting the presence of different rate-limiting steps or reaction mechanisms for L-cysteine desulfurization and the degradation of L-selenocysteine. We substituted Ala for each of Cys358 in CSD, Cys364 in CsdB, and Cys328 in IscS, residues that correspond to the catalytically essential Cys325 of Azotobacter vinelandii NifS. The enzyme activity toward L-cysteine was almost completely abolished by the mutations, whereas the activity toward L-selenocysteine was much less affected. This indicates that the reaction mechanism of L-cysteine desulfurization is different from that of L-selenocysteine decomposition, and that the conserved cysteine residues play a critical role only in L-cysteine desulfurization.
Hargono Hargono
2017-05-01
Full Text Available Starch is a potential substrate for this purpose, but the extra cost is needed to hydrolyze it into reducing sugar. As an alternative to the expensive and energy demanding conventional hydrolysis process, the low-temperature hydrolysis is being studied. Granular Starch Hydrolysing Enzyme (GSHE was used in the process to degrade starch into reducing sugar at 30°C and pH 4. The substrates included bitter cassava flour, sweet cassava starch, and gadung flour. Starch concentrations studied were 50, 100, 150, 200, 250, 300, 350, and 400 g/L, respectively, while concentration of enzyme was 1.5 % (w/w. The optimum condition of the process was hydrolysis using 200 g/L of substrate concentration and enzyme concentration of 1.5% for 12 h. It was found that the reducing sugar was 49.3 g/L and the productivity of reducing sugar (Qrs was 4.11 (gL-1 h-1. Lineweaver-Burk plot of Michaelis-Menten equation was used to study the inhibition kinetics. The Michaelis-Menten constants (Km for these three substrates were determined as 141.64 g/L, 137,64 g/L and 140.84 g/L for bitter cassava flour, sweet cassava starch, and gadung flour, respectively. The value of Vm/Km, which denotes the affinity of the enzyme to the substrate, were determined and compared, and the result showed that the affinity (Vm to the enzyme to this substrate followed the order of sweet cassava starch˃ bitter cassava flour˃ gadung flour, and all are non-competitive inhibitor, while the Ki value was 0.022 h -1.
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.
Enzyme kinetics: the whole picture reveals hidden meanings.
Pinto, Maria F; Estevinho, Berta N; Crespo, Rosa; Rocha, Fernando A; Damas, Ana M; Martins, Pedro M
2015-06-01
The methodology adopted by Michaelis and Menten in 1913 is still routinely used to characterize the catalytic power and selectivity of enzymes. These kinetic measurements must be performed soon after the purified enzyme is mixed with a large excess of substrate. Other time scales and solution compositions are no less physiologically relevant, but fall outside the range of applicability of the classical formalism. Here we show that the complete picture of an enzyme's mode of function is critically obscured by the limited scope of conventional kinetic analysis, even in the simplest case of a single active site without inhibition. This picture is now unveiled in a mathematically closed form that remains valid over the reaction time for all combinations of enzyme/substrate concentrations and rate constants. Algebraic simplicity is maintained in the new formalism when stationary reaction phases are considered. By achieving this century-old objective, the otherwise hidden role of the reversible binding step is revealed and atypical kinetic profiles are explained. Most singular kinetic behaviors are identified in a critical region of conditions that coincide with typical cell conditions. Because it is not covered by the Michaelis-Menten model, the critical region has been missed until now by low- and high-throughput screenings of new drugs. New possibilities are therefore raised for novel and once-promising inhibitors to therapeutically target enzymes.
Corella, J.; Narvaez, I.; Orio, A. [Madrid Univ. (Spain). Dept. of Chem. Eng.
1996-12-31
Calcined dolomites and commercial steam reforming catalysts are used downstream biomass gasifiers for hot catalytic raw gas cleaning. To further compare these solids under a rigorous basis, a reaction network and a kinetic model are presented. The apparent kinetic constant for the tar reduction is here proposed as a basis of comparison. Tar sampling and analysis, and the units used for the space-time in the catalytic reactor affect the kinetic constants observed. (author) (2 refs.)
Guilloux, M.J.; Michon, G. [Commissariat a l' Energie Atomique, Saclay (France). Centre d' Etudes Nucleaires
1958-07-01
A kinetic study of strontium elimination was made on rats after a single oral administration of 3 to 5 {mu}curies of carrier free Sr{sup 90}. The curve showing the body burden in function of time may be considered as the sum of three exponential terms with half-lives of 14 hours, 72 days, 153 days. The term with a half-live of 153 days represents the metabolism of strontium in the bone; it is predominant since the 17. day and its extrapolation to time zero shows that things seem to proceed as if 18 per cent of the administered amount were deposited in the skeleton. (author) [French] La cinetique de l'elimination du strontium chez le rat a ete etudiee apres une administration orale unique de 3 a 5 {mu}curies de {sup 90}Sr repute sans entraineur. La courbe representant la quantite presente dans l'organisme en fonction du temps peut etre assimilee a la somme de trois termes exponentiels de periode 14 heures, 72 jours, 153 jours. Le terme de periode 153 jours represente le metabolisme osseux du strontium, il est preponderant des le 17. jour et son extrapolation au temps zero nous montre qu'en definitive, tout se passe comme si 18 pour cent de la quantite administree etaient deposes dans le squelette. (auteur)
Phu, Jack; Al-Saleem, Noha; Kalloniatis, Michael; Khuu, Sieu K
2016-11-01
In the present study, we measured the extent of statokinetic dissociation (SKD) in normal observers and then equated the psychophysical tasks into a two-interval forced choice (2IFC) procedure. In Experiment 1, we used the Humphrey visual field analyzer in static perimetry and automated kinetic perimetry modes to measure contrast sensitivity thresholds and the Goldmann manual kinetic perimeter to measure isopters. This was carried out using a Goldmann size II target. Goldmann kinetic perimetry was performed manually with both inward (peripheral to center) and outward (center to periphery) directions of movement to deduce an "average" isopter. This revealed the presence of SKD when superimposed upon the map of static contrast threshold results. There was no evidence of any contribution of examiner technique or instrument-specific differences to SKD. In Experiment 2, we determined the psychometric curves plotting proportion seen as a function of stimulus eccentricity with static and kinetic stimuli with a 2IFC procedure and method of constant stimuli. In an additional experiment, we also showed that subjects were able to reliably discriminate whether a stimulus was static, moving inward, or moving outward, and hence, comparisons could be made between static and kinetic perimetry tasks. Overall, by making the task objective and reducing criterion bias, eccentricity thresholds were equated across static and kinetic perimetry methods; hence, no evidence of SKD was seen. We suggest SKD is inherent to the differences in methodology of threshold measurement in conventional static and kinetic perimetry and individual criterion bias.
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
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.
Leighfield, Tod A; Muha, Noah; Miles, Christopher O; Ramsdell, John S
2013-06-17
Brevetoxin B (BTX-B), produced by dinoflagellates of the species Karenia, is a highly reactive molecule, due in part to an α,β-unsaturated aldehyde group at the terminal side chain, leading to the production of metabolites in shellfish by reduction, oxidation, and conjugation. We have investigated in mice the blood elimination of three common bioactive brevetoxin metabolites found in shellfish, which have been semisynthesized from BTX-B in radioactive forms. BTX-B was reduced at C42 to yield [(3)H] dihydro-BTX-B. [(3)H] S-desoxy-BTX-B2 (cysteine brevetoxin B) was semisynthesized from BTX-B by the conjugation of cysteine at the C50 olefinic group then [(3)H] radiolabeled by C42 aldehyde reduction. [(14)C] N-Palmitoyl-S-desoxy-BTX-B2 was prepared using S-desoxy-BTX-B2 as the starting material with addition of the [(14)C] radiolabeled fatty acid via cysteine-amide linkage. The elimination of intravenously administered [(3)H] S-desoxy-BTX-B2, [(14)C] N-palmitoyl-S-desoxy-BTX-B2, or [(3)H] dihydro-BTX-B was measured in blood collected from C57BL/6 mice over a 48 h period. Each brevetoxin metabolite tested exhibited biexponential elimination kinetics and fit a two-compartment model of elimination that was applied to generate toxicokinetic parameters. The rate of transfer between the central compartment (i.e., blood) and the peripheral compartment (e.g., tissue) for each brevetoxin differed substantially, with dihydro-BTX-B exchanging rapidly with the peripheral compartment, S-desoxy-BTX-B2 eliminating rapidly from the central compartment, and N-palmitoyl-S-desoxy-BTX-B2 eliminating slowly from the central compartment. Toxicokinetic parameters were analyzed in the context of the unique structure of each brevetoxin metabolite resulting from a reduction, amino acid conjugation, or fatty acid addition to BTX-B.
Zahra Ghobadi Nejad
2014-01-01
Full Text Available Due to great commercial application of protease, it is necessary to study kinetic characterization of this enzyme in order to improve design of enzymatic reactors. In this study, mathematical modeling of protease enzyme production kinetics which is derived from Bacillus licheniformis BBRC 100053 was studied (at 37°C, pH 10 after 73 h in stationary phase, and 150 rpm. The aim of the present paper was to determine the best kinetic model and kinetic parameters for production of protease and calculating Ki (inhibition constant of different inhibitors to find the most effective one. The kinetic parameters Km (Michaelis-Menten constant and Vm (maximum rate were calculated 0.626 mM and 0.0523 mM/min. According to the experimental results, using DFP (diisopropyl fluorophosphate and PMSF (phenylmethanesulfonyl fluoride as inhibitors almost 50% of the enzyme activity could be inhibited when their concentrations were 0.525 and 0.541 mM, respectively. Ki for DFP and PMSF were 0.46 and 0.56 mM, respectively. Kinetic analysis showed that the Lineweaver-Burk model was the best fitting model for protease production kinetics DFP was more effective than PMSF and both of them should be covered in the group of noncompetitive inhibitors.
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].
Cardoso, Franciane Pinheiro; Aquino Neto, Sidney; Ciancaglini, Pietro; de Andrade, Adalgisa R
2012-08-01
The kinetic behavior of the enzyme laccase in solution and immobilized onto carbon platforms using poly(amido amine) (PAMAM) dendrimers has been investigated. The results with the immobilized enzymes have demonstrated that almost ten times more enzyme on the carbon support is required for satisfactory kinetic rates to be achieved. Furthermore, the study as a function of the substrate concentration revealed that the kinetic behavior of the enzyme in solution fits the Michaelis-Menten model. However, when the enzyme is immobilized onto the carbon surface, the catalyzed reaction follows a particular kinetic behavior with apparent positive cooperativity. The highest activity with laccase (in solution or immobilized) is achieved around pH 4.5, and the substrate conversion rate clearly diminishes with rising pH. The optimum temperature lies around 60 °C. The enzyme displays good catalytic activity in a wide range of pH and temperature values. The stability tests evidenced that there is no appreciable reduction in the enzymatic activity after immobilization within the first 30 days. Taking into account both the kinetic and stability tests, one can infer that the use of PAMAM dendrimers seems to be a very attractive approach for the immobilization of enzymes, as well as a feasible and useful methodology for the anchoring of enzymes with potential application in many biotechnological areas.
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.
Ribeiro, Fabianne; Gallego-Urrea, Julián Alberto; Goodhead, Rhys M; Van Gestel, Cornelis A M; Moger, Julian; Soares, Amadeu M V M; Loureiro, Susana
2015-01-01
Raphidocelis subcapitata is a freshwater algae species that constitutes the basis of many aquatic trophic chains. In this study, R. subcapitata was used as a model species to investigate the kinetics of uptake and elimination of silver nanoparticles (AgNP) in comparison to silver nitrate (AgNO3) with particular focus on the Ag sized-fractions in solution. AgNP used in this study were provided in a suspension of 1 mg Ag/l, with an initial size of 3-8 nm and coated with an alkane material. Algae was exposed for 48 h to both AgNP and AgNO3 and sampled at different time points to determine their internal Ag concentration over time. Samples were collected and separated into different sized fractions: total (Agtot), water column Ag (Agwater), small particulate Ag (Agsmall.part.) and dissolved Ag (Agdis). At AgNO3 exposures algae reached higher bioconcentration factor (BCF) and lower elimination rate constants than at AgNP exposures, meaning that Ag is more readily taken up by algae in its dissolved form than in its small particulate form, however slowly eliminated. When modelling the kinetics based on the Agdis fraction, a higher BCF was found. This supports our hypothesis that Ag would be internalised by algae only in its dissolved form. In addition, algae images obtained by Coherent Anti-stokes Raman Scattering (CARS) microscopy demonstrated large aggregates of nanoparticles external to the algae cells with no evidence of its internalisation, thus providing a strong suggestion that these AgNP were not able to penetrate the cells and Ag accumulation happens through the uptake of Ag ions.
Michael E.G. Lyons
2003-01-01
Full Text Available A detailed kinetic analysis of the pertinent physical processes underlying the operation of enzyme electrodes immobilized within alkane thiol self assembled monolayers is developed. These electrodes utilize a soluble mediator, which partitions into the monolayer, regenerates the active catalytic form of the enzyme and is re-oxidized at the underlying support electrode surface giving rise to a current which reflects kinetic events at the enzyme surface. Both the enzyme/substrate and enzyme mediator kinetics have been quantified fully in terms of a ping-pong mechanism for the former and Michaelis-Menten kinetics for the latter. The effect of substrate and mediator diffusion in solution have also been specifically considered and the latter processes have been shown to result in a complex expression for the reaction flux. Four limiting kinetic cases have been enumerated and simple expressions for the reaction flux in each of these rate limiting situations have been developed. Kinetic case diagrams have been presented as an aid to mechanistic diagnosis. The complicating effects of diffusive loss of reduced mediator from the enzyme layer have also been examined and the relation between the observed flux corresponding to reduced mediator oxidation at the support electrode and the substrate reaction flux in the enzyme layer have been quantified in terms of an efficiency factor. Results extracted from recently published practical realizations of immobilized monolayer enzyme systems have been discussed in the context of the proposed model analysis.
Strompen, Simon; Weiss, Markus; Ingram, Thomas; Smirnova, Irina; Gröger, Harald; Hilterhaus, Lutz; Liese, Andreas
2012-06-01
A solvent-free, chemoenzymatic reaction sequence for the enantioselective synthesis of β-amino acid esters has been kinetically and thermodynamically characterized. The coupled sequence comprises a thermal aza-Michael addition of cheap starting materials and a lipase catalyzed aminolysis for the kinetic resolution of the racemic ester. Excellent ee values of >99% were obtained for the β-amino acid ester at 60% conversion. Kinetic constants for the aza-Michael addition were obtained by straightforward numerical integration of second-order rate equations and nonlinear fitting of the progress curves. A different strategy had to be devised for the biocatalytic reaction. Initially, a simplified Michaelis-Menten model including product inhibition was developed for the reaction running in THF as an organic solvent. Activity based parameters were used instead of concentrations in order to facilitate the transfer of the kinetic model to the solvent-free system. Observed solvent effects not accounted for by the use of thermodynamic activities were incorporated into the kinetic model. Enzyme deactivation was observed to depend on the ratio of the applied substrates and also included in the kinetic model. The developed simple model is in very good agreement with the experimental data and allows the simulation and optimization of the solvent-free process.
Kinetics of aqueous chlorination of some pharmaceuticals and their elimination from water matrices.
Acero, Juan L; Benitez, F Javier; Real, Francisco J; Roldan, Gloria
2010-07-01
Apparent rate constants for the reactions of four selected pharmaceutical compounds (metoprolol, naproxen, amoxicillin, and phenacetin) with chlorine in ultra-pure (UP) water were determined as a function of the pH. It was found that amoxicillin (in the whole pH range 3-12), and naproxen (in the low pH range 2-4) presented high reaction rates, while naproxen (in the pH range 5-9), and phenacetin and metoprolol (in the pH range 2.5-12 for phenacetin, and 3-10 for metoprolol) followed intermediate and slow reaction rates. A mechanism is proposed for the chlorination reaction, which allowed the evaluation of the intrinsic rate constants for the elementary reactions of the ionized and un-ionized species of each selected pharmaceutical with chlorine. An excellent agreement is obtained between experimental and calculated rate constants by this mechanism.The elimination of these substances in several waters (a groundwater, a surface water from a public reservoir, and two effluents from municipal wastewater treatment plants) was also investigated at neutral pH. The efficiency of the chlorination process with respect to the pharmaceuticals elimination and the formation THMs was also established. It is generally observed that the increasing presence of organic and inorganic matter in the water matrices demand more oxidant agent (chlorine), and therefore, less chlorine is available for the oxidation of these compounds. Finally, half-life times and oxidant exposures (CT) required for the removal of 99% of the four pharmaceuticals are also evaluated. These parameters are useful for the establishment of safety chlorine doses in oxidation or disinfection stages of pharmaceuticals in treatment plants.
Moxley, Michael A; Beard, Daniel A; Bazil, Jason N
2016-02-05
Mammalian E3 is an essential mitochondrial enzyme responsible for catalyzing the terminal reaction in the oxidative catabolism of several metabolites. E3 is a key regulator of metabolic fuel selection as a component of the pyruvate dehydrogenase complex (PDHc). E3 regulates PDHc activity by altering the affinity of pyruvate dehydrogenase kinase, an inhibitor of the enzyme complex, through changes in reduction and acetylation state of lipoamide moieties set by the NAD(+)/NADH ratio. Thus, an accurate kinetic model of E3 is needed to predict overall mammalian PDHc activity. Here, we have combined numerous literature data sets and new equilibrium spectroscopic experiments with a multitude of independently collected forward and reverse steady-state kinetic assays using pig heart E3. The latter kinetic assays demonstrate a pH-dependent transition of NAD(+) activation to inhibition, shown here, to our knowledge, for the first time in a single consistent data set. Experimental data were analyzed to yield a thermodynamically constrained four-redox-state model of E3 that simulates pH-dependent activation/inhibition and active site redox states for various conditions. The developed model was used to determine substrate/product conditions that give maximal E3 rates and show that, due to non-Michaelis-Menten behavior, the maximal flux is different compared with the classically defined kcat.
Christensen, Hege; Mathiesen, Liv; Postvoll, Lillian W; Winther, Bjørn; Molden, Espen
2009-01-01
In vitro drug metabolism techniques with human CYP c-DNA expressed systems are frequently used to predict human drug metabolism in vivo. The aim of this study was to compare midazolam enzyme kinetics in recombinant expressed CYP3A4 microsomes from human and insect cells. The amounts of 1'- hydroxymidazolam and 4-hydroxymidazolam formed in CYP3A4 microsomes from transfected human liver epithelial cells (T5-3A4 microsomes) and baculovirus-infected insect cells (with and without coexpressed cytochrome b(5)) were analysed by LC-MS. Enzyme kinetic parameters were estimated by nonlinear regression. Mean K(m) for the formation of 1'-hydroxymidazolam was 3- and 4-fold higher in T5-3A4 microsomes than in insect microsomes (pmicrosomes was reflected by significantly lower Cl(int) compared to insect microsomes (pmicrosomes displayed Michaelis-Menten kinetics, while insect microsomes showed substrate inhibition kinetics. The different enzyme kinetics of midazolam observed in recombinant CYP3A4 microsomes from human and insect sources, especially the substantially higher K(m) obtained in human microsomes compared to insect microsomes, should be further evaluated since it may have implications for correlations to in vivo situation.
Effect of Fluosol-DA hemodilution on the kinetics of hepatically eliminated drugs.
Shrewsbury, R P
1987-03-01
The pharmacokinetics of four hepatically eliminated drugs were determined in the rat following moderate hemodilution with either Fluosol-DA or normal saline. The drugs, antipyrine, phenytoin, indocyanine green, and d-propranolol, have extraction ratios from 0.01 to 0.99 in the rat. Animals received an intravenous dose of the drug 0.5, 24, 48, or 72 hours after hemodilution and drug disposition was compared to non-exchanged animals. Antipyrine clearance was increased 48 and 72 hours after Fluosol-DA exchange probably due to enhanced microsomal enzymatic activity. Indocyanine green clearance was decreased 24 hours after Fluosol-DA exchange more likely by a change in its extraction ratio than by alterations in hepatic blood flow. Phenytoin and d-propranolol clearances were decreased at 24 and 72 hours respectively after Fluosol-DA hemodilution due to a decreased apparent volume of distribution. Saline hemodilution decreased phenytoin clearance 24, 48, and 72 hours after exchange also by decreasing the apparent volume of distribution. This volume change was thought to be due to hypovolemia or a microcirculation redistribution which was secondary to hemodilution.
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.
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.
Probing the kinetics of quantum dot-based proteolytic sensors.
Díaz, Sebastián A; Malonoski, Anthony P; Susumu, Kimihiro; Hofele, Romina V; Oh, Eunkeu; Medintz, Igor L
2015-09-01
As an enzyme superfamily, proteases are rivaled only by kinases in terms of their abundance within the human genome. Two ratiometric quantum dot (QD) Förster resonance energy transfer-based sensors designed to monitor the activity of the proteolytic enzymes collagenase and elastase are investigated here. Given the unique material constraints of these sensing constructs, assays are realized utilizing excess enzyme and fixed substrate in progress curve format to yield enzyme specificity or k cat/K m ratios. The range of k cat/Km values derived is 0.5-1.1 mM(-1) s(-1) for the collagenase sensor and 3.7-4.2 mM(-1) s(-1) for the elastase sensor. Of greater interest is the observation that the elastase sensor can be well represented by the Michaelis-Menten model while the collagenase sensor cannot. The latter demonstrates increased specificity at higher peptide substrate/QD loading values and an apparent QD-caused reversible inhibition as the reaction progresses. Understanding the detailed kinetic mechanisms that underpin these types of sensors will be important especially for their further quantitative utilization.
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
Sauer, Ticiane Pokrywiecki [Department of Chemical and Food Engineering, Federal University of Santa Catarina, Campus Universitario-Trindade, P.O. Box 476, 88040-900 Florianopolis, Santa Catarina (Brazil)]. E-mail: sauer@enq.ufsc.br; Casaril, Leonardo [Department of Chemical and Food Engineering, Federal University of Santa Catarina, Campus Universitario-Trindade, P.O. Box 476, 88040-900 Florianopolis, Santa Catarina (Brazil)]. E-mail: leonardocasaril@ufsc.grad.br; Oberziner, Andre Luiz Bertoldi [Department of Chemical and Food Engineering, Federal University of Santa Catarina, Campus Universitario-Trindade, P.O. Box 476, 88040-900 Florianopolis, Santa Catarina (Brazil)]. E-mail: andreoberzine@hotmail.com; Jose, Humberto Jorge [Department of Chemical and Food Engineering, Federal University of Santa Catarina, Campus Universitario-Trindade, P.O. Box 476, 88040-900 Florianopolis, Santa Catarina (Brazil)]. E-mail: humberto@enq.ufsc.br; Moreira, Regina de Fatima Peralta Muniz [Department of Chemical and Food Engineering, Federal University of Santa Catarina, Campus Universitario-Trindade, P.O. Box 476, 88040-900 Florianopolis, Santa Catarina (Brazil)]. E-mail: regina@enq.ufsc.br
2006-07-31
The application of advanced oxidation processes (H{sub 2}O{sub 2}/UV, TiO{sub 2}/H{sub 2}O{sub 2}/UV and TiO{sub 2}/UV) to treat tannery wastewater was investigated. The experiments were performed in batch and continuous UV reactors, using TiO{sub 2} as a catalyst. The effect of the hydrogen peroxide concentration on the degradation kinetics was evaluated in the concentration range 0-1800 mg L{sup -1}. We observed that the degradation rate increased as the hydrogen peroxide increased, but excessive H{sub 2}O{sub 2} concentration was detrimental because it acted as a hydroxyl radical scavenger since it can compete for the active sites of the TiO{sub 2}. In the H{sub 2}O{sub 2}/UV treatment, the COD removal reached around 60% in 4 h of reaction, indicating that the principal pollutants were chemically degraded as demonstrated by the results for BOD, COD, nitrate, ammonium and analysis of the absorbance at 254 nm. Artemia salina toxicity testing performed in parallel showed an increase in toxicity after AOP treatment of the tannery wastewater.
Roberts, M S; Anissimov, Y G
1999-08-01
The conventional convection-dispersion (also called axial dispersion) model is widely used to interrelate hepatic availability (F) and clearance (Cl) with the morphology and physiology of the liver and to predict effects such as changes in liver blood flow on F and Cl. An extended form of the convection-dispersion model has been developed to adequately describe the outflow concentration-time profiles for vascular markers at both short and long times after bolus injections into perfused livers. The model, based on flux concentration and a convolution of catheters and large vessels, assumes that solute elimination in hepatocytes follows either fast distribution into or radial diffusion in hepatocytes. The model includes a secondary vascular compartment, postulated to be interconnecting sinusoids. Analysis of the mean hepatic transit time (MTT) and normalized variance (CV2) of solutes with extraction showed that the discrepancy between the predictions of MTT and CV2 for the extended and unweighted conventional convection-dispersion models decreases as hepatic extraction increases. A correspondence of more than 95% in F and Cl exists for all solute extractions. In addition, the analysis showed that the outflow concentration-time profiles for both the extended and conventional models are essentially identical irrespective of the magnitude of rate constants representing permeability, volume, and clearance parameters, providing that there is significant hepatic extraction. In conclusion, the application of a newly developed extended convection-dispersion model has shown that the unweighted conventional convection-dispersion model can be used to describe the disposition of extracted solutes and, in particular, to estimate hepatic availability and clearance in both experimental and clinical situations.
