scholarly journals Architecture of Allosteric Structure. Rate Equations, Rate Constants, and Equilibrium Constants for Reaction of: Hb4 with O2 and (HbO2)4 with Dithionate, in the Presence of 2,3-Bisphosphoglycerate

2019 ◽  
Author(s):  
Francis Knowles ◽  
Samantha J. Doyle ◽  
Douglas Magde
Keyword(s):  
Rate Constants ◽  
Binding Constant ◽  
Equilibrium Constants ◽  
Rate Equations ◽  
Rate Law ◽  
First Order ◽  
Equilibrium Binding ◽  
Binding Curve ◽  
O2 Binding

Three unknown quantities are all that is required to describe the O2-equilibrium binding curve for fractional saturation of human hemoglobin in red blood cells, under standard conditions: Kα, the O2-binding constant of equivalent α-chains; KC, the equilibrium constant for the T →R conformation change; Kβ, the O2-binding constant of equivalent β-chains. The model for formulation of the equation of state is a 3-stage ordered sequence of reactions. The values of were established by determination of rate constants for the oxygenation reaction and the dithionite-mediated de oxygenation reaction. The rate law for the forward reaction in the presence of excess O2 yields The same rate law yields for the dithionite-mediated de-oxygenation reaction. The rate constants for binding O2 are pseudo-first-order. The rate constants for release of O2 are first-order. Reactions involving O2, are 2-step ordered sequences of equivalent subunits. Progress curves for a 2-step ordered sequence of equivalent chains collapse to a first order reaction. Progress curves for both oxygenation and dithionite-mediated de-oxygenation reactions return is 0.0580 for the oxygenation reaction and 0.0358 for the dithionite-mediated de-oxygenation reaction. The corresponding values from the O2-equilibrium binding curve are: and = 0.02602. Values of determined from rate constants of progress curves for oxygenation and dithionite-mediated de-oxygenation reactions are close to values of determined by analysis of the O2-equilibrium binding curves for whole blood, by the Perutz/Adair equation.<br>

scholarly journals Architecture of Allosteric Structure. Rate Equations, Rate Constants, and Equilibrium Constants for Reaction of: Hb4 with O2 and (HbO2)4 with Dithionate, in the Presence of 2,3-Bisphosphoglycerate

2019 ◽  
Author(s):  
Francis Knowles ◽  
Samantha J. Doyle ◽  
Douglas Magde
Keyword(s):  
Rate Constants ◽  
Binding Constant ◽  
Equilibrium Constants ◽  
Rate Equations ◽  
Rate Law ◽  
First Order ◽  
Equilibrium Binding ◽  
Binding Curve ◽  
O2 Binding

Three unknown quantities are all that is required to describe the O2-equilibrium binding curve for fractional saturation of human hemoglobin in red blood cells, under standard conditions: Kα, the O2-binding constant of equivalent α-chains; KC, the equilibrium constant for the T →R conformation change; Kβ, the O2-binding constant of equivalent β-chains. The model for formulation of the equation of state is a 3-stage ordered sequence of reactions. The values of were established by determination of rate constants for the oxygenation reaction and the dithionite-mediated de oxygenation reaction. The rate law for the forward reaction in the presence of excess O2 yields The same rate law yields for the dithionite-mediated de-oxygenation reaction. The rate constants for binding O2 are pseudo-first-order. The rate constants for release of O2 are first-order. Reactions involving O2, are 2-step ordered sequences of equivalent subunits. Progress curves for a 2-step ordered sequence of equivalent chains collapse to a first order reaction. Progress curves for both oxygenation and dithionite-mediated de-oxygenation reactions return is 0.0580 for the oxygenation reaction and 0.0358 for the dithionite-mediated de-oxygenation reaction. The corresponding values from the O2-equilibrium binding curve are: and = 0.02602. Values of determined from rate constants of progress curves for oxygenation and dithionite-mediated de-oxygenation reactions are close to values of determined by analysis of the O2-equilibrium binding curves for whole blood, by the Perutz/Adair equation.<br>

scholarly journals The linkage between binding of the C-terminal domain of hirudin and amidase activity in human α-thrombin

1993 ◽  
Vol 289 (2) ◽  
pp. 475-480 ◽  
Author(s):  
R de Cristofaro ◽  
B Rocca ◽  
B Bizzi ◽  
R Landolfi
Keyword(s):  
Rate Constants ◽  
Binding Constant ◽  
Amidase Activity ◽  
Equilibrium Binding ◽  
Viscosity Effects ◽  
The Individual ◽  
Individual Rate ◽  
Hydrolysis Of ◽  
Equilibrium Binding Constant

A method derived from the analysis of viscosity effects on the hydrolysis of the amide substrates D-phenylalanylpipecolyl-arginine-p-nitroaniline, tosylglycylprolylarginine-p-nitroanaline and cyclohexylglycylalanylarginine-p-nitroalanine by human alpha-thrombin was developed to dissect the Michaelis-Menten parameters Km and kcat into the individual rate constants of the binding, acylation and deacylation reactions. This method was used to analyse the effect of the C-terminal hirudin (residues 54-65) [hir-(54-65)] domain on the binding and hydrolysis of the three substrates. The results showed that the C-terminal hir-(