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.
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.
L.R.B. Gonçalves
1997-12-01
Full Text Available In this work the effects of diffusion on the hydrolysis of maltose using glucoamylase immobilized on macroporous silica at 30o C are studied. Two different kinds of experimental assays are carried out: one using free enzyme and the other using an enzyme covalently linked to macroporous silica, preactivated with glutaraldehyde. Free enzyme assays are used to estimate the kinetic parameters for hydrolysis of maltose at 30ºC, according to a Michaelis-Menten equation, with inhibition by the product. Runs with the immobilized enzyme enable us to estimate dextrin diffusivities in silica, assuming that the inherent kinetic parameters are equal to the intrinsic ones. The values of kinetic and mass transfer parameters are: K3 = 0.90x10-5 g/U.s, Km = 0.61x10-3 g/ml, Ki = 1.23x10-1 g/ml, DMs = 0.50x10-6 cm2 /s and DGs = 0.55x10-6 cm2 /s
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.
Lopes, Vanessa M; Baptista, Miguel; Repolho, Tiago; Rosa, Rui; Costa, Pedro Reis
2014-01-01
Marine phycotoxins derived from harmful algal blooms are known to be associated with mass mortalities in the higher trophic levels of marine food webs. Bivalve mollusks and planktivorous fish are the most studied vectors of marine phycotoxins. However, field surveys recently showed that cephalopod mollusks also constitute potential vectors of toxins. Thus, here we determine, for the first time, the time course of accumulation and depuration of paralytic shellfish toxins (PSTs) in the common octopus (Octopus vulgaris). Concomitantly, the underlying kinetics of toxin transfer between tissue compartments was also calculated. Naturally contaminated clams were used to orally expose the octopus to PSTs during 6 days. Afterwards, octopus specimens were fed with non-contaminated shellfish during 10 days of depuration period. Toxins reached the highest concentrations in the digestive gland surpassing the levels in the kidney by three orders of magnitude. PSTs were not detected in any other tissue analyzed. Net accumulation efficiencies of 42% for GTX5, 36% for dcSTX and 23% for C1+2 were calculated for the digestive gland. These compounds were the most abundant toxins in both digestive gland and the contaminated shellfish diet. The small differences in relative abundance of each toxin observed between the prey and the cephalopod predator indicates low conversion rates of these toxins. The depuration period was better described using an exponential decay model comprising a single compartment - the entire viscera. It is worth noting that since octopuses' excretion and depuration rates are low, the digestive gland is able to accumulate very high toxin concentrations for long periods of time. Therefore, the present study clearly shows that O. vulgaris is a high-potential vector of PSTs during and even after the occurrence of these toxic algal blooms.
Inferring latent gene regulatory network kinetics
González, Javier; Vujačić, Ivan; Wit, Ernst
2013-01-01
Regulatory networks consist of genes encoding transcription factors (TFs) and the genes they activate or repress. Various types of systems of ordinary differential equations (ODE) have been proposed to model these networks, ranging from linear to Michaelis-Menten approaches. In practice, a serious d
Farias, Daniel L; Lucena, Malson N; Garçon, Daniela P; Mantelatto, Fernando L; McNamara, John C; Leone, Francisco A
2017-08-24
We provide a kinetic characterization of (Na(+), K(+))-ATPase activity in a posterior gill microsomal fraction from the semi-terrestrial mangrove crab Cardisoma guanhumi. Sucrose density gradient centrifugation reveals two distinct membrane fractions showing considerable (Na(+), K(+))-ATPase activity, but also containing other microsomal ATPases. The (Na(+), K(+))-ATPase, notably immuno-localized to the apical region of the epithelial pillar cells, and throughout the pillar cell bodies, has an M r of around 110 kDa and hydrolyzes ATP with V M = 146.8 ± 6.3 nmol Pi min(-1) mg protein(-1) and K M = 0.05 ± 0.003 mmol L(-1) obeying Michaelis-Menten kinetics. While stimulation by Na(+) (V M = 139.4 ± 6.9 nmol Pi min(-1) mg protein(-1), K M = 4.50 ± 0.22 mmol L(-1)) also follows Michaelis-Menten kinetics, modulation of (Na(+), K(+))-ATPase activity by MgATP (V M = 136.8 ± 6.5 nmol Pi min(-1) mg protein(-1), K 0.5 = 0.27 ± 0.04 mmol L(-1)), K(+) (V M = 140.2 ± 7.0 nmol Pi min(-1) mg protein(-1), K 0.5 = 0.17 ± 0.008 mmol L(-1)), and NH4(+) (V M = 149.1 ± 7.4 nmol Pi min(-1) mg protein(-1), K 0.5 = 0.60 ± 0.03 mmol L(-1)) shows cooperative kinetics. Ouabain (K I = 52.0 ± 2.6 µmol L(-1)) and orthovanadate (K I = 1.0 ± 0.05 µmol L(-1)) inhibit total ATPase activity by around 75%. At low Mg(2+) concentrations, ATP is an allosteric modulator of the enzyme. This is the first study to provide a kinetic characterization of the gill (Na(+), K(+))-ATPase in C. guanhumi, and will be useful in better comprehending the biochemical underpinnings of osmoregulatory ability in a semi-terrestrial mangrove crab.
Kinetics of Mn(II) oxidation by spores of the marine Bacillus sp. SG-1
Toyoda, Kazuhiro; Tebo, Bradley M.
2016-09-01
The kinetics of Mn(II) oxidation by spores of the marine Bacillus sp. SG-1 was measured under controlled conditions of the initial Mn(II) concentration, spore concentration, chemical speciation, pH, O2, and temperature. Mn(II) oxidation experiments were performed with spore concentrations ranging from 0.7 to 11 × 109 spores/L, a pH range from 5.8 to 8.1, temperatures between 4 and 58 °C, a range of dissolved oxygen from 2 to 270 μM, and initial Mn(II) concentrations from 1 to 200 μM. The Mn(II) oxidation rates were directly proportional to the spore concentrations over these ranges of concentration. The Mn(II) oxidation rate increased with increasing initial Mn(II) concentration to a critical concentration, as described by the Michaelis-Menten model (Km = ca. 3 μM). Whereas with starting Mn(II) concentrations above the critical concentration, the rate was almost constant in low ionic solution (I = 0.05, 0.08). At high ionic solution (I = 0.53, 0.68), the rate was inversely correlated with Mn(II) concentration. Increase in the Mn(II) oxidation rate with the dissolved oxygen concentration followed the Michaelis-Menten model (Km = 12-19 μM DO) in both a HEPES-buffered commercial drinking (soft) water and in artificial and natural seawater. Overall, our results suggest that the mass transport limitations of Mn(II) ions due to secondary Mn oxide products accumulating on the spores cause a significant decrease of the oxidation rate at higher initial Mn(II) concentration on a spore basis, as well as in more concentrated ionic solutions. The optimum pH for Mn(II) oxidation was approximately 7.0 in low ionic solutions (I = 0.08). The high rates at the alkaline side (pH > 7.5) may suggest a contribution by heterogeneous reactions on manganese bio-oxides. The effect of temperature on the Mn(II) oxidation rate was studied in three solutions (500 mM NaCl, ASW, NSW solutions). Thermal denaturation occurred at 58 °C and spore germination was evident at 40 °C in all three
Kinetics of the intestinal uptake of zinc acexamate in normal and zinc-depleted rats.
Torres-Molina, F; Martínez-Coscollá, A; Gisbert, S; Quintana, E; Sendrós, S; Peris-Ribera, J E; Plá-Delfina, J M
1990-10-01
The uptake of zinc as acexamic acid salt in the small intestine of the anaesthetized rat was shown to be a two-phase process in normal animals. The first phase is rapid mucosal binding which satisfies the Freundlich isotherm equation and which involves about 30 per cent of the initially perfused zinc. The second phase was characterized as an apparent absorption step which obeys Michaelis-Menten and first-order combined kinetics, with the following parameters: Vm = 6.51 mg h-1; Km = 2.96 mg; ka = 0.306 h-1. In largely non-saturated conditions, an apparent global rate constant of about 2.50 h-1 was calculated. No significant interference due to endogenous zinc excretion into the small intestine was observed during the absorption period. In zinc-deficient animals, the two phases were not so well characterized. Binding was non-linear and apparent absorption efficiency was much greater at high zinc concentrations, so no evidence of saturable kinetics was found, thus confirming the hypothesis of a homeostatic zinc regulation mechanism.
Tavares, Ana P M; Silva, Cláudia G; Dražić, Goran; Silva, Adrián M T; Loureiro, José M; Faria, Joaquim L
2015-09-15
The biocatalytic performance of immobilized enzyme systems depends mostly on the intrinsic properties of both biomolecule and support, immobilization technique and immobilization conditions. Multi-walled carbon nanotubes (MWCNTs) possess unique features for enzyme immobilization by adsorption. Enhanced catalytic activity and stability can be achieved by optimization of the immobilization conditions and by investigating the effect of operational parameters. Laccase was immobilized over MWCNTs by adsorption. The hybrid material was characterized by Fourier transformed infrared (FTIR) spectroscopy, scanning and transmission electron microscopy (SEM and TEM, respectively). The effect of different operational conditions (contact time, enzyme concentration and pH) on laccase immobilization was investigated. Optimized conditions were used for thermal stability, kinetic, and storage and operational stability studies. The optimal immobilization conditions for a laccase concentration of 3.75μL/mL were a pH of 9.0 and a contact time of 30min (522 Ulac/gcarrier). A decrease in the thermal stability of laccase was observed after immobilization. Changes in ΔS and ΔH of deactivation were found for the immobilized enzyme. The Michaelis-Menten kinetic constant was higher for laccase/MWCNT system than for free laccase. Immobilized laccase maintained (or even increased) its catalytic performance up to nine cycles of utilization and revealed long-term storage stability.
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.
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.
Kinetic studies on the inhibition of GABA-T by gamma-vinyl GABA and taurine.
Sulaiman, Saba A J; Suliman, Fakhr Eldin O; Barghouthi, Samira
2003-08-01
Gamma-aminobutyric acid transaminase (GABA-T, EC 2.6.1.19) is a pyridoxal phosphate (PLP) dependent enzyme that catalyzes the degradation of gamma-aminobutyric acid. The kinetics of this reaction are studied in vitro, both in the absence, and in the presence of two inhibitors: gamma-vinyl GABA (4-aminohex-5-enoic acid), and a natural product, taurine (ethylamine-2-sulfonic acid). A kinetic model that describes the transamination process is proposed. GABA-T from Pseudomonas fluorescens is inhibited by gamma-vinyl GABA and taurine at concentrations of 51.0 and 78.5 mM. Both inhibitors show competitive inhibition behavior when GABA is the substrate and the inhibition constant (Ki) values for gamma-vinyl GABA and taurine were found to be 26 +/- 3 mM and 68 +/- 7 mM respectively. The transamination process of alpha-ketoglutarate was not affected by the presence of gamma-vinyl GABA, whereas, taurine was a noncompetitive inhibitor of GABA-T when alpha-ketoglutarate was the substrate. The inhibition dissociation constant (Kii) for this system was found to be 96 +/- 10 mM. The Michaelis-Menten constant (Km) in the absence of inhibition, was found to be 0.79 +/- 0.11 mM, and 0.47 +/- 0.10 mM for GABA and alpha-ketoglutarate respectively.
Mass action realizations of reaction kinetic system models on various time scales
Hangos, K M; Szederkenyi, G, E-mail: hangos@scl.sztaki.hu, E-mail: szeder@scl.sztaki.hu [Process Control Research Group, Computer and Automation Reseach Institute, Kende u. 13-17, H-1111 Budapest (Hungary)
2011-01-01
Complex chemical reaction networks often exhibit different dynamic behaviour on different time scales. A combined approach is proposed in this work for determining physically meaningful mass action realizations of complex chemical reaction networks that describe its dynamic behaviour on different time scales. This is achieved by appropriately reducing the detailed overall mass action kinetic scheme using quasi steady state assumptions fit to the particular time scale, and then searching for an optimal realization using mixed integer linear programing. Furthermore, the relationship between the properties (reversibility, deficiency, stability) of the obtained realizations of the same system on different time scales are also investigated and related to the same properties of the detailed overall model. It is shown that the reduced models obtained by quasi steady state assumptions may show exotic nonlinear behaviour, such as oscillations, when the original detailed is globally asymptotically stable. The proposed methods are illustrated by using a simple Michaelis-Menten type reaction kinetic example. The simplified versions of the well known Brusselator model have also been investigated and presented as a case study.
DRAGOMIRESCU MONICA
2007-01-01
Full Text Available Robust immobilization techniques that preserve the activity of biomolecules havemany potential applications. In recent years, a number of new bioimobilisationmethods in sol-gel-derived materials were reported. The interactions between thebiomolecule and the inorganic material determine the degree to which thebiomolecule retains its native properties. The newer technological developments inthe field of immobilized biocatalysts can offer the possibility of a wider and moreeconomical exploitation of biocatalysts in biological applications, food and feedindustry, medicine, and in the development of bioprocess monitoring devices, like thebiosensors.The aim of this study was to obtain immobilized enzymatic preparations by methodswhich affect enzyme conformations and kinetic parameters as less as possible. Weimmobilized the enzymatic preparation with protease activity produced by a Bacilluslicheniformis B 40 local strain by physical bonding on ceramics and entrapment intosol-gel-derived glasses obtained from tetraethyl orthosilicate (TEOS, deposited inthin layer on a ceramic support (entrapment/deposition. Both physically adsorbedand entrapped/deposited enzymes follow Michaelis-Menten kinetics, similar with thesoluble enzyme. In the case of immobilized enzymes, the apparent Michaelisconstant, Km, was greater than that of the native one, as it was expected. The kineticparameters indicate that the enzymatic preparations adsorbed on ceramic supportand entrapped/deposited show less affinity for the substrate, Km being 1.3 and 2.1times higher than that of the native enzyme, respectively. The maximum velocityincreased also by 3.5 and 7.9 times respectively, compared with the free counterpart(according to Lineweaver-Burk linearization.
Korla, Kalyani; Vadlakonda, Lakshmipathi; Mitra, Chanchal K
2015-01-01
In the present work, we have kinetically simulated two mitochondrial shuttles, malate-aspartate shuttle (used for transferring reducing equivalents) and citrate-pyruvate shuttle (used for transferring carbon skeletons). However, the functions of these shuttles are not limited to the points mentioned above, and they can be used in different arrangements to meet different cellular requirements. Both the shuttles are intricately associated with Krebs cycle through the metabolites involved. The study of this system of shuttles and Krebs cycle explores the response of the system in different metabolic environments. Here, we have simulated these subsets individually and then combined them to study the interactions among them and to bring out the dynamics of these pathways in focus. Four antiports and a pyruvate pump were modelled along with the metabolic reactions on both sides of the inner mitochondrial membrane. Michaelis-Menten approach was extended for deriving rate equations of every component of the system. Kinetic simulation was carried out using ordinary differential equation solver in GNU Octave. It was observed that all the components attained steady state, sooner or later, depending on the system conditions. Progress curves and phase plots were plotted to understand the steady state behaviour of the metabolites involved. A comparative analysis between experimental and simulated data show fair agreement thus validating the usefulness and applicability of the model.
Investigation of Horseradish Peroxidase Kinetics in an "Organelle-Like" Environment.
Baumann, Patric; Spulber, Mariana; Fischer, Ozana; Car, Anja; Meier, Wolfgang
2017-05-01
In order to mimic cell organelles, artificial nanoreactors have been investigated based on polymeric vesicles with reconstituted channel proteins (outer membrane protein F) and coencapsulated enzymes horseradish peroxidase (HRP) along with a crowding agent (Ficoll or polyethylene glycol) inside the cavity. Importantly, the presence of macromolecules has a strong impact on the enzyme kinetics, but no influence on the integrity of vesicles up to certain concentrations. This particular design allows for the first time the determination of HRP kinetics inside nanoreactors with crowded milieu. The values of the Michaelis-Menten constant (K m ) measured for HRP in a confined space (encapsulated in nanoreactors) in the absence of macromolecules are ≈50% lower than in free conditions, and the presence of a crowding agent results in a further pronounced decrease. These results clearly suggest that activities of enzymes in confined spaces can be tuned by varying the concentrations of crowding compounds. The present investigation represents an advance in nanoreactor design by considering the influence of environmental factors on enzymatic performance, and it demonstrates that both encapsulation and the presence of a crowding environment increase the enzyme-substrate affinity. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.
Sengupta, Avery; Dey, Tanmoy; Ghosh, Mahua; Ghosh, Jaydip; Ghosh, Santinath
2012-08-01
This study investigated the successful enzymatic production of furfuryl oleate and its detailed kinetic study by Michaelis-Menten model. Esterification of oleic acid and furfuryl alcohol by Candida antarctica lipase B (Novozym 435 preparation) in a solvent free system was studied in the present work at 1:1 molar ratio of furfuryl alcohol and oleic acid. About 99 % conversion (on the basis of oleic acid) has been achieved within 6 h at 5 % enzyme concentration. Ping-pong bi-bi mechanism (inhibition phenomenon taken into account) was applied to describe the ratios as a complex kinetic model. The kinetic parameters were determined using MATLAB language programme. The two initial rate constants KA and KB respectively were found out by different progress curves plotted with the help of MATLAB language programme. It was concluded from the results that furfuryl alcohol considerably inhibited the enzymatic reaction while oleic acid had negligible inhibitory effect. It was clearly seen that the initial rate was increased with the increase in the furfuryl alcohol concentration until 2 M/L after which there was a drop in the initial rate depicting the inhibitory effect of furfuryl alcohol. Surprisingly, it has been observed that addition of 0.1 mol of product activated the esterification reaction. Finally, the model was found to be statistically fitting well with the experimental data.
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.
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.
Jin, Jian; Ma, Haile; Qu, Wenjuan; Wang, Kai; Zhou, Cunshan; He, Ronghai; Luo, Lin; Owusu, John
2015-11-01
The effects of multi-frequency power ultrasound (MPU) pretreatment on the kinetics and thermodynamics of corn gluten meal (CGM) were investigated in this research. The apparent constant (KM), apparent break-down rate constant (kA), reaction rate constants (k), energy of activation (Ea), enthalpy of activation (ΔH), entropy of activation (ΔS) and Gibbs free energy of activation (ΔG) were determined by means of the Michaelis-Menten equation, first-order kinetics model, Arrhenius equation and transition state theory, respectively. The results showed that MPU pretreatment can accelerate the enzymolysis of CGM under different enzymolysis conditions, viz. substrate concentration, enzyme concentration, pH, and temperature. Kinetics analysis revealed that MPU pretreatment decreased the KM value by 26.1% and increased the kA value by 7.3%, indicating ultrasound pretreatment increased the affinity between enzyme and substrate. In addition, the values of k for ultrasound pretreatment were increased by 84.8%, 41.9%, 28.9%, and 18.8% at the temperature of 293, 303, 313 and 323 K, respectively. For the thermodynamic parameters, ultrasound decreased Ea, ΔH and ΔS by 23.0%, 24.3% and 25.3%, respectively, but ultrasound had little change in ΔG value in the temperature range of 293-323 K. In conclusion, MPU pretreatment could remarkably enhance the enzymolysis of CGM, and this method can be applied to protein proteolysis industry to produce peptides.
Jaya Gosain; Pradeep K Sharma
2003-04-01
Kinetics of oxidation of five vicinal and four non-vicinal diols, and two of their monoethers, by tetrabutylammonium tribromide (TBATB) has been studied. The vicinal diols yield products arising out of glycol-bond fission, while the non-vicinal diols produce the hydroxycarbonyl compounds. The reaction is first-order with respect to TBATB. Michaelis-Menten type kinetics is observed with respect to diols. The reaction fails to induce the polymerization of acrylonitrile. There is no effect of tetrabutylammonium chloride on the reaction rate. The proposed reactive oxidizing species is the tribromide ion. The effect of solvent composition indicates that the rate increases with increase in the polarity of the solvent. The oxidation of [1,1,2,2-2H4] ethanediol shows the absence of any primary kinetic isotope effect. Values of solvent isotope effect, (H2O)/(D2O), at 288 K for the oxidation of ethanediol, propane-1,3-diol and 3-methoxybutan-1-ol are 3.41, 0.98 and 1.02 respectively. A mechanism involving a glycol-bond fission has been proposed for the oxidation of vicinal diols. Non-vicinal diols are oxidised by a hydride-transfer mechanism, as they are monohydric alcohols.
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 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.
R. Ramachandrappa
2013-01-01
Full Text Available A kinetic study on RuCl3-catalysed oxidation of levocarnitine (LC by sodium N-bromo-p-toluenesulphonamide or bromamine-T (BAT has been carried out in HCl medium at 303 K. The reaction rate shows a first order dependence on [BAT]0 and fractional order with respect to both [LC]0 and [H+]. Addition of the reaction product, p-toluenesulphonamide, retards the rate. The addition of RuCl3 and chloride ions to the reaction mixture shows an increase in the rate of the reaction. The dielectric effect is positive. The variation of ionic strength of the medium has no significant effect on the rate of the reaction. The reaction fails to initiate polymerization of acrylamide. Michaelis-Menten type of kinetics has been proposed. Thermodynamic parameters have been computed from Arrhenius plot by studying the reaction at different temperatures. The reaction stoichiometry and oxidation products were identified. Based on the experimental observations a suitable mechanism was proposed and rate law deduced.
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.
Wang, Haina; Ji, Jianbo; Zeng, Su
2011-08-15
Zaltoprofen, available commercially as a racemic mixture, is a propionic acid derivative of non-steroidal anti-inflammatory drugs (NSAIDs). Firstly, (+)- and (-)-zaltoprofen glucuronide was biosynthesized and purified. Then a simple and rapid RP-HPLC analysis method for direct determination of (+)- and (-)-zaltoprofen glucuronide in rat hepatic microsomes was developed and validated. The calibration curves of (+)- and (-)-zaltoprofen glucuronide both showed good linearity in the concentration range from 0.15 to 31.13 μM. The lower limit of quantification was 0.15 μM. Finally, this method was used to investigate the enantioselectivity of zaltoprofen glucuronidation in rat hepatic microsomes. The kinetics of zaltoprofen glucuronidation in rat hepatic microsomes for 40 min incubation fit the Michaelis-Menten model. Kinetic analysis indicated that (-)-zaltoprofen had a higher glucuronidation rate in rat liver microsome than that of (+)-zaltoprofen. The catalyzing efficiency (V(max)/K(m)) ratio of (+)-zaltoprofen to (-)-enantiomer is 0.8 times in rat liver microsomes.
Claudia Avitia-Domínguez
2014-04-01
Full Text Available Methicillin-resistant Staphylococcus auerus (MRSA strains are having a major impact worldwide, and due to their resistance to all β-lactams, an urgent need for new drugs is emerging. In this regard, the shikimate pathway is considered to be one of the metabolic features of bacteria and is absent in humans. Therefore enzymes involved in this route, such as shikimate dehydrogenase (SDH, are considered excellent targets for discovery of novel antibacterial drugs. In this study, the SDH from MRSA (SaSDH was characterized. The results showed that the enzyme is a monomer with a molecular weight of 29 kDa, an optimum temperature of 65 °C, and a maximal pH range of 9–11 for its activity. Kinetic studies revealed that SDH showed Michaelis-Menten kinetics toward both substrates (shikimate and NADP+. Initial velocity analysis suggested that SaSDH catalysis followed a sequential random mechanism. Additionally, a tridimensional model of SaSDH was obtained by homology modeling and validated. Through virtual screening three inhibitors of SaSDH were found (compounds 238, 766 and 894 and their inhibition constants and mechanism were obtained. Flexible docking studies revealed that these molecules make interactions with catalytic residues. The data of this study could serve as starting point in the search of new chemotherapeutic agents against MRSA.
Wu, C.H.; Shreeve, W.W.
1975-06-01
Kinetic studies of the very-low-density lipoprotein triglycerides (VLDL-TG) turnover by endogenous labeling with glycerol-2-/sup 3/H were performed in 13 patients in the postabsorptive state, first after 10-14 days on a low-sucrose high-starch-diet, then again after 10-14 days of isocaloric high-sucrose low-starch diet (HSD). After HSD, a significant decrease in the fractional turnover rates of VLDL-TG was observed, as well as a modest but significant increase in its pool size, but the net turn-over rates remained unchanged. Using Michaelis-Menten formulation, we have further calculated the V/sub max/ and Km's of the removal system for VLDL-TG and found that the V/sub max/ and Km's do not differ significantly between the two dietary periods. These results suggest that the removal mechanism for VLDL-TG has not changed after 10-14 days on the HSD, at least when the patients are studied in the postabsorptive state. Measurements of postheparin lipolytic activity under fed condition in 17 patients (including the 13 patients above) have shown a decrease after HSD. However, a defect in the removal of plasma-TG related to decreased activity of tissue-lipoprotein lipase in the fed state has not been conclusively uncovered by the kinetic studies performed in the postabsorptive state, and cannot contribute significantly to the expansion of VLDL-TG pool.
Palai, Tapas; Mitra, Shubhrajyoti; Bhattacharya, Prashant K
2012-10-01
The enzymatic synthesis of galacto-oligosaccharides (GOS) from lactose was studied using commercial grade β-galactosidase (Biolacta FN5) from Bacillus circulans. The reaction was carried out under free enzyme condition varying initial lactose concentration (ILC: 55-525 g/L), enzyme concentration (0.05-1.575 g/L), temperature (30-50°C) and pH (5.0-6.0). Reaction mixture compositions were analyzed utilizing high performance liquid chromatography (HPLC). A maximum GOS formation of 39% (dry basis) was achieved at an ILC of 525 g/L converting 60% of the lactose fed. Tri-saccharides were the major types of GOS formed, accounting approximately 24%; whereas, tetra-saccharides and penta-saccharides account approximately 12% and 3%, respectively. Design correlation was developed in order to observe the quantitative effect of operating parameters on GOS yield. Further, based on Michaelis-Menten model, four-step reaction pathways were considered for simplistic understanding of the kinetics. Apart from predicting the reaction mixture composition, the approach also provided kinetic parameters though simulation using COPASI 4.7®. Excellent agreements were observed between simulated and experimental results.
Enzyme Kinetics: A critique of the quasi-steady-state approximation
Bhattacharyya, Kamal
2013-01-01
The standard two-step model of homogeneous-catalyzed reactions had been theoretically analyzed at various levels of approximations from time to time. The primary aim was to check the validity of the quasi-steady-state approximation, and hence emergence of the Michaelis-Menten kinetics, with various substrate-enzyme ratios. But, conclusions vary. We solve here the desired set of coupled nonlinear differential equations by invoking a new set of dimensionless variables. Approximate solutions are obtained via the power-series method aided by Pade approximants. The scheme works very successfully in furnishing the initial dynamics at least up to the region where existence of any steady state can be checked. A few conditions for its validity are put forward and tested against the findings. Temporal profiles of the substrate and the product are analyzed in addition to that of the complex to gain further insights into legitimacy of the above approximation. Some recent observations like the reactant stationary approxim...
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.
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.
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.
Wang, Ning-Xin; Li, Yan; Deng, Xi-Hai; Miao, Ai-Jun; Ji, Rong; Yang, Liu-Yan
2013-05-01
In the present study, the toxicity and bioaccumulation kinetics of arsenate in two green algae Chlamydomonas reinhardtii and Scenedesmus obliquus under phosphate-enriched (+P) and limited (-P) conditions were investigated. P-limitation was found to aggravate arsenate toxicity and S. obliquus was more tolerant than C. reinhardtii. Such phosphate-condition-dependent or algal-species-specific toxicity difference was narrowed when the relative inhibition of cell growth was plotted against intracellular arsenate content instead of its extracellular concentration. The discrepance was further reduced when the intracellular ratio of arsenic to phosphorus was applied. It suggests that both arsenate bioaccumulation and intracellular phosphorus played an important role in arsenate toxicity. On the other hand, arsenate uptake was induced by P-limitation and its variation with ambient arsenate concentration could be well fitted to the Michaelis-Menten model. Arsenate transporters of S. obliquus were found to have a higher affinity but lower capacity than those of C. reinhardtii, which explains its better regulation of arsenate accumulation than the latter species in the toxicity experiment. Further, arsenate depuration was facilitated and more was transformed to arsenite in C. reinhardtii or under -P condition. Intracellular proportion of arsenite was also increased after the algae were transferred from the long-term uptake media to a relatively clean solution in the efflux experiment. Both phenomena imply that algae especially the sensitive species could make physiological adjustments to alleviate the adverse effects of arsenate. Overall, our findings will facilitate the application of algae in arsenate remediation.
Savic, Sasa; Vojinovic, Katarina; Milenkovic, Sanja; Smelcerovic, Andrija; Lamshoeft, Marc; Petronijevic, Zivomir
2013-12-15
Flavonoid oxidation is important issue in food processing and quality. The kinetic mechanism of enzymatic oxidation of rutin by horseradish peroxidase (HRP) was studied. Rutin oxidation reaction was followed by recording of spectral changes over the time at 360 nm. The studied oxidation is mostly enzymatic and less part non-enzymatic. The reaction with HRP has a higher rate compared with the reaction without of HRP, whereby is part of non-enzymatic reaction about 10% of the total reaction. Kinetic parameters were determined from graphics of linear Michaelis-Menten equation, and it was found that investigated reactions of rutin oxidation by HRP take place in a ping-pong kinetic mechanism. High resolution HPLC-MS analysis of the mixture of oxidized products of rutin revealed the presence of rutin dimer. Because of widely distribution of rutin as well as presence of peroxidases and hydrogen peroxide in fresh foods identification of this enzymatic modification product can be beneficial for foods quality and safety.
Maier-Salamon, Alexandra; Böhmdorfer, Michaela; Thalhammer, Theresia; Szekeres, Thomas; Jaeger, Walter
2011-01-01
The enzyme kinetic profiles of the formation of resveratrol-3-O-glucuronide (R3G) and resveratrol-4'-O-glucuronide (R4'G) by liver microsomes from humans, dogs, and rodents were investigated. Glucuronidation by human and dog liver microsomes to R3G and R4'G occurred for about 65% of applied resveratrol, and was significantly reduced to 10% when substrate concentration was increased 10-fold. In contrast, rodent microsomes glucuronidated about 90% of applied resveratrol independently of substrate concentration. Furthermore, in mouse and rat liver microsomes, resveratrol was almost exclusively conjugated at position 3, whereas human and dog livers also glucuronidated resveratrol at position 4' (ratio R3G:R4'G = 5:1). Interspecies differences were also found when calculating the enzyme kinetic profiles of both conjugates. Formation of R4'G in human and dog microsomes followed Michaelis-Menten kinetics, while R3G showed substrate inhibition at higher resveratrol concentrations. In mouse and rat microsomes, however, both R3G and R4'G formation exhibited auto-activation kinetics. Formation of R3G and R4'G by recombinant UGT1A1 also showed substrate inhibition kinetics that led to decreased intrinsic clearance values, while UGT1A9-catalyzed glucuronidation demonstrated substrate inhibition kinetics at position 3 and Hill kinetics for the formation of R4'G. In conclusion, resveratrol glucuronidation exhibited species-dependent differences, with the dog as the animal model that most closely represents humans in terms of this process.
Modelling phytate degradation kinetics in soaked wheat and barley
Blaabjerg, Karoline; Strathe, A B; Poulsen, Hanne Damgaard
2012-01-01
) function, a first-order (FO) function and a Generalised Michaelis Menten (GMM) function were considered. The GMM fitted the data best. The GMM function was used to derive the relative instantaneously degradable fraction of phytate (F0) and the half-life (t1/2) of phytate in hours (K). Addition of Phytase 1...
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
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
Takayanagi, Toshiaki
2011-07-01
Cell-mediated cytotoxicity assays are widely implemented to evaluate cell-mediated cytotoxic activity, and some assays are analyzed using the analogy of enzyme kinetics. In the analogy, the effector cell is regarded as the enzyme, the target cell as the substrate, the effector cell-target cell conjugate as the enzyme-substrate complex and the dead target cell as the product. However, the assumptions analogous to those of enzyme kinetics are not always true in cell-mediated cytotoxicity assays, and the parameter analogous to the Michaelis-Menten constant is not constant but is dependent on the number of effector cells. Therefore I present novel mathematical models for cell-mediated cytotoxicity assays without applying enzyme kinetics. I instead use combinations and probability, because analysis of cell-mediated cytotoxicity assays by applying enzyme kinetics seems controversial. With my original models, I demonstrate simulations of the data in previously published papers. The results are exhibited in the same forms as the corresponding data. Comparing the simulation results with the published data, the results seem to agree well with the data. From simulations of cytotoxic assays with bulk effector cells, it appears that bystanders in bulk effector cells increase both the cytotoxic activity and the motility of effector cells.
Research progress of the atypical kinetic profiles of cytochrome P450 enzymes%细胞色素P450酶的非典型动力学研究进展
曾彩雯; 何芳; 夏春华; 熊玉卿
2012-01-01
Cytochrome P450 enzymes are composed of many isozyraes and involved in the biotransformation of both exogenous and endogenous substances. A growing number of studies have found that the P450 enzymes do not always follow the classical Michaelis-Menten kinetics, but show atypical kinetic behavior, which is also the current research hotspot. In this paper, the category and mechanisms of atypical kinetics of the P450 enzyme were reviewed, providing theoretical basis for the research of enzyme kinetics.%细胞色素P450酶是一组由许多同工酶组成的超基因大家族,在外源性和内源性物质的代谢中起着极其重要的作用.越来越多的研究发现,P450酶并不总是遵循经典的米氏动力学,动力学模式经常以别构形式出现,即表现出非典型动力学行为,这也是当今的一个研究热点.本文就P450酶的非典型动力学表现形式及其发生机制做一综述,为酶动力学研究提供科学依据.
Kinetic Modeling of Enzymatic Hydrolysis of Coconut Oil with Lipase%脂肪酶水解椰子油动力学研究
武林贺; 白新鹏; 吴谦; 徐小梦; 马若影; 李雪
2016-01-01
A kinetic study on hydrolysis for the production of derivatives catalyzed by Lipase was investigated. The effects of substrate concentration,enzyme concentration,temperature and time on the hydrolysis rate of co-conut oil by lipase were analyzed. Based on this,the Michaelis constant(km) and maximum rate(Vm) were de-duced by Lineweaver-Burk plotting and Wilkinson statistical method. Results showed that,under the optimal conditions of enzyme concentration 1%and temperature 50℃,the km and Vm were 1.273 9 [mg/(g·mL)] and 0.969 6 [mg/(g·mL·min)] respectively. The Michaelis-Menten equation was:v= 0.969 6[S]1.273 9+[S] . The model-pre-dicted values were consistent with the actually measured values from confirmation tests. Though the simulation of Michaelis-Menten equation to the hydrolysis process,goodness of fit were greater than 0.99,it found that ap-plication of Michaelis-Menten equation in hydrolysis process was reasonable. It can provide research foundation for the fat digestion process.%为了探究脂肪酶水解椰子油的动力学过程，在研究了底物质量浓度、酶添加量、酶解温度及酶解时间对脂肪酶水解椰子油反应速率影响的基础上，本试验采用Lineweaver-Burk法和Wilkinson统计法两种方法对酶解过程进行拟合，计算酶解过程的动力学常数km和Vm，并求解脂肪酶水解椰子油动力学方程。结果表明：在酶添加量为1%、温度为50℃的条件下，动力学常数km为1.2739[mg/（g·mL）]，Vm为0.9696[mg/（g·mL·min）]，米氏方程为：v=0.9696[S]1.2739+[S]。经过试验验证得出米氏方程的拟合度大于0.99，说明方程的预测值与测定值基本吻合，米氏方程适合脂肪酶水解椰子油动力学研究，为油脂酶解过程提供理论模型。
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
Krishna, Honnur; Nagaraja, Padmarajaiah; Shivakumar, Anantharaman; Chamaraja, Nelligere A.; Aradhana, Narayan
2013-02-01
The intermolecular coupling of 2,5-dimethoxyaniline (DMA) as mediated electron transfer reaction in presence of H2O2 and peroxidase in acetate buffer of pH 4.2 resulting green colored product having maximum absorption at λmax = 740 nm was investigated by spectrophotometer. Under optimum conditions, linearity range for the quantification of H2O2 was 2.0-288.0 μM and for peroxidase were 0.59-9.46 and 0.443-9.46 nM by kinetic and fixed-time method, respectively. The catalytic efficiency and catalytic power were KeffD = 2.354 × 105 M-1 min-1 and KpowD = 4.59 × 10-4 min-1, respectively. From the plot of d(1/Do) vs d(1/Vo) and d(1/Ho) vs d(1/Vo), Michaelis-Menten constants for DMA and H2O2were found that KmD = 1458 μM and KmHO = 301 μM. Applicability of the method was tested for peroxidase activity in some plant extracts and compared with guaiacol/peroxidase system. Regarding superiority of the method, it is suggested that DMA/peroxidase system can be a better hydrogen donor for HRP assay than guaiacol system as evident from kinetic data.
Eibes, G; Moreira, M T; Feijoo, G; Lema, J M
2008-07-01
Polycyclic aromatic hydrocarbons (PAHs) are toxic compounds presenting low water solubility and high hydrophobicity, which greatly hampers their natural biodegradation. The enzymatic degradation of a model compound, anthracene, was evaluated in presence of a miscible solvent for an increased solubility. Manganese peroxidase, a ligninolytic enzyme from white-rot fungi, was used as biocatalyst in a medium containing acetone. The kinetic parameters of the enzymatic degradation of anthracene, obtained from fed-batch experiments, were applied to model the operation of a continuous reactor. Kinetics comprised a Michaelis-Menten equation, modified with an autocatalytic term, assumed to the effect of quinones acting as electron carriers, and a logistic function related to enzyme activity. The continuous reactor has been operated for 108 h, attaining a 90% of anthracene degradation, which demonstrated the feasibility of the system for its application in the removal of poorly soluble compounds. The model of this reactor permitted to predict accurately anthracene degradation in different conditions, such as external addition of anthraquinone and different enzymatic activities.
Krishna, Honnur; Nagaraja, Padmarajaiah; Shivakumar, Anantharaman; Chamaraja, Nelligere A; Aradhana, Narayan
2013-02-01
The intermolecular coupling of 2,5-dimethoxyaniline (DMA) as mediated electron transfer reaction in presence of H(2)O(2) and peroxidase in acetate buffer of pH 4.2 resulting green colored product having maximum absorption at λ(max)=740 nm was investigated by spectrophotometer. Under optimum conditions, linearity range for the quantification of H(2)O(2) was 2.0-288.0 μM and for peroxidase were 0.59-9.46 and 0.443-9.46 nM by kinetic and fixed-time method, respectively. The catalytic efficiency and catalytic power were K(eff)(D)=2.354 × 10(5)M(-1)min(-1) and K(pow)(D)=4.59 × 10(-4)min(-1), respectively. From the plot of d(1/D(o)) vs d(1/V(o)) and d(1/H(o)) vs d(1/V(o)), Michaelis-Menten constants for DMA and H(2)O(2)were found that K(m)(D)=1,458 μM and [Formula: see text] =301 μM. Applicability of the method was tested for peroxidase activity in some plant extracts and compared with guaiacol/peroxidase system. Regarding superiority of the method, it is suggested that DMA/peroxidase system can be a better hydrogen donor for HRP assay than guaiacol system as evident from kinetic data.
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.
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.
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.
Kim, Hyojin; Seo, Kyung-Ah; Kim, Hyunmi; Lee, Hye Suk; Lee, Choong-Hwan; Shin, Jae-Gook; Liu, Kwang-Hyeon
2007-04-01
KR-32570 (5-(2-Methoxy-5-chlorophenyl)furan-2-ylcarbonyl)guanidine) is a new cardioprotective agent for preventing ischemia-reperfusion injury. Human liver microsomal incubation of KR-32570 in the presence of NADPH resulted in the formation of two metabolites, hydroxy-KR-32570 and O-desmethyl-KR-32570. In this study, a kinetic analysis of the metabolism of two metabolites from KR-32570 was performed in human liver microsomes, and recombinant CYP1A2, and CYP3A4. The metabolism for hydroxy- and O-desmethyl-KR-32570 formation from KR-32570 by human liver microsomes was best described by a Michaelis-Menten equation and a Hill equation, respectively. The Cl(int) values of hydroxy- and O-desmethyl-KR-32570 formation were similar to each other (0.03 vs 0.04 microL/min/pmol CYP, respectively). CYP3A4 mediated the formation of hydroxy-KR-32570 from KR-32570 with Cl(int) = 0.24 microL/min/pmol CYP3A4. The intrinsic clearance for O-desmethyl-KR-32570 formation by CYP1A2 was 0.83 AL/min/pmol CYP1A2. These findings suggest that CYP3A4 and CYP1A2 enzymes are major enzymes contributing to the metabolism of KR-32570.
Rolando Mendoza
2012-01-01
Full Text Available El objetivo de este trabajo fue determinar la cinética de inactivación de la enzima peroxidasa y la cinética del color y textura en tubérculos de papa criolla (Solanum tuberosum grupo phureja sometidos a escaldado mediante agua a 80°C, 90°C y vapor saturado a 93°C. Los coeficientes de transferencia de calor para el escaldado en agua oscilaron entre 214 y 230 W °C-1 m-2 mientras que para vapor saturado fueron en promedio 84.5 W °C-1 m-2. A diferentes tiempos de precocción el tubérculo de papa criolla presentó una zona en donde ocurrió pardeamiento enzimático, hecho que fue modelado según la cinética de Michaelis-Menten y otra zona en donde el cambio de color disminuyó debido a la inactivación enzimática que correspondió a una cinética de primer orden, de manera similar al comportamiento de la textura. La inactivación de la enzima peroxidasa obedeció al mecanismo de Lumry-Eyring.The objective of this work was to determine the inactivation kinetics of peroxidase enzyme and the change in color and texture in golden potato tubers (Solanum tuberosum phureja group exposed to blanching with water at 80°C, 90°C and to saturated steam at 93°C. The heat transfer coefficients for the blanch water ranged between 214 and 230 W °C-1 m-2 while for saturated steam they showed an average of 84.5 W °C-1 m-2. At different pre-cooking times the golden potato tuber showed an area that developed enzymatic browning, which was fitted to the Michaelis-Menten kinetic model and another area where the color change decreased due to enzyme inactivation, which corresponded to first order kinetics, in a similar way as the texture behavior. The inactivation of peroxidase enzyme followed the Lumry-Eyring mechanism.
Prévoteau, Antonin; Geirnaert, Annelies; Arends, Jan B. A.; Lannebère, Sylvain; van de Wiele, Tom; Rabaey, Korneel
2015-07-01
Monitoring in vitro the metabolic activity of microorganisms aids bioprocesses and enables better understanding of microbial metabolism. Redox mediators can be used for this purpose via different electrochemical techniques that are either complex or only provide non-continuous data. Hydrodynamic chronoamperometry using a rotating disc electrode (RDE) can alleviate these issues but was seldom used and is poorly characterized. The kinetics of Faecalibacterium prausnitzii A2-165, a beneficial gut microbe, were determined using a RDE with riboflavin as redox probe. This butyrate producer anaerobically ferments glucose and reduces riboflavin whose continuous monitoring on a RDE provided highly accurate kinetic measurements of its metabolism, even at low cell densities. The metabolic reaction rate increased linearly over a broad range of cell concentrations (9 × 104 to 5 × 107 cells.mL-1). Apparent Michaelis-Menten kinetics was observed with respect to riboflavin (KM = 6 μM kcat = 5.3×105 s-1, at 37 °C) and glucose (KM = 6 μM kcat = 2.4 × 105 s-1). The short temporal resolution allows continuous monitoring of fast cellular events such as kinetics inhibition with butyrate. Furthermore, we detected for the first time riboflavin reduction by another potential probiotic, Butyricicoccus pullicaecorum. The ability of the RDE for fast, accurate, simple and continuous measurements makes it an ad hoc tool for assessing bioprocesses at high resolution.
Galmés, Jeroni; Hermida-Carrera, Carmen; Laanisto, Lauri; Niinemets, Ülo
2016-09-01
The present study provides a synthesis of the in vitro and in vivo temperature responses of Rubisco Michaelis-Menten constants for CO2 (Kc) and O2 (Ko), specificity factor (Sc,o) and maximum carboxylase turnover rate (kcatc) for 49 species from all the main photosynthetic kingdoms of life. Novel correction routines were developed for in vitro data to remove the effects of study-to-study differences in Rubisco assays. The compilation revealed differences in the energy of activation (∆Ha) of Rubisco kinetics between higher plants and other photosynthetic groups, although photosynthetic bacteria and algae were under-represented and very few species have been investigated so far. Within plants, the variation in Rubisco temperature responses was related to species' climate and photosynthetic mechanism, with differences in ∆Ha for kcatc among C3 plants from cool and warm environments, and in ∆Ha for kcatc and Kc among C3 and C4 plants. A negative correlation was observed among ∆Ha for Sc/o and species' growth temperature for all data pooled, supporting the convergent adjustment of the temperature sensitivity of Rubisco kinetics to species' thermal history. Simulations of the influence of varying temperature dependences of Rubisco kinetics on Rubisco-limited photosynthesis suggested improved photosynthetic performance of C3 plants from cool habitats at lower temperatures, and C3 plants from warm habitats at higher temperatures, especially at higher CO2 concentration. Thus, variation in Rubisco kinetics for different groups of photosynthetic organisms might need consideration to improve prediction of photosynthesis in future climates. Comparisons between in vitro and in vivo data revealed common trends, but also highlighted a large variability among both types of Rubisco kinetics currently used to simulate photosynthesis, emphasizing the need for more experimental work to fill in the gaps in Rubisco datasets and improve scaling from enzyme kinetics to realized
Siddiqui, Khawar Sohail; Ertan, Haluk; Charlton, Timothy; Poljak, Anne; Daud Khaled, A K; Yang, Xuexia; Marshall, Gavin; Cavicchioli, Ricardo
2014-05-20
The kinetic constants of a hybrid versatile-peroxidase (VP) which oxidizes complex polymeric humic substances (HS) derived from lignin (humic and fulvic acids) and industrial wastes were determined for the first time using isothermal titration calorimetry (iTC). The reaction conditions were manipulated to enable manganese-peroxidase (MnP) and/or lignin-peroxidase (LiP) activities to be evaluated. The peroxidase reactions exhibited varying degrees of product inhibition or activation; properties which have not previously been reported for VP enzymes. In contrast to previous work (Ertan et al., 2012) on small non-polymeric substrates (MnSO4, veratryl alcohol and dyes), all kinetic plots for polymeric HS were sigmoidal, lacked Michaelis-Menten characteristics, and were indicative of positive cooperativity. Under conditions when both LiP and MnP were active, the kinetic data fitted to a novel biphasic Hill Equation, and the rate of enzymatic reaction was significantly greater than the sum of individual LiP plus MnP activities implying synergistic activation. By employing size-exclusion chromatography and electrospray ionization mass spectrometry, the characteristics of the oxidative degradation products of the HS were also monitored. Our study showed that the allosteric behaviour of the VP enzyme promotes a high level of regulation of activity during the breakdown of model and industrial ligninolytic substrates. The work was extended to examine the kinetics of breakdown of industrial wastes (effluent from a pulp and paper plant, and fouled membrane solids extracted from a ground water treatment membrane) revealing unique, VP-mediated, kinetic responses. This work demonstrates that iTC can be successfully employed to study the kinetic properties of VP enzymes in order to devise reaction conditions optimized for oxidative degradation of HS present in materials used in a wide range of industries. Crown Copyright © 2014. Published by Elsevier B.V. All rights reserved.
Kinetic characterization of a novel acid ectophosphatase from Enterobacter asburiae.
Sato, Vanessa Sayuri; Galdiano Júnior, Renato F; Rodrigues, Gisele Regina; Lemos, Eliana G M; Pizauro Junior, João Martins
2016-02-01
Expression of acid ectophosphatase by Enterobacter asburiae, isolated from Cattleya walkeriana (Orchidaceae) roots and identified by the 16S rRNA gene sequencing analysis, was strictly regulated by phosphorus ions, with its optimal activity being observed at an inorganic phosphate concentration of 7 mM. At the optimum pH 3.5, intact cells released p-nitrophenol at a rate of 350.76 ± 13.53 nmol of p-nitrophenolate (pNP)/min/10(8) cells. The membrane-bound enzyme was obtained by centrifugation at 100,000 × g for 1 h at 4 °C. p-Nitrophenylphosphate (pNPP) hydrolysis by the enzyme follows "Michaelis-Menten" kinetics with V = 61.2 U/mg and K0.5 = 60 μM, while ATP hydrolysis showed V = 19.7 U/mg, K0.5 = 110 μM, and nH = 1.6 and pyrophosphate hydrolysis showed V = 29.7 U/mg, K0.5 = 84 μM, and nH = 2.3. Arsenate and phosphate were competitive inhibitors with K i = 0.6 mM and K i = 1.8 mM, respectively. p-Nitrophenyl phosphatase (pNPPase) activity was inhibited by vanadate, while p-hydroxymercuribenzoate, EDTA, calcium, copper, and cobalt had no inhibitory effects. Magnesium ions were stimulatory (K0.5 = 2.2 mM and nH = 0.5). Production of an acid ectophosphatase can be a mechanism for the solubilization of mineral phosphates by microorganisms such as Enterobacter asburiae that are versatile in the solubilization of insoluble minerals, which, in turn, increases the availability of nutrients for plants, particularly in soils that are poor in phosphorus.
Kranawetvogl, Andreas; Müller, Susanne; Kubik, Stefan; Spruit, Helma; Thiermann, Horst; Worek, Franz; Noort, Daan; Reiter, Georg
2015-11-19
Detoxification mechanisms of the chemical warfare agent cyclosarin (GF) in presence of 6-OxP-CD were investigated in detail in in vitro model systems. Most important finding was the preference of 6-Ox-P-CD to eliminate the more toxic (-)-GF. However, elimination of GF enantiomers was dependent on the 6-OxP-CD:GF ratios showing decreasing stereoselectivity and speed of the reaction with increasing GF concentrations. Formation of covalent mono, bis, tris and tetrakis conjugates ((CHMP)n-6-OxP-CD) and appearance of small molecular fragments (SMF) as possible decomposition products after consumption of 6-OxP-CD could be observed.. Interestingly, the non-toxic metabolite O-cyclohexyl methylphosphonic acid (CHMPA) and covalent mono and bis conjugates of 6-OxP-CD and GF were immediately formed, indicating that GF elimination proceeds along different pathways. These important new insights provide information about the mode of action of 6-Ox-P-CD including the role of the pyridinium aldoxime group on the cyclodextrin ring. They are the basis for further investigations in biological media, which could eventually lead to approval of 6-OxP-CD as a new antidote against nerve agent toxicity.
Haseba, Takeshi; Kameyama, Kouji; Mashimo, Keiko; Ohno, Youkichi
2012-01-01
ADH 1 and ADH 3 are major two ADH isozymes in the liver, which participate in systemic alcohol metabolism, mainly distributing in parenchymal and in sinusoidal endothelial cells of the liver, respectively. We investigated how these two ADHs contribute to the elimination kinetics of blood ethanol by administering ethanol to mice at various doses, and by measuring liver ADH activity and liver contents of both ADHs. The normalized AUC (AUC/dose) showed a concave increase with an increase in ethanol dose, inversely correlating with β. CL(T) (dose/AUC) linearly correlated with liver ADH activity and also with both the ADH-1 and -3 contents (mg/kg B.W.). When ADH-1 activity was calculated by multiplying ADH-1 content by its V(max)/mg (4.0) and normalized by the ratio of liver ADH activity of each ethanol dose to that of the control, the theoretical ADH-1 activity decreased dose-dependently, correlating with β. On the other hand, the theoretical ADH-3 activity, which was calculated by subtracting ADH-1 activity from liver ADH activity and normalized, increased dose-dependently, correlating with the normalized AUC. These results suggested that the elimination kinetics of blood ethanol in mice was dose-dependently changed, accompanied by a shift of the dominant metabolizing enzyme from ADH 1 to ADH 3.
Gamarra, L.F. [Instituto de Ensino e Pesquisa, Hospital Israelita Albert Einstein, Sao Paulo 05651-901 (Brazil); Instituto de Fisica, Universidade de Sao Paulo, Sao Paulo 05315-970 (Brazil)], E-mail: lgamarra@if.usp.br; Pontuschka, W.M. [Instituto de Fisica, Universidade de Sao Paulo, Sao Paulo 05315-970 (Brazil); Amaro, E. [Instituto de Ensino e Pesquisa, Hospital Israelita Albert Einstein, Sao Paulo 05651-901 (Brazil); Instituto de Radiologia, Faculdade de Medicina, Universidade de Sao Paulo, Sao Paulo 05403-001 (Brazil); Costa-Filho, A.J. [Instituto de Fisica de Sao Carlos, Universidade de Sao Paulo, Sao Carlos 13560-970 (Brazil); Brito, G.E.S. [Instituto de Fisica, Universidade de Sao Paulo, Sao Paulo 05315-970 (Brazil); Vieira, E.D. [Instituto de Fisica de Sao Carlos, Universidade de Sao Paulo, Sao Carlos 13560-970 (Brazil); Carneiro, S.M. [Laboratorio de Biologia Celular, Instituto Butantan, Sao Paulo 05503-900 (Brazil); Escriba, D.M. [Instituto de Fisica, Universidade de Sao Paulo, Sao Paulo 05315-970 (Brazil); Falleiros, A.M.F. [Centro de Ciencias Biologicas, Universidade Estadual de Londrina 86051-990 (Brazil); Salvador, V.L. [Centro de aplicacoes e Lasers, IPEN, Sao Paulo 05508-000 (Brazil)
2008-05-01
In this study, we evaluated the biodistribution and the elimination kinetics of a biocompatible magnetic fluid, Endorem{sup TM}, based on dextran-coated Fe{sub 3}O{sub 4} nanoparticles endovenously injected into Winstar rats. The iron content in blood and liver samples was recorded using electron paramagnetic resonance (EPR) and X-ray fluorescence (XRF) techniques. The EPR line intensity at g = 2.1 was found to be proportional to the concentration of magnetic nanoparticles and the best temperature for spectra acquisition was 298 K. Both EPR and XRF analysis indicated that the maximum concentration of iron in the liver occurred 95 min after the ferrofluid administration. The half-life of the magnetic nanoparticles (MNP) in the blood was (11.6 {+-} 0.6) min measured by EPR and (12.6 {+-} 0.6) min determined by XRF. These results indicate that both EPR and XRF are very useful and appropriate techniques for the study of kinetics of ferrofluid elimination and biodistribution after its administration into the organism.
Takeshi Haseba
2012-01-01
Full Text Available ADH 1 and ADH 3 are major two ADH isozymes in the liver, which participate in systemic alcohol metabolism, mainly distributing in parenchymal and in sinusoidal endothelial cells of the liver, respectively. We investigated how these two ADHs contribute to the elimination kinetics of blood ethanol by administering ethanol to mice at various doses, and by measuring liver ADH activity and liver contents of both ADHs. The normalized AUC (AUC/dose showed a concave increase with an increase in ethanol dose, inversely correlating with β. CLT (dose/AUC linearly correlated with liver ADH activity and also with both the ADH-1 and -3 contents (mg/kg B.W.. When ADH-1 activity was calculated by multiplying ADH-1 content by its Vmax/mg (4.0 and normalized by the ratio of liver ADH activity of each ethanol dose to that of the control, the theoretical ADH-1 activity decreased dose-dependently, correlating with β. On the other hand, the theoretical ADH-3 activity, which was calculated by subtracting ADH-1 activity from liver ADH activity and normalized, increased dose-dependently, correlating with the normalized AUC. These results suggested that the elimination kinetics of blood ethanol in mice was dose-dependently changed, accompanied by a shift of the dominant metabolizing enzyme from ADH 1 to ADH 3.
Controlling enzymatic activity and kinetics in swollen mesophases by physical nano-confinement
Sun, Wenjie; Vallooran, Jijo J.; Zabara, Alexandru; Mezzenga, Raffaele
2014-05-01
Bicontinuous lipid cubic mesophases are widely investigated as hosting matrices for functional enzymes to build biosensors and bio-devices due to their unique structural characteristics. However, the enzymatic activity within standard mesophases (in-meso) is severely hindered by the relatively small diameter of the mesophase aqueous channels, which provide only limited space for enzymes, and restrict them into a highly confined environment. We show that the enzymatic activity of a model enzyme, horseradish peroxidase (HRP), can be accurately controlled by relaxing its confinement within the cubic phases' water channels, when the aqueous channel diameters are systematically swollen with varying amount of hydration-enhancing sugar ester. The in-meso activity and kinetics of HRP are then systematically investigated by UV-vis spectroscopy, as a function of the size of the aqueous mesophase channels. The enzymatic activity of HRP increases with the swelling of the water channels. In swollen mesophases with water channel diameter larger than the HRP size, the enzymatic activity is more than double that measured in standard mesophases, approaching again the enzymatic activity of free HRP in bulk water. We also show that the physically-entrapped enzymes in the mesophases exhibit a restricted-diffusion-induced initial lag period and report the first observation of in-meso enzymatic kinetics significantly deviating from the normal Michaelis-Menten behaviour observed in free solutions, with deviations vanishing when enzyme confinement is released by swelling the mesophase.Bicontinuous lipid cubic mesophases are widely investigated as hosting matrices for functional enzymes to build biosensors and bio-devices due to their unique structural characteristics. However, the enzymatic activity within standard mesophases (in-meso) is severely hindered by the relatively small diameter of the mesophase aqueous channels, which provide only limited space for enzymes, and restrict them
Li, Su-Juan; Wang, Chen; Wu, Zeng-Qiang; Xu, Jing-Juan; Xia, Xing-Hua; Chen, Hong-Yuan
2010-09-01
To understand the fundamentals of enzymatic reactions confined in micro-/nanosystems, the construction of a small enzyme reactor coupled with an integrated real-time detection system for monitoring the kinetic information is a significant challenge. Nano-enzyme array reactors were fabricated by covalently linking enzymes to the inner channels of a porous anodic alumina (PAA) membrane. The mechanical stability of this nanodevice enables us to integrate an electrochemical detector for the real-time monitoring of the formation of the enzyme reaction product by sputtering a thin Pt film on one side of the PAA membrane. Because the enzymatic reaction is confined in a limited nanospace, the mass transport of the substrate would influence the reaction kinetics considerably. Therefore, the oxidation of glucose by dissolved oxygen catalyzed by immobilized glucose oxidase was used as a model to investigate the mass-transport-related enzymatic reaction kinetics in confined nanospaces. The activity and stability of the enzyme immobilized in the nanochannels was enhanced. In this nano-enzyme reactor, the enzymatic reaction was controlled by mass transport if the flux was low. With an increase in the flux (e.g., >50 microL min(-1)), the enzymatic reaction kinetics became the rate-determining step. This change resulted in the decrease in the conversion efficiency of the nano-enzyme reactor and the apparent Michaelis-Menten constant with an increase in substrate flux. This nanodevice integrated with an electrochemical detector could help to understand the fundamentals of enzymatic reactions confined in nanospaces and provide a platform for the design of highly efficient enzyme reactors. In addition, we believe that such nanodevices will find widespread applications in biosensing, drug screening, and biochemical synthesis.
Pedruzzi, Israel; da Silva, Eduardo A Borges; Rodrigues, Alírio E
2011-07-10
In this work, we have investigated the kinetics of the biotechnological production of lactobionic acid (LBA) and sorbitol by the catalytic action of glucose-fructose oxidoreductase (GFOR) and glucono-δ-lactonase (GL) enzymes. The cells of bacterium Zymomonas mobilis ATCC 29191 containing this enzymatic complex were submitted to permeabilization and reticulation procedures. The effect of the concentration of substrates on the rate of product formation using a mobilized cell system was investigated. The application of higher fructose concentration seems to not affect the initial rate of formation of the bionic acid. Under conditions of low initial concentration of lactose, the experimental kinetic data of the bi-substrate reaction were modelled by assuming a rate equation of the classical ping-pong mechanism. The found kinetic parameters displayed a low affinity of the GFOR enzyme for both substrates. The enzymatic system did not exhibit normal Michaelis-Menten kinetics in response to a change of concentration of lactose, when fructose was held constant, presenting a sigmoid relationship between initial velocity and substrate concentration. A rate equation based on Hill kinetics was used to describe the kinetic behaviour of this enzyme-substituted reaction at higher lactose concentrations. The results from batch experiments using immobilized cells within Ca-alginate beads revealed that there is no pronounced occurrence of mass transfer limitations on LBA production for beads with 1.2 mm in average diameter. This discussion aids for defining the best operating conditions to maximize the productivity for LBA and sorbitol in this bioconversion and also for reducing the complexity of downstream separation processes.
Metin, Ayşegül Ülkü; Alver, Erol
2016-07-01
Papain, which is an industrially important enzyme, has been immobilized on fibrous polymer-modified composite beads, namely poly(methacrylic acid)-grafted chitosan/clay. Characterization studies have been done using FTIR and SEM analysis. Operating parameters such as pH and initial concentration of papain have been varied to obtain the finest papain immobilized polymer-modified composite beads. The immobilization capacity of composite beads has been determined as 34.47 ± 1.18 (n = 3) mg/g. The proteolytic activity of immobilized papain was operated using bovine serum albumin (BSA) and maximum velocity (V max) and Michaelis-Menten constant (Km) values of the free and immobilized enzymes were determined using Lineweaver-Burk and Eadie-Hofstee equations. Usability of papain immobilized polymer-modified composite beads as adsorbents for the elimination of mercury was investigated. The maximum removal capacity of PIPMC beads has been found to be 4.88 ± 0.21 mg Hg/g when the initial metal concentration and weight of polymer-modified composite beads were 50 mg/L and 0.04 g at pH 7, respectively. Mercury removal performance of the papain immobilized polymer-modified composite beads was investigated in conjunction with Cu (II), Zn (II) and Cd (II) ions. The mercury adsorption capacity of papain immobilized polymer-modified composite beads was a slight reduction from 1.15 to 0.89 mg/g in presence of multiple metal salts.
An Integrated Circuit for Chip-Based Analysis of Enzyme Kinetics and Metabolite Quantification.
Cheah, Boon Chong; Macdonald, Alasdair Iain; Martin, Christopher; Streklas, Angelos J; Campbell, Gordon; Al-Rawhani, Mohammed A; Nemeth, Balazs; Grant, James P; Barrett, Michael P; Cumming, David R S
2016-06-01
We have created a novel chip-based diagnostic tools based upon quantification of metabolites using enzymes specific for their chemical conversion. Using this device we show for the first time that a solid-state circuit can be used to measure enzyme kinetics and calculate the Michaelis-Menten constant. Substrate concentration dependency of enzyme reaction rates is central to this aim. Ion-sensitive field effect transistors (ISFET) are excellent transducers for biosensing applications that are reliant upon enzyme assays, especially since they can be fabricated using mainstream microelectronics technology to ensure low unit cost, mass-manufacture, scaling to make many sensors and straightforward miniaturisation for use in point-of-care devices. Here, we describe an integrated ISFET array comprising 2(16) sensors. The device was fabricated with a complementary metal oxide semiconductor (CMOS) process. Unlike traditional CMOS ISFET sensors that use the Si3N4 passivation of the foundry for ion detection, the device reported here was processed with a layer of Ta2O5 that increased the detection sensitivity to 45 mV/pH unit at the sensor readout. The drift was reduced to 0.8 mV/hour with a linear pH response between pH 2-12. A high-speed instrumentation system capable of acquiring nearly 500 fps was developed to stream out the data. The device was then used to measure glucose concentration through the activity of hexokinase in the range of 0.05 mM-231 mM, encompassing glucose's physiological range in blood. Localised and temporal enzyme kinetics of hexokinase was studied in detail. These results present a roadmap towards a viable personal metabolome machine.
Kinetic study of enzymatic hydrolysis of acid-pretreated coconut coir
Fatmawati, Akbarningrum; Agustriyanto, Rudy
2015-12-01
Biomass waste utilization for biofuel production such as bioethanol, has become more prominent currently. Coconut coir is one of lignocellulosic food wastes, which is abundant in Indonesia. Bioethanol production from such materials consists of more than one step. Pretreatment and enzymatic hydrolysis is crucial steps to produce sugar which can then be fermented into bioethanol. In this research, ground coconut coir was pretreated using dilute sulfuric acid at 121°C. This pretreatment had increased the cellulose content and decreased the lignin content of coconut coir. The pretreated coconut coir was hydrolyzed using a mix of two commercial cellulase enzymes at pH of 4.8 and temperature of 50°C. The enzymatic hydrolysis was conducted at several initial coconut coir slurry concentrations (0.1-2 g/100 mL) and reaction times (2-72 hours). The reducing sugar concentration profiles had been produced and can be used to obtain reaction rates. The highest reducing sugar concentration obtained was 1,152.567 mg/L, which was produced at initial slurry concentration of 2 g/100 mL and 72 hours reaction time. In this paper, the reducing sugar concentrations were empirically modeled as a function of reaction time using power equations. Michaelis-Menten kinetic model for enzymatic hydrolysis reaction is adopted. The kinetic parameters of that model for sulfuric acid-pretreated coconut coir enzymatic hydrolysis had been obtained which are Vm of 3.587×104 mg/L.h, and KM of 130.6 mg/L.
Li, Hui; Luo, Na; Zhang, Li Jun; Zhao, Hai Ming; Li, Yan Wen; Cai, Quan Ying; Wong, Ming Hung; Mo, Ce Hui
2016-11-15
Rice (Oryza sativa L.) plants were inoculated with two species of arbuscular mycorrhizal fungi (AMF) - Rhizophagus intraradices (RI) and Funneliformis mosseae (FM) and grown for 60days to ensure strong colonization. Subsequently, a short-term hydroponic experiment was carried out to investigate the effects of AMF on cadmium (Cd) uptake kinetics, subcellular distribution and chemical forms in rice exposed to six Cd levels (0, 0.005, 0.01, 0.025, 0.05, 0.1mM) for three days. The results showed that the uptake kinetics of Cd fitted the Michaelis-Menten model well (R(2)>0.89). AMF significantly decreased the Cd concentrations both in shoots and roots in Cd solutions. Furthermore, the decrement of Cd concentrations by FM was significantly higher than RI treatment in roots. AMF reduced the Cd concentrations markedly in the cell wall fractions at high Cd substrate (≥0.025mM). The main subcellular fraction contributed to Cd detoxification was cell wall at low Cd substrate (<0.05mM), while vacuoles at high Cd substrate (≥0.05mM). Moreover, the concentrations and proportions of Cd in inorganic and water-soluble form also reduced by AMF colonization at high Cd substrate (≥0.05mM), both in shoots and roots. This suggested that AMF could convert Cd into inactive forms which were less toxic. Therefore, AMF could enhance rice resistance to Cd through altering subcellular distribution and chemical forms of Cd in rice.
Marcos De Souza
2013-10-01
Full Text Available The cyclodextrins (CDs are cyclic maltooligosaccharides obtained by cyclization of linear chains of starch, catalyzed by the enzyme cyclomaltodextringlucanotransferase (CGTase. The interest in CD production results from the formation of inclusion complexes, which allow many important applications, especially in food, pharmaceutical and cosmetic industries. The substances complexed generally have their properties modified by complexation. It is appreciated if increased solubility and higher thermal and chemical stabilities are obtained. In this work, a kinetic model was developed for the production of cyclodextrins in the presence of CGTase from alkalophilic Bacillus sp., taking into account the reversibility of the cyclization reaction, the simultaneous production of b and g-CD and also the inhibitory influence of the substrate and products (CDs, on the enzymatic activity of the CGTase. The substrate formed from a solution of maltodextrins was treated as a single substrate. The model was compared with experimental results of 24h of reaction and this comparison demonstrated that there was a very good representation of the data throughout the test period. The model also allowed explaining the observation of different experimental values for each Michaelis-Menten constant and substrate inhibition constant for each CD, although the CDs are produced from the same substrate.
Gorden, P J; van der List, M; Lehman, F D; Lantz, R K; Constable, P D
2013-07-01
The objective of this study was to determine the elimination kinetics of extended therapy with intramammary (IMM) cephapirin in lactating dairy cattle. Eight healthy Holstein-Friesian cows were administered cephapirin (200mg) into all 4 mammary glands every 24 h after milking. Cows were milked 3 times per day and concentrations of cephapirin and desacetyl cephapirin were determined in bucket milk using liquid chromatography-mass spectrometry. Milk concentration-time data after the last of the 8 IMM infusions were fitted using compartment and noncompartmental models. The maximum cephapirin concentration was 128±57 µg/mL (mean ± SD), the elimination rate constant from the central compartment was 0.278±0.046 (h(-1)), clearance was 0.053±0.023 L/h, the half time for elimination was 2.55±0.40 h, and the mean residence time was 2.65±0.79 h. The cephapirin concentration was below the approved tolerance in all cows by 96 h after the last infusion, which is the labeled withholding time for the preparation used. Extended therapy for 8 d provided milk cephapirin concentrations above the minimum inhibitory concentration for common gram-positive mastitis pathogens (0.1 to 1.0 µg/mL) for the duration of therapy and for an additional 16 to 32 h after the end of treatment. Our findings suggest that this IMM cephapirin sodium formulation, which is labeled for 2 doses 12 h apart, could be administered at a 24-h interval for up to 8 d in cows milked 3 times per day, with no significant effect on residue levels by 96 h after the last treatment. Longer withdrawal times would be prudent for cows with low milk production.
SBMLsqueezer: A CellDesigner plug-in to generate kinetic rate equations for biochemical networks
Schröder Adrian
2008-04-01
Full Text Available Abstract Background The development of complex biochemical models has been facilitated through the standardization of machine-readable representations like SBML (Systems Biology Markup Language. This effort is accompanied by the ongoing development of the human-readable diagrammatic representation SBGN (Systems Biology Graphical Notation. The graphical SBML editor CellDesigner allows direct translation of SBGN into SBML, and vice versa. For the assignment of kinetic rate laws, however, this process is not straightforward, as it often requires manual assembly and specific knowledge of kinetic equations. Results SBMLsqueezer facilitates exactly this modeling step via automated equation generation, overcoming the highly error-prone and cumbersome process of manually assigning kinetic equations. For each reaction the kinetic equation is derived from the stoichiometry, the participating species (e.g., proteins, mRNA or simple molecules as well as the regulatory relations (activation, inhibition or other modulations of the SBGN diagram. Such information allows distinctions between, for example, translation, phosphorylation or state transitions. The types of kinetics considered are numerous, for instance generalized mass-action, Hill, convenience and several Michaelis-Menten-based kinetics, each including activation and inhibition. These kinetics allow SBMLsqueezer to cover metabolic, gene regulatory, signal transduction and mixed networks. Whenever multiple kinetics are applicable to one reaction, parameter settings allow for user-defined specifications. After invoking SBMLsqueezer, the kinetic formulas are generated and assigned to the model, which can then be simulated in CellDesigner or with external ODE solvers. Furthermore, the equations can be exported to SBML, LaTeX or plain text format. Conclusion SBMLsqueezer considers the annotation of all participating reactants, products and regulators when generating rate laws for reactions. Thus, for
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
Löppmann, Sebastian; Blagodatskaya, Evgenia; Kuzyakov, Yakov
2014-05-01
Rhizosphere and detritusphere are soil microsites with very high resource availability for microorganisms affecting their biomass, composition and functions. In the rhizosphere low molecular compounds occur with root exudates and low available polymeric compounds, as belowground plant senescence. In detritusphere the substrate for decomposition is mainly a polymeric material of low availability. We hypothesized that microorganisms adapted to contrasting quality and availability of substrates in the rhizosphere and detritusphere are strongly different in affinity of hydrolytic enzymes responsible for decomposition of organic compounds. According to common ecological principles easily available substrates are quickly consumed by microorganisms with enzymes of low substrate affinity (i.e. r-strategists). The slow-growing K-strategists with enzymes of high substrate affinity are better adapted for growth on substrates of low availability. Estimation of affinity of enzyme systems to the substrate is based on Michaelis-Menten kinetics, reflecting the dependency of decomposition rates on substrate amount. As enzymes-mediated reactions are substrate-dependent, we further hypothesized that the largest differences in hydrolytic activity between the rhizosphere and detritusphere occur at substrate saturation and that these differences are smoothed with increasing limitation of substrate. Affected by substrate limitation, microbial species follow a certain adaptation strategy. To achieve different depth gradients of substrate availability 12 plots on an agricultural field were established in the north-west of Göttingen, Germany: 1) 4 plots planted with maize, reflecting lower substrate availability with depth; 2) 4 unplanted plots with maize litter input (0.8 kg m-2 dry maize residues), corresponding to detritusphere; 3) 4 bare fallow plots as control. Maize litter was grubbed homogenously into the soil at the first 5 cm to ensure comparable conditions for the herbivore and
Gillis, Patricia L. [Department of Biology, McMaster University, Hamilton, ON, L8S-4K1 (Canada)], E-mail: patty.gillis@ec.gc.ca; Wood, Chris M. [Department of Biology, McMaster University, Hamilton, ON, L8S-4K1 (Canada)
2008-09-17
The uptake kinetics of waterborne Ca and Cd, both independently and in combination, were examined in C. riparius larvae, which are extremely Cd tolerant. Larvae exposed to Ca (100-2500 {mu}mol L{sup -1}), exhibited classic Michaelis-Menten saturation kinetics for Ca influx, measured using {sup 45}Ca as a radio-tracer. The maximum rate of Ca influx (J{sub max}{sup Ca}) was 0.39 {mu}mol g{sup -1} h{sup -1}, and the Ca concentration where the carrier reached half saturation (K{sub M}{sup Ca}) was 289 {mu}mol L{sup -1}. Cd influx was measured using {sup 109}Cd as a radio-tracer in larvae exposed to Cd (0-1400 {mu}mol L{sup -1}) while the Ca concentration was set to the K{sub M}{sup Ca}. This revealed a J{sub max}{sup Cd} (2.26 {mu}mol g{sup -1} h{sup -1}) which was nearly 6-fold higher that of Ca. This unusually high capacity for Cd uptake is in accordance with the huge tissue Cd burdens that chironomid larvae are able to accumulate during high level exposures. The apparent K{sub M}{sup Cd} (1133 {mu}mol Cd L{sup -1}), when recalculated to account for the background Ca level, was still high (567 {mu}mol Cd L{sup -1}), suggesting that this organism has a low affinity for Cd relative to most aquatic animals, indeed lower or comparable to its affinity for Ca. In consequence, even well above environmentally relevant Cd exposures, C. riparius does not accumulate Cd at the expense of Ca, thereby avoiding internal hypocalcaemia, in contrast to most other organisms which are much more sensitive to Cd. However, Ca influx was significantly reduced when 1200 {mu}mol Cd L{sup -1} was added to Ca exposures (96-2410 {mu}mol L{sup -1}). Michaelis-Menten analysis revealed a similar J{sub max}{sup Ca} in Cd-exposed and control larvae (i.e. exposed only to Ca), but that the apparent K{sub M}{sup Ca} was many-fold higher in larvae which were simultaneously exposed to Ca and Cd. Conversely, increasing Ca concentrations (96-2410 {mu}mol L{sup -1}) progressively inhibited Cd uptake from a
Leong, Sze Ying; Oey, Indrawati
2014-03-01
The objective of this research was to study the enzyme kinetics and thermostability of endogenous ascorbic acid oxidase (AAO) in carrot purée (Daucus carota cv. Nantes) after being treated with pulsed electric field (PEF) processing. Various PEF treatments using electric field strength between 0.2 and 1.2kV/cm and pulsed electrical energy between 1 and 520kJ/kg were conducted. The enzyme kinetics and the kinetics of AAO thermal inactivation (55-70°C) were described using Michaelis-Menten model and first order reaction model, respectively. Overall, the estimated Vmax and KM values were situated in the same order of magnitude as the untreated carrot purée after being exposed to pulsed electrical energy between 1 and 400kJ/kg, but slightly changed at pulsed electrical energy above 500kJ/kg. However, AAO presented different thermostability depending on the electric field strength applied. After PEF treatment at the electric field strength between 0.2 and 0.5kV/cm, AAO became thermolabile (i.e. increase in inactivation rate (k value) at reference temperature) but the temperature dependence of k value (Ea value) for AAO inactivation in carrot purée decreased, indicating that the changes in k values were less temperature dependent. It is obvious that PEF treatment affects the temperature stability of endogenous AAO. The changes in enzyme kinetics and thermostability of AAO in carrot purée could be related to the resulting carrot purée composition, alteration in intracellular environment and the effective concentration of AAO released after being subjected to PEF treatment. Copyright © 2013 Elsevier Ltd. All rights reserved.
Prenafeta-Boldú, Frances X; Illa, Josep; van Groenestijn, Johan W; Flotats, Xavier
2008-05-01
The biodegradation of toluene was studied in two lab-scale air biofilters operated in parallel, packed respectively with perlite granules (PEG) and polyurethane foam cubes (PUC) and inoculated with the same toluene-degrading fungus. Differences on the material pore size, from micrometres in PEG to millimetres in PUC, were responsible for distinct biomass growth patterns. A compact biofilm was formed around PEG, being the interstitial spaces progressively filled with biomass. Microbial growth concentrated at the core of PUC and the excess of biomass was washed-off, remaining the gas pressure drop comparatively low. Air dispersion in the bed was characterised by tracer studies and modelled as a series of completely stirred tanks (CSTR). The obtained number of CSTR (n) in the PEG packing increased from 33 to 86 along with the applied gas flow (equivalent to empty bed retention times from 48 to 12 s) and with operation time (up to 6 months). In the PUC bed, n varied between 9 and 13, indicating that a stronger and steadier gas dispersion was achieved. Michaelis-Menten half saturation constant (km) estimates ranged 71-113 mg m(-3), depending on the experimental conditions, but such differences were not significant at a 95% confidence interval. The maximum volumetric elimination rate (rm) varied from 23 to 50 g m(-3) h(-1). Comparison between volumetric and biomass specific biodegradation activities indicated that toluene mass transfer was slower with PEG than with PUC as a consequence of a smaller biofilm surface and to the presence of larger zones of stagnant air.
Prenafeta-Boldu, F.X. [GIRO Technological Centre, Mollet del Valles, Barcelona (Spain); IRTA, Barcelona (Spain); Illa, J. [Lleida Univ. (Spain); Groenestijn, J.W. van [TNO, Zeist (Netherlands). Dept. of Microbiology; Flotats, X. [GIRO Technological Centre, Mollet del Valles, Barcelona (Spain); Lleida Univ. (Spain)
2008-05-15
The biodegradation of toluene was studied in two lab-scale air biofilters operated in parallel, packed respectively with perlite granules (PEG) and polyurethane foam cubes (PUC) and inoculated with the same toluene-degrading fungus. Differences on the material pore size, from micrometres in PEG to millimetres in PUC, were responsible for distinct biomass growth patterns. A compact biofilm was formed around PEG, being the interstitial spaces progressively filled with biomass. Microbial growth concentrated at the core of PUC and the excess of biomass was washed-off, remaining the gas pressure drop comparatively low. Air dispersion in the bed was characterised by tracer studies and modelled as a series of completely stirred tanks (CSTR). The obtained number of CSTR (n) in the PEG packing increased from 33 to 86 along with the applied gas flow (equivalent to empty bed retention times from 48 to 12 s) and with operation time (up to 6 months). In the PUC bed, n varied between 9 and 13, indicating that a stronger and steadier gas dispersion was achieved. Michaelis-Menten half saturation constant (k{sub m}) estimates ranged 71-113 mg m{sup -3}, depending on the experimental conditions, but such differences were not significant at a 95% confidence interval. The maximum volumetric elimination rate (r{sub m}) varied from 23 to 50 g m{sup -3} h{sup -1}. Comparison between volumetric and biomass specific biodegradation activities indicated that toluene mass transfer was slower with PEG than with PUC as a consequence of a smaller biofilm surface and to the presence of larger zones of stagnant air. (orig.)
Amin, Faiza; Bhatti, Haq Nawaz; Bilal, Muhammad; Asgher, Muhammad
2017-03-18
An extracellular exo-polygalacturonase (exo-PG) produced by Penicillium notatum was purified (3.07-folds) by ammonium sulfate fractionation, ion exchange, and gel filtration chromatography. Two distinct isoforms of the enzyme, namely exo-PGI and exo-PGII, were identified during column purification with molecular weights of 85 and 20 kDa, respectively, on sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE). The enzyme displayed its optimum activity at pH 6.0 and 50 °C and was found to be stable in the slightly acidic pH (ranging from 4.5 to 6.0). Michaelis-Menten parameters, i.e., K m (app) and V max for pectin hydrolysis, were calculated to be 16.6 mg/mL and 20 μmol/mL/min, respectively. The enzyme followed biphasic deactivation kinetics. Phase I of the exo-PGI showed half-lives of 6.83 and 2.39 min at 55 and 80 °C, respectively, whereas phase II of the enzyme exhibited a half-life of 63.57 and 22.72 min at 55 and 80 °C, respectively. The activation energy for denaturation was 51.66 and 44.06 kJ/mol for phase I and phase II of the exo-PGI, respectively. The enzyme activity was considerably enhanced by Mn(2+), whereas exposure to a hydrophobic environment (urea and sodium azide solution) drastically suppressed the enzyme activity. Results suggest that exo-PGI might be considered as a potential candidate for various applications, particularly in the food and textile industries.
Tang, Wen-Tao; Dai, Ji; Liu, Rulong; Chen, Guang-Hao
2015-12-15
Our previous study has confirmed the feasibility of using seawater as an economical precipitant for urine phosphorus (P) precipitation. However, we still understand very little about the ureolysis in the Seawater-based Urine Phosphorus Recovery (SUPR) system despite its being a crucial step for urine P recovery. In this study, batch experiments were conducted to investigate the kinetics of microbial ureolysis in the seawater-urine system. Indigenous bacteria from urine and seawater exhibited relatively low ureolytic activity, but they adapted quickly to the urine-seawater mixture during batch cultivation. During cultivation, both the abundance and specific ureolysis rate of the indigenous bacteria were greatly enhanced as confirmed by a biomass-dependent Michaelis-Menten model. The period for fully ureolysis was decreased from 180 h to 2.5 h after four cycles of cultivation. Based on the successful cultivation, a lab-scale SUPR reactor was set up to verify the fast ureolysis and efficient P recovery in the SUPR system. Nearly complete urine P removal was achieved in the reactor in 6 h without adding any chemicals. Terminal Restriction Fragment Length Polymorphism (TRFLP) analysis revealed that the predominant groups of bacteria in the SUPR reactor likely originated from seawater rather than urine. Moreover, batch tests confirmed the high ureolysis rates and high phosphorus removal efficiency induced by cultivated bacteria in the SUPR reactor under seawater-to-urine mixing ratios ranging from 1:1 to 9:1. This study has proved that the enrichment of indigenous bacteria in the SUPR system can lead to sufficient ureolytic activity for phosphate precipitation, thus providing an efficient and economical method for urine P recovery.
Van den Eede, Nele; Tomy, Gregg; Tao, Fang; Halldorson, Thor; Harrad, Stuart; Neels, Hugo; Covaci, Adrian
2016-02-01
Tris(1-chloro-2-propyl) phosphate (TCIPP) is an emerging contaminant which is ubiquitous in the indoor and outdoor environment. Moreover, its presence in human body fluids and biota has been evidenced. Since no quantitative data exist on the biotransformation or stability of TCIPP in the human body, we performed an in vitro incubation of TCIPP with human liver microsomes (HLM) and human serum (HS). Two metabolites, namely bis(2-chloro-isopropyl) phosphate (BCIPP) and bis(1-chloro-2-propyl) 1-hydroxy-2-propyl phosphate (BCIPHIPP), were quantified in a kinetic study using HLM or HS (only BCIPP, the hydrolysis product) and LC-MS. The Michaelis-Menten model fitted best the NADPH-dependent formation of BCIPHIPP and BCIPP in HLM, with respective V(MAX) of 154 ± 4 and 1470 ± 110 pmol/min/mg protein and respective apparent K(m) of 80.2 ± 4.4 and 96.1 ± 14.5 μM. Hydrolases, which are naturally present in HLM, were also involved in the production of BCIPP. A HS paraoxonase assay could not detect any BCIPP formation above 38.6 ± 10.8 pmol/min/μL serum. Our data indicate that BCIPP is the major metabolite of TCIPP formed in the liver. To our knowledge, this is the first quantitative assessment of the stability of TCIPP in tissues of humans or any other species. Further research is needed to confirm whether these biotransformation reactions are associated with a decrease or increase in toxicity.
Gulledge, Jay; Hrywna, Yarek; Cavanaugh, Colleen; Steudler, Paul A
2004-09-01
To determine whether repeated, long-term NH(4) (+) fertilization alters the enzymatic function of the atmospheric CH(4) oxidizer community in soil, we examined CH(4) uptake kinetics in temperate pine and hardwood forest soils amended with 150 kg N ha(-1) y(-1) as NH(4)NO(3) for more than a decade. The highest rates of atmospheric CH(4) consumption occurred in the upper 5 cm mineral soil of the control plots. In contrast to the results of several previous studies, surface organic soils in the control plots also exhibited high consumption rates. Fertilization decreased in situ CH(4) consumption in the pine and hardwood sites relative to the control plots by 86% and 49%, respectively. Fertilization increased net N mineralization and relative nitrification rates and decreased CH(4) uptake most dramatically in the organic horizon, which contributed substantially to the overall decrease in field flux rates. In all cases, CH(4) oxidation followed Michaelis-Menten kinetics, with apparent K(m) (K(m(app))) values typical of high-affinity soil CH(4) oxidizers. Both K(m(app)) and V(max(app)) were significantly lower in fertilized soils than in unfertilized soils. The physiology of the methane consumer community in the fertilized soils was distinct from short-term responses to NH(4) (+) addition. Whereas the immediate response to NH(4) (+) was an increase in K(m(app)), resulting from apparent enzymatic substrate competition, the long-term response to fertilization was a community-level shift to a lower K(m(app)), a possible adaptation to diminish the competitiveness of NH(4) (+) for enzyme active sites.
Kinetics of propionate conversion in anaerobic continuously stirred tank reactors
Bangsø Nielsen, Henrik; Mladenovska, Zuzana; Ahring, Birgitte Kiær
2008-01-01
(max), and the half saturation constant, K-m, were initially estimated by applying the integrated Michaelis-Menten equation. A(max) was in the range from 22.8 to 29.1 mu mol gVS(-1) h(-1) while K-m, was in the range from 0.46-0.95 mM. In general, A(max) gave a good reflection of the reactor performances. Secondly...
Tang, J. Y.; Riley, W. J.
2013-12-01
We demonstrate that substrate uptake kinetics in any consumer-substrate network subject to the total quasi-steady-state assumption can be formulated as an equilibrium chemistry (EC) problem. If the consumer-substrate complexes equilibrate much faster than other metabolic processes, then the relationships between consumers, substrates, and consumer-substrate complexes are in quasi-equilibrium and the change of a given total substrate (free plus consumer-bounded) is determined by the degradation of all its consumer-substrate complexes. In this EC formulation, the corresponding equilibrium reaction constants are the conventional Michaelis-Menten (MM) substrate affinity constants. When all of the elements in a given network are either consumer or substrate (but not both), we derived a first-order accurate EC approximation (ECA). The ECA kinetics is compatible with almost every existing extension of MM kinetics. In particular, for microbial organic matter decomposition modeling, ECA kinetics explicitly predicts a specific microbe's uptake for a specific substrate as a function of the microbe's affinity for the substrate, other microbes' affinity for the substrate, and the shielding effect on substrate uptake by environmental factors, such as mineral surface adsorption. By taking the EC solution as a reference, we evaluated MM and ECA kinetics for their abilities to represent several differently configured enzyme-substrate reaction networks. In applying the ECA and MM kinetics to microbial models of different complexities, we found (i) both the ECA and MM kinetics accurately reproduced the EC solution when multiple microbes are competing for a single substrate; (ii) ECA outperformed MM kinetics in reproducing the EC solution when a single microbe is feeding on multiple substrates; (iii) the MM kinetics failed, while the ECA kinetics succeeded, in reproducing the EC solution when multiple consumers (i.e., microbes and mineral surfaces) were competing for multiple
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.
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
Andric, Pavle; Meyer, Anne S.; Jensen, Peter Arendt
2010-01-01
, during 96 h of reaction. When glucose was removed by dialysis during the enzymatic hydrolysis, the cellulose conversion rates and glucose yields increased. In fact, with dialytic in situ glucose removal, the rate of enzyme-catalyzed glucose release during 48-72 h of reaction recovered from 20......-40% to become approximate to 70% of the rate recorded during 6-24 h of reaction. Although Michaelis-Menten kinetics do not suffice to model the kinetics of the complex multi-enzymatic degradation of cellulose, the data for the glucose inhibition were surprisingly well described by simple Michaelis......-Menten inhibition models without great significance of the inhibition mechanism. Moreover, the experimental in situ removal of glucose could be simulated by a Michaelis-Menten inhibition model. The data provide an important base for design of novel reactors and operating regimes which include continuous product...
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.
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....
Geusau, A. [Dept. of Dermatology, Univ. of Vienna, Vienna (Austria); Schmaldienst, S.; Derfler, K. [Dept. of Internal Medicine, Univ. of Vienna, Vienna (Austria); Paepke, O. [ERGO Forschungsgesellschaft mbH, Hamburg (Germany); Abraham, K. [Dept. of Pediatric Pneumology and Immunology, Children' s Hospital, Charite, Humboldt Univ., Berlin (Germany)
2002-06-01
In spring 1998, two women were diagnosed with severe 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) intoxication. Over the following 3 years, TCDD levels were monitored under various attempts to enhance its elimination, and the half-lives were evaluated. Olestra, a non-digestible, non-absorbable dietary fat substitute, was continuously administered to the patients either as pure substance or in potato-chips. Additionally, in the more severely contaminated patient, we studied whether low-density lipoprotein (LDL)-apheresis, an extracorporeal means of blood lipid elimination, was effective in reducing the TCDD body burden. The blood concentrations initially measured in spring 1998 were 144,000 pg/g blood fat in patient 1 and 26,000 pg/g in patient 2, the highest levels ever measured in adults. In March 2001, concentrations in blood fat were 35,900 and 9,500 pg/g, corresponding to overall elimination half-lives of 560 days (1.5 years) in patient 1 and 1050 days (2.9 years) in patient 2, which are considerably shorter than median values of 7-9 years reported for background and moderate exposure levels. Calculations of the TCDD half-lives and measurements of TCDD elimination via different routes allowed the calculation of an unidentified route of elimination, representing 78 and 62% of the overall elimination in patient 1 and 2, respectively, probably due to an induced hepatic metabolism caused by the high TCDD exposure. As previously reported, administration of olestra was found to be effective in increasing the fecal excretion of TCDD. Due to the short half-lives in our patients, the effect of olestra on the overall elimination was relatively small, but is expected to be much greater for 'normal' half-lives. LDL-apheresis was shown to eliminate TCDD, corresponding to the eliminated blood fat. When employed twice a week, the amount of TCDD excreted by this method was comparable to fecal excretion. In view of costs and time involved, LDL-apheresis does not seem to
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
彭尚; 孙丽霞; 熊珍爱; 周利琴; 兰雄雕; 孙建华; 童张法; 廖丹葵
2016-01-01
采用等温滴定量热法(ITC)测定猪肺血管紧张素转化酶（angiotensin converting enzyme，ACE）催化水解其体外模拟底物马尿酰-组氨酰-亮氨酸（Hip-His-Leu，HHL）反应的热动力学参数，考察了温度对动力学参数的影响。结果表明，该反应的摩尔水解焓ΔHhydr为正值，是吸热反应，且随温度升高ΔHhydr增大，等压比热容 cp为0.2126kJ/(mol·K)；ACE 催化 HHL 的水解反应符合 Michaelis-Menten 机理，在实验温度范围内（298.15～313.15K），米氏常数Km随温度升高而减小，催化常数kcat随温度的升高先增大后减少，在308.15K时达到最大值2.534s−1。将该法与传统的初始速率法进行比较，传统法存在的局限性使测得的 Km相对偏大。同时使用 ITC结合动力学分析测得ACE抑制剂药物依那普利拉为竞争性抑制剂，抑制常数KI为12.1 nmol/L，与文献比较证明该法可用于抑制剂类型的判断，是一种开发 ACE 抑制剂的新方法。应用该方法确定活性多肽Arg-Tyr-Leu-Gly-Tyr（RY-5)为非竞争性抑制剂，抑制常数KI为1.0μmol/L。%Thermodynamic and kinetic parameters of angiotensin converting enzyme(ACE)catalyzed hydrolysis of simulating substrate Hippuryl-Histidyl-Leucine(HHL)in vitro were determined by isothermal titration calorimetry(ITC). The effect of temperature on kinetic parameters was investigated; the results showed that the ACE-catalyzed reaction was endothermic with a small constant pressure specific heat capacity [cp=0.2126kJ/(mol·K)]. The value of molar hydrolysis enthalpyΔHhydrwas positive and increased as temperature rose. The reaction mechanism was in accordance with the Michaelis-Menten model in the temperature range(298.15—313.15K);the effect of temperature on the Michaelis constant(Km)was negative,while catalytic constant(kcat)first increased then decreased with the increase of temperature,reaching the maximum value of 2.534s−1 at 308.15K. Initial rate
Pedersen, Morten Gram; Bersani, A.M.; Bersani, E.
2008-01-01
Enzyme reactions play a pivotal role in intracellular signal transduction. Many enzymes are known to possess Michaelis-Menten (MM) kinetics and the MM approximation is often used when modeling enzyme reactions. However, it is known that the MM approximation is only valid at low enzyme concentrati......Enzyme reactions play a pivotal role in intracellular signal transduction. Many enzymes are known to possess Michaelis-Menten (MM) kinetics and the MM approximation is often used when modeling enzyme reactions. However, it is known that the MM approximation is only valid at low enzyme...
王龙; 高子平; 李文华; 徐莜; 张长波; 杨庆文; 汤继华; 刘仲齐
2016-01-01
kinetic characteristics of roots in rice seed-lings from different genotypes was well described with Michaelis-Menten equation when Cd2+ concentration around root varied from 0 μmol·L-1 to 4.45 μmol·L-1, but Cd2+ uptake kinetic parametersFmax andKm among genotypes had obvious differences.Fmax varied from 37.8 nmol·g-1 (DW)·h-1to 87.5 nmol·g-1 (DW)·h-1. The above-ground Cd2+ accumulation kinetic characteristics was also well fitted by Michaelis-Menten equation when the rootFmax was higher than 55.5 nmol·g-1 (DW)·h-1. However, the above-ground Cd2+ accumulation ki-netic characteristics was well fitted by a linear equation whenFmax was lower than 50.8 nmol·g-1 (DW)·h-1. There was a close relationship between intercept a andKm value at this time. The intercept a of above-ground was positive whenKm varied from 0.5 μmol·L-1 to 1.3 μmol·L-1 but negative whenKm varied from 2.9 μmol·L-1 to 3.9 μmol·L-1. When Cd2+ concentration around root was 4.45 μmol·L-1, the Cd accumulation in root and above-ground was signiifcantly and linearly correlated with theFmax of Michaelis-Menten equation as well as with the slope b of linear equation. Cd transport efifciency was associated with Cd2+ concentration in environ-ment, and also with Cd accumulation characteristics of above-ground. The Cd transport efifciency of rice vari-eties was rising with the increase of Cd2+ concentration in the environment when their above-ground Cd2+ab-sorption kinetic characteristics was well iftted with linear equation, but increased ifrst and then decreased when their above-ground Cd2+ absorption kinetic characteristics was accorded with Michaelis-Menten equation. These results suggest that there are different control mechanisms in root and above-ground for Cd absorption. Cd2+ ab-sorption features and transport efifciency have abundant genetic diversity among genotypes. Most rice core ger-mplasms with small rootFmax and slop b in the linear equation of above ground Cd2+ absorption are the
Distinction between esterases and lipases: a kinetic study with vinyl esters and TAG.
Chahinian, Henri; Nini, Lylia; Boitard, Elisabeth; Dubès, Jean-Paul; Comeau, Louis-Claude; Sarda, Louis
2002-07-01
The better to characterize enzymes hydrolyzing carboxyl ester bonds (carboxyl ester hydrolases), we have compared the kinetic behavior of various lipases and esterases against solutions and emulsions of vinyl esters and TAG. Short-chain vinyl esters are hydrolyzed at comparable rates by esterases and lipases and have higher limits of solubility in water than corresponding TAG. Therefore, they are suited to study the influence of the physical state of the substrate on carboxyl ester hydrolase activity within a large concentration range. Enzymes used in this study are TAG lipases from microorganisms, lipases from human and guinea pig pancreas, pig liver esterase, and acetylcholinesterase. This study also includes cutinase, a fungal enzyme that displays functional properties between esterases and lipases. Esterases display maximal activity against solutions of short-chain vinyl esters (vinyl acetate, vinyl propionate, and vinyl butyrate) and TAG (triacetin, tripropionin, and tributyrin). Half-maximal activity is reached at ester concentrations far below the solubility limit. The transition from solution to emulsion at substrate concentrations exceeding the solubility limit has no effect on esterase activity. Lipases are active on solutions of short-chain vinyl esters and TAG but, in contrast to esterases, they all display maximal activity against emulsified substrates and half-maximal activity is reached at substrate concentrations near the solubility limit of the esters. The kinetics of hydrolysis of soluble substrates by lipases are either hyperbolic or deviate from the Michaelis-Menten model and show no or weak interfacial activation. The presence of molecular aggregates in solutions of short-chain substrates, as evidenced by a spectral dye method, likely accounts for the activity of lipases against soluble esters. Unlike esterases, lipases hydrolyze emulsions of water-insoluble medium- and long-chain vinyl esters and TAG such as vinyl laurate, trioctanoin, and
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
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.
Ulmert, David; Vickers, Andrew J; Scher, Howard I
2012-01-01
The utility of conventional prostate-specific antigen (PSA) measurements in blood for monitoring rapid responses to treatment for prostate cancer is limited because of its slow elimination rate. Prior studies have shown that free PSA (fPSA), intact PSA (iPSA) and human kallikrein-related peptidase...... of tPSA, fPSA, iPSA and hK2 after rapid induction of castration with degarelix (Firmagon(®)), a novel GnRH antagonist....
Donna R. Kashian; Peter Landrum; Duane Gossiaux; Julianne Dyble; Steven Pothoven
2011-01-01
Fish consumption is a potential route of human exposure to the hepatotoxic microcystins, especially in lakes and reservoirs that routinely experience significant toxic Microcystis blooms. Understanding the rates of uptake and elimination for microcystins as well as the transfer efficiency into tissues of consumers are important for determining the potential for microcystins to be transferred up the food web and for predicting potential human health impacts. The main objective of this work was...
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...
Model-order reduction of biochemical reaction networks
Rao, Shodhan; Schaft, Arjan van der; Eunen, Karen van; Bakker, Barbara M.; Jayawardhana, Bayu
2013-01-01
In this paper we propose a model-order reduction method for chemical reaction networks governed by general enzyme kinetics, including the mass-action and Michaelis-Menten kinetics. The model-order reduction method is based on the Kron reduction of the weighted Laplacian matrix which describes the gr
DE KOK, LJ; RENNENBERG, H; KUIPER, PJC
1991-01-01
Spinach (Spinacia oleracea) leaves formed an active sink for atmospheric H2S. Upon short-term exposure, H2S flux to the leaves showed saturation kinetics with respect to the H2S concentrations and could be described by the Michaelis-Menten equation. The kinetics of H2S flux to spinach leaves were
Hayashi, N; Aso, H; Higashida, M; Kinoshita, H; Ohdo, S; Yukawa, E; Higuchi, S
2001-05-01
The clearance of recombinant human granulocyte-colony stimulating factor (rhG-CSF) is known to decrease with dose increase, and to be saturable. The average clearance after intravenous administration will be lower than that after subcutaneous administration. Therefore, the apparent absolute bioavailability with subcutaneous administration calculated from the AUC ratio is expected to be an underestimate. The absorption pharmacokinetics after subcutaneous administration was examined using the results of the bioequivalency study between two rhG-CSF formulations with a dose of 2 microg/kg. The analysis was performed using a modified Wagner-Nelson method with the nonlinear elimination model. The apparent absolute bioavailability for subcutaneous administration was 56.9 and 67.5% for each formulation, and the ratio between them was approximately 120%. The true absolute bioavailability was, however, estimated to be 89.8 and 96.9%, respectively, and the ratio was approximately 108%. The absorption pattern was applied to other doses, and the predicted clearance values for subcutaneous and intravenous administrations were then similar to the values for several doses reported in the literature. The underestimation of bioavailability was around 30%, and the amplification of difference was 2.5 times, from 8 to 20%, because of the nonlinear pharmacokinetics. The neutrophil increases for each formulation were identical, despite the different bioavailabilities. The reason for this is probably that the amount eliminated through the saturable process, which might indicate the amount consumed by the G-CSF receptor, was identical for each formulation.
Shiroudi, Abolfazl; Zahedi, Ehsan; Oliaey, Ahmad Reza; Deleuze, Michael S.
2017-03-01
The thermal decomposition kinetics of 2-chloroethylsilane and derivatives in the gas phase has been studied computationally using density functional theory, along with various exchange-correlation functionals (UM06-2x and ωB97XD) and the aug-cc-pVTZ basis set. The calculated energy profile has been supplemented with calculations of kinetic rate constants under atmospheric pressure and in the fall-off regime, using transition state theory (TST) and statistical Rice-Ramsperger-Kassel-Marcus (RRKM) theory. Activation energies and rate constants obtained using the UM06-2x/aug-cc-pVTZ approach are in good agreement with the experimental data. The decomposition of 2-chloroethyltriethylsilane species into the related products [C2H4 + Et3SiCl] is characterized by 6 successive structural stability domains associated to the sequence of catastrophes C8H19SiCl: 6-C†FCC†[FF]-0: C6H15SiCl + C2H4. Breaking of Si-C bonds and formation of Si-Cl bonds occur in the vicinity of the transition state.
Structural simplification of chemical reaction networks in partial steady states.
Madelaine, Guillaume; Lhoussaine, Cédric; Niehren, Joachim; Tonello, Elisa
2016-11-01
We study the structural simplification of chemical reaction networks with partial steady state semantics assuming that the concentrations of some but not all species are constant. We present a simplification rule that can eliminate intermediate species that are in partial steady state, while preserving the dynamics of all other species. Our simplification rule can be applied to general reaction networks with some but few restrictions on the possible kinetic laws. We can also simplify reaction networks subject to conservation laws. We prove that our simplification rule is correct when applied to a module of a reaction network, as long as the partial steady state is assumed with respect to the complete network. Michaelis-Menten's simplification rule for enzymatic reactions falls out as a special case. We have implemented an algorithm that applies our simplification rules repeatedly and applied it to reaction networks from systems biology.
Russo, Karen Ann
Methacrylate-based monomers are routinely used in medical biomaterials. Monomers undergo polymerization reactions to form the solid resin. These polymerization reactions can be incomplete thus making unpolymerized monomer available for possible biodistribution. Understanding the fate of these monomers is essential not only for their toxicological profile but also for development of future biomaterials. Aromatic methacrylate-based monomers included in this study were bisphenol A dimethacrylate and bisphenol A diglycidyl dimethathacrylate; aliphatic methacrylate monomers were 2-hydroxyethyl methacrylate and triethyleneglycol dimethacrylate. These compounds contain ester moieties thought to be susceptible to esterase-mediated hydrolysis. The hypothesis was that the ester bond of the methacrylate monomers can be hydrolyzed by esterases and these reactions would occur in a measurable, time-dependent manner confirmed by specific Michaelis-Menten kinetic relationships. Including aliphatic and aromatic methacrylate monomers in this work allowed for structure-based comparisons. In vitro enzymolysis of the test compounds by acetylcholinesterase and cholesterol esterase was performed in buffered solutions. The hydrolysis reactions were monitored by high performance liquid chromatography with ultraviolet detection. The disappearance of parent compound and appearance of hydrolysis products were quantitated. The aromatic methacrylate monomers, bisphenol A dimethacrylate and bisphenol A diglycidyl dimethacrylate, were resistant to acetylcholine esterase hydrolysis but were converted by cholesterol esterase. The putative xenoestrogen, bisphenol A, was identified as a hydrolysis product from bisphenol A dimethacrylate conversion. Cholesterol esterase induced hydrolysis of bisphenol A diglycidyl dimethacrylate yielded a Km value of 1584 muM and Vmax of 14 muM min-1. Triethyleneglycol was converted by both esterases with calculated Km values of 394 and 1311 muM for acetylcholine
Munschy, C., E-mail: cmunschy@ifremer.f [Institut Francais de Recherche pour l' Exploitation de la Mer (IFREMER), Laboratory of Biogeochemistry of Organic Contaminants, Rue de l' Ile d' Yeu, BP 21105, 44311 Nantes Cedex 3 (France); Heas-Moisan, K.; Tixier, C.; Olivier, N. [Institut Francais de Recherche pour l' Exploitation de la Mer (IFREMER), Laboratory of Biogeochemistry of Organic Contaminants, Rue de l' Ile d' Yeu, BP 21105, 44311 Nantes Cedex 3 (France); Gastineau, O.; Le Bayon, N.; Buchet, V. [Institut Francais de Recherche pour l' Exploitation de la Mer (IFREMER), Laboratory of Adaptation, Reproduction and Nutrition of marine fish, BP 70, 29280 Plouzane (France)
2011-01-15
The uptake and elimination of six PBDE congeners (BDE-28, -47, -99, -100, -153, -209) were studied in juvenile common sole (Solea solea L.) exposed to spiked contaminated food over a three-month period, then depurated over a five-month period. The results show that all of the studied PBDEs accumulate in fish tissues, including the higher brominated congener BDE-209. Several additional PBDE congeners were identified in the tissues of exposed fish, revealing PBDE transformation, mainly via debromination. The identified congeners originating from PBDE debromination include BDE-49 and BDE-202 and a series of unidentified tetra-, penta-, and hepta- BDEs. Contaminant assimilation efficiencies (AEs) were related to their hydrophobicity (log K{sub ow}) and influenced by PBDE biotransformation. Metabolism via debromination appears to be a major degradation route of PBDEs in juvenile sole in comparison to biotransformation into hydroxylated metabolites. - Juvenile sole exposed to artificially-contaminated food accumulate PBDEs, including the higher brominated congeners, and have a debromination capacity.
Diagnosis of Enzyme Inhibition Using Excel Solver: A Combined Dry and Wet Laboratory Exercise
Dias, Albino A.; Pinto, Paula A.; Fraga, Irene; Bezerra, Rui M. F.
2014-01-01
In enzyme kinetic studies, linear transformations of the Michaelis-Menten equation, such as the Lineweaver-Burk double-reciprocal transformation, present some constraints. The linear transformation distorts the experimental error and the relationship between "x" and "y" axes; consequently, linear regression of transformed data…
Helms, Hans Cc; Aldana, Blanca I; Groth, Simon
2017-01-01
-application of transporter inhibitors and competing amino acids. Endothelial abluminal L-glutamate uptake was almost abolished by co-application of an EAAT-1 specific inhibitor, whereas luminal uptake was inhibited by L-glutamate and L-aspartate (1 mM). L-glutamate uptake followed Michaelis-Menten-like kinetics with high...
Enzymatic Production of Ceramide from Sphingomyelin
Zhang, Long; Hellgren, Lars; Xu, Xuebing
activity. After seven recycles, immobilized enzyme retains around 70% of its initial activity. Through kinetic study, it has been found that the hydrolysis reactions catalyzed by both soluble and immobilized enzyme follow the Michaelis-Menten equation. The presentation will describe the research background...
Cyclodextrin Aldehydes are Oxidase Mimics
Fenger, Thomas Hauch; Bjerre, Jeannette; Bols, Mikael
2009-01-01
Cyclodextrins containing 6-aldehyde groups were found to catalyse oxidation of aminophenols in the presence of hydrogen peroxide. The catalysis followed Michaelis-Menten kinetics and is related to the catalysis previously observed with cyclodextrin ketones. A range of different cyclodextrin...
Diagnosis of Enzyme Inhibition Using Excel Solver: A Combined Dry and Wet Laboratory Exercise
Dias, Albino A.; Pinto, Paula A.; Fraga, Irene; Bezerra, Rui M. F.
2014-01-01
In enzyme kinetic studies, linear transformations of the Michaelis-Menten equation, such as the Lineweaver-Burk double-reciprocal transformation, present some constraints. The linear transformation distorts the experimental error and the relationship between "x" and "y" axes; consequently, linear regression of transformed data…
Bjelke, Jais R; Christensen, Jesper; Nielsen, Per F
2006-01-01
of the two proteins can be expressed as active peptidases, which are 882 and 892 amino acids in length for dipeptidyl peptidase 8 and 9 respectively. We show further that the purified proteins are active dimers and that they show similar Michaelis-Menten kinetics and substrate specificity. Both cleave...
van Beusekom, C D; Fink-Gremmels, J; Schrickx, J A
2014-01-01
This study aimed to assess the overall glucuronidation capacity of cats, using prototypic substrates identified for human UDP-glucuronosyltransferases (UGTs). To this end, Michaelis-Menten kinetics were established for the substrates using feline hepatic microsomal fractions, and results were compar
van Beusekom, C D|info:eu-repo/dai/nl/314836497; Fink-Gremmels, J|info:eu-repo/dai/nl/119949997; Schrickx, J A|info:eu-repo/dai/nl/30483114X
This study aimed to assess the overall glucuronidation capacity of cats, using prototypic substrates identified for human UDP-glucuronosyltransferases (UGTs). To this end, Michaelis-Menten kinetics were established for the substrates using feline hepatic microsomal fractions, and results were
Moog, P.R.; Van der Kooij, T.A.W.; Bruggemann, W.; Schiefelbein, J.W.; Kuiper, P.J.C.
1995-01-01
Arabidopsis thaliana (L.) Heynh. Columbia wild type and a root hair-less mutant RM57 were grown on iron-containing and iron-deficient nutrient solutions. In both genotypes, ferric chelate reductase (FCR) of intact roots was induced upon iron deficiency and followed a Michaelis-Menten kinetic with a
Zhang, Yi; Tay, Joo Hwa
2016-03-15
Aerobic granule is a novel form of microbial aggregate capable of degrading toxic and recalcitrant substances. Aerobic granules have been formed on phenol as the growth substrate, and used to co-metabolically degrade trichloroethylene (TCE), a synthetic solvent not supporting aerobic microbial growth. Granule formation process, rate limiting factors and the comprehensive toxic effects of phenol and TCE had been systematically studied. To further explore their potential at the level of microbial population and functions, phenol degraders were isolated and purified from mature granules in this study. Phenol and TCE degradation kinetics of 15 strains were determined, together with their TCE transformation capacities and other physiological characteristics. Isolation in the presence of phenol and TCE exerted stress on microbial populations, but the procedure was able to preserve their diversity. Wide variation was found with the isolates' kinetic behaviors, with the parameters often spanning 3 orders of magnitude. Haldane kinetics described phenol degradation well, and the isolates exhibited actual maximum phenol-dependent oxygen utilization rates of 9-449 mg DO g DW(-1) h(-1), in phenol concentration range of 4.8-406 mg L(-1). Both Michaelis-Menten and Haldane types were observed for TCE transformation, with the actual maximum rate of 1.04-21.1 mg TCE g DW(-1) h(-1) occurring between TCE concentrations of 0.42-4.90 mg L(-1). The TCE transformation capacities and growth yields on phenol ranged from 20-115 mg TCE g DW(-1) and 0.46-1.22 g DW g phenol(-1), respectively, resulting in TCE transformation yields of 10-70 mg TCE g phenol(-1). Contact angles of the isolates were between 34° and 82°, suggesting both hydrophobic and hydrophilic cell surface. The diversity in the isolates is a great advantage, as it enables granules to be versatile and adaptive under different operational conditions.
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
吴梅芬; 王晓岗; 刘亚菲; 许新华
2015-01-01
The mechanism of a-chymotrypsin-catalyzed hydrolysis of 4-nitrophenyl trimethylacetate includes the following steps:the reversible enzyme-substrate binding and the enzyme acylation and enzyme deacylation.This mechanism is quite different from the conventional Michaelis-Menten mechanism for enzyme-catalyzed reactions.The corresponding kinetic parameters can be expressed precisely on the basis of chemical kinetics theory,such as Michaelis constant KM ,equilibrium constant K,catalytic rate constant kcat ,and the rate constants of the elementary reactions k 2 and k 3 .The reaction is carried out at 25 °C in a pH = 8.5 buffer of tris(hydroxymethyl)aminomethane (TRIS)by means of spectrophotometry.The kinetic curves are fitted linearly and non-linearly.The kinetic parameters are in agreement with the theoretical prediction.The enzyme product used in this experiment is cheap and the activity is stable. The experimental method is simple enough to be applied in undergraduate physical chemistry laboratory courses.As an ideal model of complex reaction,the experiment will help the students to enhance the understanding and knowledge of chemical kinetics theories.%通过严格的化学反应动力学推导,得到了a-糜蛋白酶催化三甲基乙酸对硝基苯酯水解反应相关的动力学参数的表达式,包括表观米氏常数 KM、酶-底物络合物稳定常数 K 、催化速率常数 kcat 、以及基元反应步骤速率常 k2和 k3等.实验在25℃,pH ＝8．5的三羟基氨基甲烷缓冲液中进行,用分光光度法测定反应的动力学曲线.数据经过非线性拟合和线性拟合,得到相关的动力学参数,该参数与理论预测一致.该实验酶制剂价格低廉,活性稳定,实验方法简单,可作为本科物理化学实验课程中复杂反应动力学测量的一个很好的实例,加深学生对化学反应动力学相关理论和概念的理解和掌握.
Malea, Paraskevi; Adamakis, Ioannis-Dimosthenis S; Kevrekidis, Theodoros
2013-11-15
The kinetics of cadmium accumulation and its effects on microtubule cytoskeleton and cell viability in leaf blades of the seagrass Cymodocea nodosa were investigated under laboratory conditions in exposure concentrations ranging from 0.5 to 40 mg L(-1). An initial rapid accumulation of cadmium was followed by a steady state. The Michaelis-Menten model adequately described metal accumulation; equilibrium concentration and uptake velocity tended to increase, whereas bioconcentration factor at equilibrium to decrease, as the exposure concentration increased. Cadmium depolymerized microtubules after 3-9 d of exposure, depending on trace metal concentration, indicating that microtubules could be used as an early biomarker of cadmium stress; cell death, occurring at later time than microtubule disturbance, was also observed. Microtubule depolymerization expressed as percentage of reduction of fluorescence intensity and cell mortality expressed as percentage of live cells increased with time. The lowest experimental tissue concentration associated with the onset of microtubule depolymerization and cell death (98.5-128.9μgg(-1)drywt, 0.5 mg L(-1) treatment, 7th and 9th d) was within the wide range of reported cadmium concentrations in leaves of seagrass species from various geographical areas. This lowest tissue concentration was exceeded up to the 3rd d at higher exposure concentrations, but toxic effects were generally detected at later time. The time periods required for the onset of depolymerization and for 10 and 50% of cells to die tended to decrease as the uptake velocity increased; in particular, significant negative correlations were found between these variables. These results suggest that toxicity appears to be a function of cadmium uptake rate rather than of the total tissue metal concentration. Hence, tissue residues should be interpreted in relation to the time frame of the exposure, while the estimation of metal uptake velocity could be utilized for
Phosphorus Uptake Kinetics of Different Types of Duckweed.%不同品种浮萍磷素吸收动力学特征
蔡树美; 刘文桃; 张震; 柏彦超; 钱晓晴
2011-01-01
以长江三角洲地区常见的3种浮萍--稀脉浮萍(Lemna aequinoctialis)、少根紫萍(Spirodela oligorrhiza)和紫萍(Spriodela polyrrhiza)为对象,研究不同品种浮萍对HPO42-的吸收动力学影响.结果表明,3种浮萍对无机磷的吸收动力学特征基本可采用Michaelis-Menten方程描述,3种浮萍无机磷吸收速率V对磷浓度S双倒数曲线的拟合关系均在α=0.01水平上显著.稀脉浮萍对无机磷的亲和力较强,适宜应用于对低磷浓度污水的净化;紫萍对无机磷的最大吸收速率Vmax较高,适宜应用于对高磷浓度污水的净化.%An increasing attention has been paid to the use of duckweed in treating eutrophicated water as a tool of bio-remediation of domestic wastewater.Phosphorus uptake kinetics was studied,of different species of duckweeds, i.e.Lemna aequinoctialis, Spirodela oligorrhiza and Spriodela polyrrhiza, which are common in the Yangtze River Delta area.Results show that the phosphorus uptake kinetics of the duckweeds could be expressed with the Michaelis-Menten equation; and the relation between phosphorus uptake rate (V) of the duckweeds and inorganic phosphorus(Pi) concentration (S), was well fitted with a double-reciprocal curve with at =0.01; the Km value for Pi uptake of Lemna aequinoctialis was lower than that of Spirodela oligorrhiza and Spriodela polyrrhiza, making it a better candidate for treating wastewater low in Pi concentration.The maximum phosphorus uptake rate of Spriodela polyrrhiza was higher than that of the other two species, which allows Spriodela polyrrhiza better performance in purifying wastewater higher in Pi concentration.
Study on the kinetics of saccharifying enzymes of Luzhou-flavor daqu%浓香型大曲糖化动力学研究
任飞; 张晓宇
2013-01-01
In order to study on the kinetics of saccharifying enzymes of Luzhou-flavor Daqu, using the enzymes of 5% Daqu hydrolyzed soluble starch, at pH 4. 6, 30℃ , an Michaelis-Menten equation was deduced. The optimum pH value for the catalysis of saccharifying enzymes of Luzhou-flavor Daqu was 6. 0. Studying the catalytic reaction rate under different temperatures, the calculation results showed that the activation energy of the enzyme catalytic reaction was 40. 966 kJ/mol. The kinetics of saccharifying enzymes of Luzhou-fla-vor Daqu was similar to a single enzyme, During the production of Luzhou-flavor liquor, it will contribute to manage the saccharification and fermentation process simultaneously by controlling the conditions of pits input into the cellar, such as the concentration of starch and starter, initial acidity and temperature.%为研究浓香型大曲的糖化动力学,用5％的大曲浸出液水解可溶性淀粉,在pH4.6、30℃的条件下,用菲林试剂法测定还原糖的含量,得出米氏方程；浓香型大曲糖化反应的最适pH值为6.0；在不同温度下测定糖化反应速率,计算得到活化能E为40.966 kJ/mol.试验证明,浓香型大曲糖化酶类的糖化反应动力学与单一酶相似.通过控制淀粉浓度(投粮量)、用曲量、入窖酸度和温度可以使浓香型大曲酒的糖化、发酵过程协调进行.
Estimating the turnover number in enzyme kinetic reactions using transient and stationary state data
Sibel Uludag-Demirer
2009-12-01
Full Text Available Substrate and product concentration data obtained by simulating enzyme-substrate reaction rate equations were used to test two proposed kinetic rate constant estimation techniques in this study. In the first technique, the turnover number, k3, was calculated using early transient time domain data, which are difficult to obtain experimentally. The technique used an iterative approach to calculate k3 with a pair of data and the value of k3 could be retrieved with 35% error. The second technique calculated k3 using stationary domain data and the value of k3 could be retrieved with less than 5% error. This second technique also offered internal consistency in the calculation of k3 by calculating k3 both from the intercept and the slope of the linear plot derived in this study. A series of sensitivity analyses was conducted to understand the robustness of the second technique in estimating k3 from simulated data to the changes in the reaction rate constants (k1, k2, and k3 and the initial concentration of enzyme used for simulation. It was found that the second technique generally worked well in the estimation of k3 except for the simulated data for fast substrate conversions such as in the large k3 and [E]0 cases . This latter method, thus, shows promise for the use of late time experimental substrate/product concentration data to obtain k3. Exclusively using late time data avoids the need for difficult and expensive rapid early time measurement techniques for estimating k3. Once a reasonable estimate for k3 is obtained, the initial enzyme value can easily be determined from the maximum velocity constant established from fitting the Michaelis-Menten or Briggs-Haldane equations to substrate and product stationary state domain (late time data. While the first technique can estimate k3 with only one point in the transient domain, it is suggested that the second method generally be favored since it only requires late-time stationary domain data and
Glucose Oxidase Catalyzed Self-Assembly of Bioelectroactive Gold Nanostructures
2010-01-01
value of 15 mM at which point the kinetics of catalytic activity plateau as expected as a result of enzymatic Michaelis - Menten kinetics (Fig. 5D... kinetics of the nucleation process. This process occurs in the absence of glucose or peroxide, formed as a result of enzymatic oxidation of glucose or any...remained inconclusive, as the reactionwas complicated by the requirement forDMSO in the reactionmixture.Amore detailed investigation of the kinetics and
Oikawa, P. Y.; Jenerette, D.; Knox, S. H.; Sturtevant, C. S.; Verfaillie, J. G.; Baldocchi, D. D.
2014-12-01
Under California's Cap-and-Trade program, companies are looking to invest in land-use practices that will reduce greenhouse gas (GHG) emissions. The Sacramento-San Joaquin River Delta is a drained cultivated peatland system and a large source of CO2. To slow soil subsidence and reduce CO2 emissions, there is growing interest in converting drained peatlands to wetlands. However, wetlands are large sources of CH4 that could offset CO2-based GHG reductions. The goal of our research is to provide accurate measurements and model predictions of the changes in GHG budgets that occur when drained peatlands are restored to wetland conditions. We have installed a network of eddy covariance towers across multiple land use types in the Delta and have been measuring CO2 and CH4 ecosystem exchange for multiple years. In order to upscale these measurements through space and time we are using these data to parameterize and validate a process-based biogeochemical model. To predict gross primary productivity (GPP), we are using a simple light use efficiency (LUE) model which requires estimates of light, leaf area index and air temperature and can explain 90% of the observed variation in GPP in a mature wetland. To predict ecosystem respiration we have adapted the Dual Arrhenius Michaelis-Menten (DAMM) model. The LUE-DAMM model allows accurate simulation of half-hourly net ecosystem exchange (NEE) in a mature wetland (r2=0.85). We are working to expand the model to pasture, rice and alfalfa systems in the Delta. To predict methanogenesis, we again apply a modified DAMM model, using simple enzyme kinetics. However CH4 exchange is complex and we have thus expanded the model to predict not only microbial CH4 production, but also CH4 oxidation, CH4 storage and the physical processes regulating the release of CH4 to the atmosphere. The CH4-DAMM model allows accurate simulation of daily CH4 ecosystem exchange in a mature wetland (r2=0.55) and robust estimates of annual CH4 budgets. The LUE
Wang, Zhican; Wong, Timothy; Hashizume, Takanori; Dickmann, Leslie Z; Scian, Michele; Koszewski, Nicholas J; Goff, Jesse P; Horst, Ronald L; Chaudhry, Amarjit S; Schuetz, Erin G; Thummel, Kenneth E
2014-06-01
25-Hydroxyvitamin D3 (25OHD3) is used as a clinical biomarker for assessment of vitamin D status. Blood levels of 25OHD3 represent a balance between its formation rate and clearance by several oxidative and conjugative processes. In the present study, the identity of human uridine 5'-diphosphoglucuronyltransferases (UGTs) capable of catalyzing the 25OHD3 glucuronidation reaction was investigated. Two isozymes, UGT1A4 and UGT1A3, were identified as the principal catalysts of 25OHD3 glucuronidation in human liver. Three 25OHD3 monoglucuronides (25OHD3-25-glucuronide, 25OHD3-3-glucuronide, and 5,6-trans-25OHD3-25-glucuronide) were generated by recombinant UGT1A4/UGT1A3, human liver microsomes, and human hepatocytes. The kinetics of 25OHD3 glucuronide formation in all systems tested conformed to the Michaelis-Menten model. An association between the UGT1A4*3 (Leu48Val) gene polymorphism with the rates of glucuronide formation was also investigated using human liver microsomes isolated from 80 genotyped livers. A variant allele dose effect was observed: the homozygous UGT1A4*3 livers (GG) had the highest glucuronidation activity, whereas the wild type (TT) had the lowest activity. Induction of UGT1A4 and UGT1A3 gene expression was also determined in human hepatocytes treated with pregnane X receptor/constitutive androstane receptor agonists, such as rifampin, carbamazepine, and phenobarbital. Although UGT mRNA levels were increased significantly by all of the known pregnane X receptor/constitutive androstane receptor agonists tested, rifampin, the most potent of the inducers, significantly induced total 25OHD3 glucuronide formation activity in human hepatocytes measured after 2, but not 4 and 24 hours, of incubation. Finally, the presence of 25OHD3-3-glucuronide in both human plasma and bile was confirmed, suggesting that the glucuronidation pathway might be physiologically relevant and contribute to vitamin D homeostasis in humans.
Funk, M; Gath, I; Seidel, A; Platt, K L; Oesch, F; Zeller, H D
1994-02-09
The enzyme-catalysed conjugation of each of the four stereoisomers of trans-3,4-dihydroxy-1,2-epoxy-1,2,3,4-tetrahydrobenzo[c]phenanthrene (B[c]PhDE) with glutathione (GSH) by HTP II, a novel isolated mu-class GSH transferase from the liver of untreated rat, was studied. All four stereoisomers were substrates for GSH transferase HTP II. The enzymatic reaction shows three different types of enzyme kinetics: substrate inhibition for (-)-anti-B[c]PhDE with (R,S,S,R)-absolute configuration, allosteric behavior using (+)-anti-B[c]PhDE with (S,R,R,S)-absolute configuration and Henri-Michaelis-Menten kinetics with both the (-)-syn- and (+)-syn-enantiomers, with (S,R,S,R)- and (R,S,R,S)-absolute configuration, respectively. When the concentration of these diolepoxides was varied (using 2 mM GSH), the apparent Vmax values were 1975 nmol/min x mg for (-)-anti-B[c]PhDE and about 60 nmol/min x mg for both (-)-syn- and (+)-syn-B[c]PhDE, with the corresponding Km values of 1.05 and 0.20 mM. The reaction of (+)-anti-B[c]PhDE determined by applying the Hill equation had an estimated Vmax value of 930 nmol/min x mg. On varying the concentration of GSH, linear Lineweaver-Burk plots were obtained. No competitive effect could be observed using a mixture of (-)-anti- and (+)-anti-enantiomers, indicating that their binding sites are different and independent. It was also shown, that the binding sites of (+)-anti- and both syn-enantiomers were different and independent of each other, while there was a small effect on the binding of the syn-enantiomers caused by (-)-anti-B[c]PhDE. All products of the reaction between GSH and the dihydrodiol epoxides of benzo[c]phenanthrene could be resolved by HPLC and were identified and quantitated using the corresponding synthetic GSH conjugates.
Farazdaghi, Hadi
2011-02-01
Photosynthesis is the origin of oxygenic life on the planet, and its models are the core of all models of plant biology, agriculture, environmental quality and global climate change. A theory is presented here, based on single process biochemical reactions of Rubisco, recognizing that: In the light, Rubisco activase helps separate Rubisco from the stored ribulose-1,5-bisphosphate (RuBP), activates Rubisco with carbamylation and addition of Mg²(+), and then produces two products, in two steps: (Step 1) Reaction of Rubisco with RuBP produces a Rubisco-enediol complex, which is the carboxylase-oxygenase enzyme (Enco) and (Step 2) Enco captures CO₂ and/or O₂ and produces intermediate products leading to production and release of 3-phosphoglycerate (PGA) and Rubisco. PGA interactively controls (1) the carboxylation-oxygenation, (2) electron transport, and (3) triosephosphate pathway of the Calvin-Benson cycle that leads to the release of glucose and regeneration of RuBP. Initially, the total enzyme participates in the two steps of the reaction transitionally and its rate follows Michaelis-Menten kinetics. But, for a continuous steady state, Rubisco must be divided into two concurrently active segments for the two steps. This causes a deviation of the steady state from the transitional rate. Kinetic models are developed that integrate the transitional and the steady state reactions. They are tested and successfully validated with verifiable experimental data. The single-process theory is compared to the widely used two-process theory of Farquhar et al. (1980. Planta 149, 78-90), which assumes that the carboxylation rate is either Rubisco-limited at low CO₂ levels such as CO₂ compensation point, or RuBP regeneration-limited at high CO₂. Since the photosynthesis rate cannot increase beyond the two-process theory's Rubisco limit at the CO₂ compensation point, net photosynthesis cannot increase above zero in daylight, and since there is always respiration at
王丹; 赵玲; 尹平河; 肖娟宜; 黄思明
2012-01-01
在实验室模拟条件下,以粉煤灰改性污泥为垃圾填埋场生物覆盖材料,分析了初始甲烷浓度、初始氧气浓度对甲烷氧化效率的影响,并测定了甲烷氧化动力学方程及动力学参数,旨在为材料实际工程应用提供理论依据.结果表明:初始CH4、O2浓度制约生物覆盖材料的甲烷氧化效率,初始CH4、O2浓度越高,材料甲烷氧化能力越强；甲烷氧化过程符合2级动力学方程-dV(CH4)/dt=kV(CH4)V(O2)；利用Michaelis-Menten模型得出覆盖层材料的最大氧化速率Vmax为2.54 μmol g-1h-1,半速常数Km为0.49 μmol.%In this study, laboratory-scale experiments were carried out to examine the effects of initial methane and oxygen contents on methane oxidation efficiency in landfill bio-cover sewage sludge, and the kinetic equation and corresponding parameters were also determined, aiming to provide scientific basis for the practical engineering application. The results showed that the methane and oxygen contents strongly affected the methane oxidation efficiency. The higher methane and oxygen contents resulted in stronger methane oxidation efficiency. The kinetics of methane oxidation was - dV( CH4)/di = kV{ CH4 ) V( 02) , which fit the second-order reaction. As calculated from Michaelis-Menten equation, the largest methane oxidation rate ( Kmax ) was 2. 54 μmol g ‐ 1h‐ 1, and the half saturation constant ( Km ) was found at 0. 49 μmol.
Thermodynamic Basis for the Emergence of Genomes during Prebiotic Evolution
2012-05-01
affected by the action of polymerases. If one ignores the reverse reaction under the condition of ½PPi?0, the Michaelis - Menten kinetics applies for the...spontaneity of changes. Following a recent theoretical approach, we applied the quasispecies theory combined with kinetic /thermodynamic descriptions of...RNA replication to analyze the collective behavior of RNA replicators based on known experimental kinetics data. We find that, with increasing fidelity
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
Chan-Huot, Monique; Lesot, Philippe; Pelupessy, Philippe; Duma, Luminita; Bodenhausen, Geoffrey; Duchambon, Patricia; Toney, Michael D; Reddy, U Venkateswara; Suryaprakash, N
2013-05-07
We report the in situ and real-time monitoring of the interconversion of L- and D-alanine-d3 by alanine racemase from Bacillus stearothermophilus directly observed by (2)H NMR spectroscopy in anisotropic phase. The enantiomers are distinguished by the difference of their (2)H quadrupolar splittings in a chiral liquid crystal containing short DNA fragments. The proof-of-principle, the reliability, and the robustness of this new method is demonstrated by the determination of the turnover rates of the enzyme using the Michaelis-Menten model.
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.
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.
张亚娟; 刘存歧; 李洪波; 吴亦红; 王亚斌
2011-01-01
以蕹菜(Ipomoea aquatica)为材料,采用改进的常规耗竭法,对氨氮、硝酸盐氮和无机磷的吸收动力学特性进行了研究.通过室内静态实验测定了蕹菜对富营养化水体的氮磷去除效率.用Michaelis-Menten方程来描述蕹菜对氨氮、硝酸盐氮和无机磷的吸收速率与溶液浓度的相互关系.结果表明:蕹菜对氨氮、硝酸盐氮和无机磷的最大吸收常数Vmax为23.59、2.88和1.52μmol/(g FW·h),亲和力常数Km为1.90、10.94和0.97μmol/L,可见蕹菜对氨氮的吸收速率和亲和力均高于硝酸盐氮,对无机磷的吸收速率较小;蕹菜对富营养化水体总氮、氨氮、总磷和有机磷的去除率分别为38.13%、44.85%、63.77%和53.95%;蕹菜对受试水体表现了良好的适应性和净化能力.%The absorption kinetics of ammonium, nitrate and phosphorus by Ipomoea aquatica were studied,after that ammonium, nitrate and inorganic phosphorus removal from eutrophic water was examined under indoor static simulation experimental condition. The relationship between the uptake rate and the concentration was depicted using the Michaelis-Menten equation. The purposes of this study were to provide a scientific foundation for the removal mechanism of ammonium ,nitrate and inorganic phosphorus from water. The results showed that the maximum velocities (Vmax) of absorption on ammonium, nitrate and inorganic phosphorus were 23.59, 2.88 and 1.52μmol/( g FW·h), the Michaelis constant(Km ) were 1.90,10. 94 and 0. 97μmol/L. The results of static state removals of TN, NH4+-N, TP, DOP by I aquatica were 38.13％ ,44. 85％ ,63.77％ and 53.95％ , respectively. It is proved that I. aquatica could be used to purify the eutrophicated water body.
龚盛昭; 程江; 杨卓如
2006-01-01
Aim To evaluate the effect of paeonol on the activity of tyrosinase and provide experimental evidence for the treatment of hyperpigmentation disorders. Methods Tyrosinase activity was estimated by measuring the oxidation rate of L-3,4-dihydroxyphenylalanine (L-Dopa). The inhibitory effects of paeonol on the activity of mushroom tyrosinase and Michaelis-Menten kinetics were deduced from the Lineweaver-Burk plots. Results The inhibitory concentration of paeonol leading to 50% enzyme Paeonol is a potential mixed inhibitor of mushroom tyrosinase. The mixed inhibition function may originate from its ability to form a Schiff base with a primary amino group and to chelate copper at the active site of tyrosinase.%目的研究丹皮酚对酪氨酸酶活性的影响,为色素增加性皮肤病的治疗提供实验依据.方法选用酪氨酸酶催化氧化3,4-二羟基苯丙氨酸(L-Dopa)速率法体外测定酪氨酸酶活性.应用Lineweaver-Burk曲线推导丹皮酚对酪氨酸酶活性的抑制效应及Michaelis-Menten动力学.结果导致酪氨酸酶活力下降50%的丹皮酚浓度为0.60mmol·L-1.丹皮酚对游离酶的抑制常数(KI)和对酶底物络合物的抑制常数(KIS)分别为0.084和0.12 mmol·L-1.结论丹皮酚是酪氨酸酶的混合型抑制剂,该抑制作用源于其能与酶中氨基结合生成席夫碱及能与活性中心的铜生成络合物.
Modeling Heavy Metal Removal in Wetlands.
1992-05-01
1976 a,b,c) and Pettersson (1976) treated heavy metals uptake according to Michaelis-Menten kinetics ( Lehninger , 1975), discussed later in detail...copper kinetics equation as used in this modeling effort is presented below, after Lehninger (1975): dv_ dV, Ca (5) dt dt C.+K, where: v = rate of copper...the bulk solution, Cb, using either the Lineweaver-Burk double reciprocal or Eadie-Hofstee graphical methods ( Lehninger , 1975). Nielsen (1976 b) used
The Effect of Saquinavir on the Rate of Metabolism of Midazolam
2013-01-31
Hensyl, 1990). Saquinavir and Midazolam 8 Ki The inhibition constant for Michaelis - Menten kinetics which describes the ability of a drug to inhibit...Redacted] PREFACE This study was conducted to provide information regarding the kinetic interaction between midazolam and saquinavir. Midazolam is a...the catalysis of a second drug (Fabre et. al., 1988). Km The Michaelis constant that describes the affinity of an enzyme to a particular substrate
Optimizing the Electron Transfer Reactions at the Cathode of Microbial Fuel Cells
2015-05-15
intact bacterium conformed to the Michaelis - Menten formalism. The reduced intracellular red cytochrome represented the Michaelis complex whose...expressed spectrally different biomolecules that were redox-active during aerobic respiration on iron. In all six cases, compelling kinetic evidence...that of the electro- chemically reduced cytochrome observed in the presence of Fe(II). The kinetics of aerobic respiration on soluble iron by the
Hawaii Energy and Environmental Technologies (HEET) Initiative
2010-08-01
14) to zero, the Langmuir isotherm of the present adsorption problem is: X=j-^h— (15) *ads A Michaelis - Menten formalism is recovered for methane...systems. Methane hydrates work included: hydrate thermochemistry and kinetics ; environmental impacts of methane release from seafloor hydrates...5.1 Scope of Work and Approach 82 5.1.1 Hydrate Thermochemistry and Kinetics 82 5.1.2 Environmental Impacts of Methane Release from Seafloor Hydrates
Heule, Marijn; Biere, Armin
2010-01-01
Generalizing the novel clause elimination procedures developed in [M. Heule, M. J\\"arvisalo, and A. Biere. Clause elimination procedures for CNF formulas. In Proc. LPAR-17, volume 6397 of LNCS, pages 357-371. Springer, 2010.], we introduce explicit (CCE), hidden (HCCE), and asymmetric (ACCE) variants of a procedure that eliminates covered clauses from CNF formulas. We show that these procedures are more effective in reducing CNF formulas than the respective variants of blocked clause elimination, and may hence be interesting as new preprocessing/simplification techniques for SAT solving.
Department of Homeland Security — USCIS is streamlining the way immigration benefits are delivered. By working smarter and eliminating redundancies, USCIS is bringing a business model to government....
Hydrolysis of Toxic Natural Glucosides Catalyzed by Cyclodextrin Dicyanohydrins
Bjerre, Jeannette; Nielsen, Erik Holm; Bols, Mikael
2008-01-01
The hydrolysis of toxic 7-hydroxycoumarin glucosides and other aryl and alkyl glucosides, catalyzed by modified a- and ß-cyclodextrin dicyanohydrins, was investigated using different UV, redox, or HPAEC detection assays. The catalyzed reactions all followed Michaelis-Menten kinetics, and an impre......The hydrolysis of toxic 7-hydroxycoumarin glucosides and other aryl and alkyl glucosides, catalyzed by modified a- and ß-cyclodextrin dicyanohydrins, was investigated using different UV, redox, or HPAEC detection assays. The catalyzed reactions all followed Michaelis-Menten kinetics......, and an impressive rate increase of up to 7569 (kcat/kuncat) was found for the hydroxycoumarin glucoside substrate 4-MUGP. Good and moderate degrees of catalysis (kcat/kuncat) of up to 1259 were found for the natural glucosides phloridzin and skimmin. By using a newly developed catechol detection UV-assay, a weak...
Fernandez, J.A. [Area de Ecologia, Facultad de Biologia, Univ. Santiago de Compostela, 15782 Santiago de Compostela (Spain)]. E-mail: bfjafe@usc.es; Vazquez, M.D. [Area de Ecologia, Escuela Politecnica Superior, Univ. Santiago de Compostela, 27002 Lugo (Spain); Lopez, J. [Area de Ecologia, Facultad de Ciencias, Univ. de Vigo, 36200 Vigo (Spain); Carballeira, A. [Area de Ecologia, Facultad de Biologia, Univ. Santiago de Compostela, 15782 Santiago de Compostela (Spain)
2006-01-15
Samples of the aquatic bryophyte Fontinalis antipyretica Hedw. were transplanted to different sites with the aim of characterizing the kinetics of the uptake and discharge of heavy metals in the extra and intracellular compartments. The accumulation of metals in extracellular compartments, characterized by an initial rapid accumulation, then a gradual slowing down over time, fitted perfectly to a Michaelis-Menten model. The discharge of metals from the same compartment followed an inverse linear model or an inverse Michaelis-Menten model, depending on the metal. In intracellular sites both uptake and discharge occurred more slowly and progressively, following a linear model. We also observed that the acidity of the environment greatly affected metal accumulation in extracellular sites, even when the metals were present at relatively high concentrations, whereas the uptake of metals within cells was much less affected by pH. - The kinetics of uptake and discharge of heavy metals, in different cellular locations, were studied in transplanted aquatic mosses.
Immobilization of lipase from Fusarium solani FS1 Imobilização de lipase de Fusarium solani FS1
Kirsty Knight
2000-09-01
Full Text Available Lipase from Fusarium solani FS1 was immobilized by covalent attachment to polyacrylamide beads and onto magnetized Dacron, retaining 12% and 97% of activity, respectively. Lipase was also entrapped within polyacrylamide beads, retaining 53% of activity. Investigations of the kinetic characteristics of the immobilized derivatives using triolein as substrate showed that lipase immobilized onto polyacrilamide beads and Dacron did not follow Michaelis-Menten kinetics.Lipase de Fusarium solani FS1 foi imobilizada por ligação covalente usando esferas de poliacrilamida e Dacron magnetizado, retendo 12%, e 97% de atividade, respectivamente. A lipase foi também enclausurada em esferas de poliacrilamida e reteve 53% de sua atividade específica. Investigações sobre o comportamento cinético usando trioleína como substrato mostraram que as lipases imobilizadas não seguem a cinética de Michaelis-Menten.
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.
翟爱华; 李新华
2012-01-01
The response mechanism and kinetic behavior of bioactive peptides by protease were studied. Rice bran protein was used as raw material. Based on the classic Michaelis - Menten equation, the enzymatic kinetics of the system of rice bran protein and alkaline protease was researched by the method of mathematical derivation combined with experiment. The mechanism model of single substrate hydrolysis of protein and inactivation of protease were considered to build the kinetics model of R =aexp[ -b(DH) ] ,and the parameters "a" and "b" of the kinetics model were determined. Origin 8. 0 software was applied to fit the deduced formula and calculate related parameters of enzyme kinetic model. It was shown that the rate of hydrolysis kinetic model was R = (94. 754e0 - 0. 0597s0 ) exp [ -0. 157 (DH)] and the kinetic model of degree of hydrolysis and time of hydrolysis was DH = 6. 37× ln[1 +(14. 88e0/s0 -0. 009)t]. The kinetic constants of the system of rice bran protein and alkaline protease were fitted by experiments and the results showed that the constant K4 of enzyme inactivation was 16. 144 min-1 and the constant k2 of enzymatic reaction rate was 94. 754 min-1 .%研究蛋白酶水解制备生物活性多肽反应机制与动力学行为,基于经典的米氏方程理论,应用数学推导结合试验研究的方法,以米糠蛋白为原料,对米糠蛋白-碱性蛋白酶体系进行酶解动力学研究.考虑蛋白质单底物水解、蛋白酶失活的机理模型,构建动力学模型R=aexp[-b(DH)],其中对参数a值和b值进行确定.利用Origin 8.0软件,对推导出的公式进行拟合得到水解速率动力学模型为R=(94.754e0-0.0597s0)exp[-0.157(DH)],水解度-水解时间的动力学模型:DH =6.37ln[1+(14.88e0/s0-0.009)t].对于米糠蛋白-碱性蛋白酶模型体系,经试验拟合,并求得该体系动力学常数:酶失活常数K4为16.144 min-1,酶解反应速率常数k2为94.754 min-1.
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).
Manipulating single enzymes by an external harmonic force
Lomholt, Michael A; Urbakh, Michael; Metzler, Ralf
2007-01-01
We study a Michaelis-Menten reaction for a single two-state enzyme molecule, whose transition rates between the two conformations are modulated by an harmonically oscillating external force. In particular, we obtain a range of optimal driving frequencies for changing the conformation of the enzyme......, thereby controlling the enzymatic activity (i.e., product formation). This analysis demonstrates that it is, in principle, possible to obtain information about particular rates within the kinetic scheme....
Slow-Binding Inhibition: A Theoretical and Practical Course for Students
Golicnik, Marko; Stojan, Jure
2004-01-01
Tyrosinase (EC 1.14.18.1) catalyzes the oxidation of L-3,4-dihydroxyphenylalanine (L-DOPA) to 2,3,5,6-tetrahydro-5,6-dioxo-1H-indole-2-carboxylate (dopachrome), according to the classical Michaelis-Menten kinetic mechanism. The enzyme is strongly but slowly inhibited by alpha-amino-beta-[N-(3-hydroxy-4-pyridone)] propionic acid (L-mimosine), a…
Asymptotic Behaviour Near a Nonlinear Sink
Calder, Matt S
2010-01-01
In this paper, we will explore an iterative procedure to determine the detailed asymptotic behaviour of solutions of a certain class of nonlinear vector differential equations which approach a nonlinear sink as time tends to infinity. This procedure is indifferent to resonance in the eigenvalues. Moreover, we will address the writing of one component in terms of the other in the case of a planar system. Examples will be given, notably the Michaelis-Menten mechanism of enzyme kinetics.
Amino acid uptake and energy coupling dependent on photosynthesis in Anacystis nidulans.
Lee-Kaden, J; Simonis, W
1982-01-01
The photoautotrophic cyanobacterium Anacystis nidulans was used to investigate the membrane transport of branched-chain, neutral amino acids and its dependence on photosynthetic reactions. The uptake of alpha-amino [1-14C]isobutyric acid and L-[1-14C]leucine followed Michaelis, Menten kinetics and resulted in an energy-dependent accumulation. As in bacteria, different uptake systems for neutral amino acids were present: two DAG (D-alanine, aminoisobutyric acid, and glycine) systems responsibl...
Fernández, J A; Vázquez, M D; López, J; Carballeira, A
2006-01-01
Samples of the aquatic bryophyte Fontinalis antipyretica Hedw. were transplanted to different sites with the aim of characterizing the kinetics of the uptake and discharge of heavy metals in the extra and intracellular compartments. The accumulation of metals in extracellular compartments, characterized by an initial rapid accumulation, then a gradual slowing down over time, fitted perfectly to a Michaelis-Menten model. The discharge of metals from the same compartment followed an inverse linear model or an inverse Michaelis-Menten model, depending on the metal. In intracellular sites both uptake and discharge occurred more slowly and progressively, following a linear model. We also observed that the acidity of the environment greatly affected metal accumulation in extracellular sites, even when the metals were present at relatively high concentrations, whereas the uptake of metals within cells was much less affected by pH.
Babú, Yogeeta N; Nemec, Michal; Solich, Petr; Wsól, Vladimír
2008-04-15
Glucuronidation of the non-steroidal anti-inflammatory chiral drug flobufen and its major metabolite M17203 has been implicated as an important mechanism of flobufen elimination. To characterize flobufen metabolism by O-glucuronidation, new liquid chromatographic method (LC) coupled with ESI-MS was developed to detect the conjugates of flobufen and its metabolites formed in vitro in rat liver microsomes. Discovery DSC-18 LT cartridge columns were utilized for solid phase extraction (SPE) and Discovery C18 column (150 mm x 2.1 mm, 5 microm particle size) was used for LC separation. Chiral inversion of flobufen and its metabolites enantiomers was checked by special 1-allyl-(5R,8S,10R)-terguride column (150 mm x 4.6 mm). O-Glucuronidation of the S-enantiomer displayed a typical Michaelis-Menten kinetics, whereas the R-enantiomer exhibited a substrate inhibition type of kinetics. The study of glucuronidation of M17203 led to kinetics with sigmoidal characteristics.
黄曲霉毒素氧化酶的酶动力学研究%Enzymatic kinetics of aflatoxin oxidase
胡丽莎; 谢春芳; 刘大岭
2012-01-01
Aflatoxin oxidase ( AFO) is a protein enzyme derived from the Armillariella tabescens, and demonstrating aflatoxin degradation effect. AFO has been successfully cloned and expressed in a prokary-otic system in our previous studies. The enzymatic kinetics has been investigated by determination of the apparent reaction rate. The traditional analysis method was carried out by end point reaction, which was not suitable for the continuous monitor of enzyme reaction. The experimental process of traditional method was more cumbersome and could be influenced by many factors. Therefore, isothermal titration microcalo-ri-metry (ITC) was used to examine the enzymatic kinetics of AFO in this study through substrate titration and direct monitoring of enzyme reactions in the process of heat change. A complete Michaelis-Ment-en curve was produced by the titration, and measured by fitting analysis. The aflatoxin oxidase activity on AFB1 (KmAFB1) and the ST Michaelis-Menten constant (KmST) were found at 3. 34 x 10-7 mol/L and 1. 06 x 10-7 mol/L, respectively. AFB1 and ST conversion factors were KcatAFB1 -2. 7 min-1 and KcatST = 1.7 min-1 respectively. The combination letters were found at AHAFB1 = - 1.686 x 107 J/mol andΔH5T = -9. 092 x 106 J/mol, respectively. Compared with the traditional methods, application of ITC in enzymatic kinetics demonstrates significant advantages, due to its simpleness, speediness, accuracy and universality.%黄曲霉毒素氧化酶(AFO)是来自Armillariella tabescens的具有降解黄曲霉毒素作用的蛋白质酶.本实验室成功克隆和以原核系统表达了黄曲霉毒素氧化酶,前期的工作中用传统测量表观酶促反应速度的方法对AFO进行了酶动力学的研究,采用了在酶反应的结束点进行分析,因此不能够连续监测酶的反应过程,且实验过程较为繁琐,影响因素较多,对动力学常数的测量存在不够准确的可能.本实验使用等温滴定微量热技术对该
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
Gonze, Didier; Abou-Jaoudé, Wassim; Ouattara, Djomangan Adama; Halloy, José
2011-01-01
The recent advance of genetic studies and the rapid accumulation of molecular data, together with the increasing performance of computers, led researchers to design more and more detailed mathematical models of biological systems. Many modeling approaches rely on ordinary differential equations (ODE) which are based on standard enzyme kinetics. Michaelis-Menten and Hill functions are indeed commonly used in dynamical models in systems and synthetic biology because they provide the necessary nonlinearity to make the dynamics nontrivial (i.e., limit-cycle oscillations or multistability). For most of the systems modeled, the actual molecular mechanism is unknown, and the enzyme equations should be regarded as phenomenological. In this chapter, we discuss the validity and accuracy of these approximations. In particular, we focus on the validity of the Michaelis-Menten function for open systems and on the use of Hill kinetics to describe transcription rates of regulated genes. Our discussion is illustrated by numerical simulations of prototype systems, including the Repressilator (a genetic oscillator) and the Toggle Switch model (a bistable system). We systematically compare the results obtained with the compact version (based on Michaelis-Menten and Hill functions) with its corresponding developed versions (based on "elementary" reaction steps and mass action laws). We also discuss the use of compact approaches to perform stochastic simulations (Gillespie algorithm). On the basis of these results, we argue that using compact models is suitable to model qualitatively biological systems.
Minding Rachlin's Eliminative Materialism
McDowell, J. J.
2012-01-01
Rachlin's teleological behaviorism eliminates the first-person ontology of conscious experience by identifying mental states with extended patterns of behavior, and thereby maintains the materialist ontology of science. An alternate view, informed by brain-based and externalist philosophies of mind, is shown also to maintain the materialist…
Minding Rachlin's Eliminative Materialism
McDowell, J. J.
2012-01-01
Rachlin's teleological behaviorism eliminates the first-person ontology of conscious experience by identifying mental states with extended patterns of behavior, and thereby maintains the materialist ontology of science. An alternate view, informed by brain-based and externalist philosophies of mind, is shown also to maintain the materialist…
Somerville, Kevin; Francombe, Paula
2005-01-01
The effect of the elimination of mortality from heart disease and cancer was modelled mathematically to allow for the effect of other competing causes of death. The model allows for potential dependence between heart disease or cancer and other causes of death by using cupola functions, which analyse the individual risk itself and the dependence structure between causes of death by using correlation coefficients. As the strength of these risk associations is unknown, the study investigated both full positive and negative dependence and compared this with no dependence. Depending upon the degree and type of correlation assumed, positive or negative, the life expectancy at birth is increased by between 3 months and 6.5 years if cancer mortality was eliminated, and between 5 months and 7.5 years in the case of heart disease. In addition, estimates of these effects on life insurance premia can be made with the greatest reduction for women with the elimination of cancer mortality. These figures provide a range of improvements in life expectancy and the consequent effect on life insurance risk premium rates which elimination of either of these important diseases would produce.
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
Efficacy of wood charcoal and its modified form as packing media for biofiltration of isoprene.
Srivastva, Navnita; Singh, Ram S; Dubey, Suresh K
2017-07-01
The efficacy of wood charcoal (WC) and nutrient-enriched wood charcoal (NWC) as biofilter packing media were assessed for isoprene biodegradation in a bioreactor comprising bioscrubber and a biofilter connected in series and inoculated with Pseudomonas sp. The bioreactors using WC and NWC exhibited >90% removal efficiency and around 369 g m(-3) h(-1) elimination capacity at around 404 g m(-3) h(-1) inlet loading rate. In both the bioreactors, the biofilter component showed better degradation capacity compared to the bioscrubber unit. The kinetic parameters, maximum elimination capacity, ECmax; substrate constant, Ks and ECmax/Ks for Michaelis-Menten model were evaluated. The lower Ks for the WC packed bioreactor indicated that ECmax achieved, was faster compared to others, while higher ECmax and ECmax/Ks for the NWC packed bioreactor suggests its superiority in isoprene abatement in the continuous mode. A comparison of the available published information on biofiltration of isoprene reflected polyurethane foam as the superior packing media. Copyright © 2017 Elsevier Ltd. All rights reserved.
Near-Critical Phenomena in Intracellular Metabolite Pools
Elf, Johan; Paulsson, Johan; Berg, Otto G.; Ehrenberg, Måns
2003-01-01
The supply and consumption of metabolites in living cells are catalyzed by enzymes. Here we consider two of the simplest schemes where one substrate is eliminated through Michaelis-Menten kinetics, and where two types of substrates are joined together by an enzyme. It is demonstrated how steady-state substrate concentrations can change ultrasensitively in response to changes in their supply rates and how this is coupled to slow relaxation back to steady state after a perturbation. In the one-substrate system, such near-critical behavior occurs when the supply rate approaches the maximal elimination rate, and in the two-substrate system it occurs when the rates of substrate supply are almost balanced. As systems that operate near criticality tend to display large random fluctuations, we also carried out a stochastic analysis using analytical approximations of master equations and compared the results with molecular-level Monte Carlo simulations. It was found that the significance of random fluctuations was directly coupled to the steady-state sensitivity and that the two substrates can fluctuate greatly because they are anticorrelated in such a way that the product formation rate displays only small variation. Basic relations are highlighted and biological implications are discussed. PMID:12524272
Eliminating Perinatal HIV Transmission
2012-11-26
In this podcast, CDCâs Dr. Steve Nesheim discusses perinatal HIV transmission, including the importance of preventing HIV among women, preconception care, and timely HIV testing of the mother. Dr. Nesheim also introduces the revised curriculum Eliminating Perinatal HIV Transmission intended for faculty of OB/GYN and pediatric residents and nurse midwifery students. Created: 11/26/2012 by Division of HIV/AIDS Prevention. Date Released: 11/26/2012.
Targeting rubella for elimination
Davendra K Taneja
2012-01-01
Full Text Available Rubella is an acute, usually mild viral disease. However, when rubella infection occurs just before conception or during the first 8-10 weeks of gestation, it causes multiple fetal defects in up to 90% of cases, known as Congenital Rubella Syndrome (CRS. It may result in fetal wastage, stillbirths and sensorineural hearing deficit up to 20 weeks of gestation. Rubella vaccine (RA 27/3 is highly effective and has resulted in elimination of rubella and CRS from the western hemisphere and several European countries. Review of several studies documents the duration of protection over 10-21 years following one dose of RA27/3 vaccination, and persistent seropositivity in over 95% cases. Studies in India show seronegativity to rubella among adolescent girls to vary from 10% to 36%. Although due to early age of infection resulting in protection in the reproductive age group, incidence of rubella in India is not very high. However, due to severity of CRS coupled with introduction of RCV in private sector and in some of the states which is likely to lead to sub-optimal coverage and resulting higher risk of rubella during pregnancy in the coming decades, it is imperative to adopt the goal of rubella elimination. As in order to control measles, the country has adopted strategy of delivering second dose of measles through measles campaigns covering children 9 months to 10 years of age in 14 states, it is recommended to synergize efforts for elimination of rubella with these campaigns by replacing measles vaccine by MR or MMR vaccine. Other states which are to give second dose of measles through routine immunization will also have to adopt campaign mode in order to eliminate rubella from the country over 10-20 years. Subsequently, measles vaccine can be replaced by MR or MMR vaccine in the national schedule.
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
Lin, Maozi; Wang, Zhiwei; He, Lingchao; Xu, Kang; Cheng, Dongliang; Wang, Genxuan
2015-01-01
Photosynthesis-irradiance (PI) curves are extensively used in field and laboratory research to evaluate the photon-use efficiency of plants. However, most existing models for PI curves focus on the relationship between the photosynthetic rate (Pn) and photosynthetically active radiation (PAR), and do not take account of the influence of environmental factors on the curve. In the present study, we used a new non-competitive inhibited Michaelis-Menten model (NIMM) to predict the co-variation of Pn, PAR, and the relative pollution index (I). We then evaluated the model with published data and our own experimental data. The results indicate that the Pn of plants decreased with increasing I in the environment and, as predicted, were all fitted well by the NIMM model. Therefore, our model provides a robust basis to evaluate and understand the influence of environmental pollution on plant photosynthesis.
Maozi Lin
Full Text Available Photosynthesis-irradiance (PI curves are extensively used in field and laboratory research to evaluate the photon-use efficiency of plants. However, most existing models for PI curves focus on the relationship between the photosynthetic rate (Pn and photosynthetically active radiation (PAR, and do not take account of the influence of environmental factors on the curve. In the present study, we used a new non-competitive inhibited Michaelis-Menten model (NIMM to predict the co-variation of Pn, PAR, and the relative pollution index (I. We then evaluated the model with published data and our own experimental data. The results indicate that the Pn of plants decreased with increasing I in the environment and, as predicted, were all fitted well by the NIMM model. Therefore, our model provides a robust basis to evaluate and understand the influence of environmental pollution on plant photosynthesis.
Efforts to Eliminate Illiteracy
无
2000-01-01
FOLLOWING the Chinese women's emancipation movement, the Chinese women's illiteracy elimination drive has also gone through a history of 50 years. Although this task is a huge and arduous one, due to various historical, economic and ideological reasons, the rate of illiteracy amongst Chinese women has declined from 90 percent immediately after the founding of New China in 1949 to the present level of 23 percent. The rate of girls going to school has risen from 20 percent to 96.8 percent. Among
Risks: diagnosing and eliminating
Yuriy A. Tikhomirov
2016-01-01
Full Text Available Objective to develop conceptual theoretical and legal provisions and scientific recommendations on the identification analysis and elimination of risk. Methods universal dialectic method of cognition as well as scientific and private research methods based on it. Results the system was researched of risks diagnostics in the legal sphere and mechanism of influencing the quotrisk situationsquot and their consequences damage to the environment and harm to society. The concept of risk in the legal sphere was formulated the author39s classification of risks in the legal sphere is presented. The rules of analysis evaluation and prevention of risks and the model risk management framework are elaborated. Scientific novelty the mechanism for the identification analysis and elimination of risk has been developed and introduced into scientific circulation the author has proposed the classification and types of risks the reasons and the conditions promoting the risk occurrence. Practical significance the provisions and conclusions of the article can be used in the scientific lawmaking and lawenforcement activity as well as in the educational process of higher educational establishments. nbsp
宋保军; 娄洁; 文清芝
2011-01-01
通过建立数学模型,描述了HIV-1感染者使用抗病毒治疗药物——融合酶抑制剂(T-20)的治疗效果.使用脉冲微分方程描述了T-20的使用过程,并考虑了两种不同的药物消除动力学:一级消除动力学与米-曼(Michaelis-Menten)消除动力学.此模型是个非自治微分方程系统,主要关注其无病平衡态,并研究当接受治疗者在服药完全依从的治疗过程中无病平衡态的稳定性.分别针对药物剂量与服药间隔得到了使得无病平衡态稳定的阈值条件.此外,还研究了间歇治疗的效果.研究表明,间歇治疗的效果甚至可以比完全不治疗还要糟糕.%A mathematical model that describes the antiretroviral therapy of the fusion inhibitor enfuvirtide on HIV-1 patients and the effect of enfuvirtide (formerly T-20) using impulsive differential equations were developed, taking into account two different drug elimination kinetics: first order and Michaelis-Menten. The model was a non-autonomous system of differential equations. For the time-dependent system, the disease-free equilibrium and its stability when therapy was taken with perfect adherence were focused on. Analytical thresholds for dosage and dosing intervals were determined to ensure that the disease-free equilibrium remains stable. The effects of supervised treatment interruption were also explored. It is shown that supervised treatment interruption may be worse than no therapy at all, thus strongly supporting no interruption strategies.
王岚; 王伟; 黄承和; 常春荣
2012-01-01
The characteristics of nitrate uptake kinetic in the solution of five ratios of ammonium and nitrate by modified depleting way treated with 0.2 mtnol/L CaSO4 solution for three days were studied to discover the ammonium and' nitrate nutrition properties of banana seedlings. The result showed that the nitrate uptake kinetic characteristics of all treatments with five ratios of ammonium and nitrate followed the enzyme kinetic model of Michaelis-Menten. Increasing ammonium ratio remarkably influenced Vmax. and Kmi would be reduced more to the Hoagland solution adding 10% ammonium than that in placement of 10% ammonium with 10% nitrate, although Kn had no distinct difference between these two treatments. The nitrate uptake rate would be reduced in soil of 100% nitrate treated with increasing ammonium ratios. The nitrate affinity, would be decreased treated with 10% more ammonium, while that for the 25% ammonium treatment was in the opposite direction. The nitrate uptake for banana seedlings belonged to low affinity system.%将香蕉苗移植到0.2 mmol/L CaSO4溶液中饥饿3d,采用改进耗竭法研究了香蕉幼苗期在5种铵硝配比营养液中的硝态氮的吸收动力学特征,以探讨香蕉铵硝营养特点.结果表明,香蕉幼苗所有铵硝配比处理的硝态氮吸收曲线特征均符合Michaelis-Menten酶动力学模型的描述.加铵不仅显著影响香蕉幼苗硝态氮吸收动力学参数Vax,对Km的影响也达显著水平.在霍格兰营养液的基础上直接添加10％NH4+-N比将10％NO3-N用NIH4+-N替换更能降低香蕉对硝态氮的吸收速率,但这两种处理对Km的影响不显著.在100％硝态氮的基础上,增铵降低了香蕉对硝态氮的吸收速率,增10％NH4+-N降低香蕉对硝态氮的亲和力,增25％ NH+4-N对香蕉对硝态氮的亲和力的影响则相反.在本实验条件下,香蕉硝态氮吸收系统属于低亲和吸收系统.
Golgi-resident PAP-specific 3'-phosphatase-coupled sulfotransferase assays.
Prather, Brittany; Ethen, Cheryl M; Machacek, Miranda; Wu, Zhengliang L
2012-04-01
Sulfotransferases are a large group of enzymes that transfer a sulfonate group from the donor substrate, 3'-phosphoadenosine-5'-phosphosulfate (PAPS)(1), to various acceptor substrates, generating 3'-phosphoadenosine-5'-phosphate (PAP) as a by-product. A universal phosphatase-coupled sulfotransferase assay is described here. In this method, Golgi-resident PAP-specific 3'-phosphatase (gPAPP) is used to couple to a sulfotransferase reaction by releasing the 3'-phosphate from PAP. The released phosphate is then detected using malachite green reagents. The enzyme kinetics of gPAPP have been determined, which allows calculation of the coupling rate, the ratio of product-to-signal conversion, of the coupled reaction. This assay is convenient, as it eliminates the need for radioisotope labeling and substrate-product separation, and is more accurate through removal of product inhibition and correction of the results with the coupling rate. This assay is also highly reproducible, as a linear correlation factor above 0.98 is routinely achievable. Using this method, we measured the Michaelis-Menten constants for recombinant human CHST10 and SULT1C4 with the substrates phenolphthalein glucuronic acid and α-naphthol, respectively. The activities obtained with the method were also validated by performing simultaneous radioisotope assays. Finally, the removal of PAP product inhibition by gPAPP was clearly demonstrated in radioisotope assays.
Similarity transformation approach to identifiability analysis of nonlinear compartmental models.
Vajda, S; Godfrey, K R; Rabitz, H
1989-04-01
Through use of the local state isomorphism theorem instead of the algebraic equivalence theorem of linear systems theory, the similarity transformation approach is extended to nonlinear models, resulting in finitely verifiable sufficient and necessary conditions for global and local identifiability. The approach requires testing of certain controllability and observability conditions, but in many practical examples these conditions prove very easy to verify. In principle the method also involves nonlinear state variable transformations, but in all of the examples presented in the paper the transformations turn out to be linear. The method is applied to an unidentifiable nonlinear model and a locally identifiable nonlinear model, and these are the first nonlinear models other than bilinear models where the reason for lack of global identifiability is nontrivial. The method is also applied to two models with Michaelis-Menten elimination kinetics, both of considerable importance in pharmacokinetics, and for both of which the complicated nature of the algebraic equations arising from the Taylor series approach has hitherto defeated attempts to establish identifiability results for specific input functions.
Oliver-Calixte, Nyoté J; Uba, Franklin I; Battle, Katrina N; Weerakoon-Ratnayake, Kumuditha M; Soper, Steven A
2014-05-06
The process of immobilizing enzymes onto solid supports for bioreactions has some compelling advantages compared to their solution-based counterpart including the facile separation of enzyme from products, elimination of enzyme autodigestion, and increased enzyme stability and activity. We report the immobilization of λ-exonuclease onto poly(methylmethacrylate) (PMMA) micropillars populated within a microfluidic device for the on-chip digestion of double-stranded DNA. Enzyme immobilization was successfully accomplished using 3-(3-dimethylaminopropyl) carbodiimide/N-hydroxysuccinimide (EDC/NHS) coupling to carboxylic acid functionalized PMMA micropillars. Our results suggest that the efficiency for the catalysis of dsDNA digestion using λ-exonuclease, including its processivity and reaction rate, were higher when the enzyme was attached to a solid support compared to the free solution digestion. We obtained a clipping rate of 1.0 × 10(3) nucleotides s(-1) for the digestion of λ-DNA (48.5 kbp) by λ-exonuclease. The kinetic behavior of the solid-phase reactor could be described by a fractal Michaelis-Menten model with a catalytic efficiency nearly 17% better than the homogeneous solution-phase reaction. The results from this work will have important ramifications in new single-molecule DNA sequencing strategies that employ free mononucleotide identification.
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.
Dynamics of Hydrogen Elimination from Unsaturated Hydrocarbons
Cromwell, Evan Francis
dissociation of rm C_2H_4 . Differences in the vibrational, rotational and translational energies for these two channels are extracted. The D atom elimination from rm C_2D_4 is examined and kinetic energy distribution for this product is measured.
Banu, Kazi Sabnam; Chattopadhyay, Tanmay; Banerjee, Arpita; Bhattacharya, Santanu; Suresh, Eringathodi; Nethaji, Munirathinam; Zangrando, Ennio; Das, Debasis
2008-08-18
very efficiently. The substrate TCC forms an adduct with 2- 5 without performing further oxidation to TCQ due to the high reduction potential of TCC (in comparison with 3,5-DTBC). But most interestingly, 1 is observed to be effective even in TCC oxidation, a process never reported earlier. Kinetic experiments have been performed to determine initial rate of reactions (3,5-DTBC as substrate, in methanol medium) and the activity sequence is 1 > 5 > 2 = 4 > 3. A treatment on the basis of Michaelis-Menten model has been applied for kinetic study, suggesting that all five complexes exhibit very high turnover number, especially 1, which exhibits turnover number or K cat of 3.24 x 10 (4) (h (-1)), which is approximately 3.5 times higher than the most efficient catalyst reported to date for catecholase activity in methanol medium.
黄立新; 张欣欣; 吴小员; 郭峰
2013-01-01
Wheat flour was modified by acid and heat-moisture treatment in thermal water kettle.Polarization microscope,scanning electron micrograph,differential scanning calorimetry (DSC) instrument,Brabender viscosity instrument,X-ray diffraction (XRD),infrared spectrometer were used to study the properties enzymatic kinetics of wheat flour before and after the treatment.It was found that,after modification,the protein content was reduced and part of starch granules had shallow crack.Polarization cross was blurring.DSC showed endothermic peak moved backward and absorption enthalpy (ΔH) decreased 2.976 J/g.Brabender viscosity curve indicated that pasting temperature increased from 82.6 ℃ to 87 ℃ and viscosity decreased from 82 BU to 63 BU.XRD showed crystalline structure of starch increased 3.8％.Under in vitro digestion conditions,α-Amylase hydrolyzation of treatment product followed Michaelis-Menten,and enzymatic kinetic equation of product with α-Amylase was obtained as V=0.161[S]/(1.093+[S]).Compared with that without modification,Michealis constant (Km) and maximum rate (Vm) decreased.%本文采用水热反应釜酸湿热处理小麦面粉,分析了小麦面粉处理前后基本成分变化、显微形貌、热力学性质、糊粘度曲线、结晶性质、红外图谱和酶解动力学方程.研究表明,经过酸湿热处理后的作用产物,蛋白质含量减少,部分颗粒出现浅层裂痕,偏光十字模糊；差示扫描量热分析显示,处理产物与原面粉相比吸热峰后移,吸热焓ΔH降低了2.976 J/g;布拉班德粘度曲线表明,产物的起糊温度由82.6℃增加到87℃,峰值粘度由82 BU降到63 BU;X射线衍射分析显示产物结晶度增大3.8％；红外图谱变化不大.酶解动力学研究发现,在模拟体外消化条件下,a-淀粉酶对小麦面粉处理前后样品的降解遵循Michaelis-Menten规律,产物的a-淀粉酶酶解动力学方程为V=0.161[S]/(1.093+ [S]),与处理前比,米氏常数Km及最大反应速率Vm均降低.
Eliminating rabies in Estonia.
Florence Cliquet
Full Text Available The compulsory vaccination of pets, the recommended vaccination of farm animals in grazing areas and the extermination of stray animals did not succeed in eliminating rabies in Estonia because the virus was maintained in two main wildlife reservoirs, foxes and raccoon dogs. These two species became a priority target therefore in order to control rabies. Supported by the European Community, successive oral vaccination (OV campaigns were conducted twice a year using Rabigen® SAG2 baits, beginning in autumn 2005 in North Estonia. They were then extended to the whole territory from spring 2006. Following the vaccination campaigns, the incidence of rabies cases dramatically decreased, with 266 cases in 2005, 114 in 2006, four in 2007 and three in 2008. Since March 2008, no rabies cases have been detected in Estonia other than three cases reported in summer 2009 and one case in January 2011, all in areas close to the South-Eastern border with Russia. The bait uptake was satisfactory, with tetracycline positivity rates ranging from 85% to 93% in foxes and from 82% to 88% in raccoon dogs. Immunisation rates evaluated by ELISA ranged from 34% to 55% in foxes and from 38% to 55% in raccoon dogs. The rabies situation in Estonia was compared to that of the other two Baltic States, Latvia and Lithuania. Despite regular OV campaigns conducted throughout their territory since 2006, and an improvement in the epidemiological situation, rabies has still not been eradicated in these countries. An analysis of the number of baits distributed and the funding allocated by the European Commission showed that the strategy for rabies control is more cost-effective in Estonia than in Latvia and Lithuania.
Quantum State Detection Via Elimination
Ettinger, J M; Hoyer, Peter
1999-01-01
We present the view of quantum algorithms as a search-theoretic problem. We show that the Fourier transform, used to solve the Abelian hidden subgroup problem, is an example of an efficient elimination observable which eliminates a constant fraction of the candidate secret states with high probability. Finally, we show that elimination observables do not always exist by considering the geometry of the hidden subgroup states of the dihedral group D_N.
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.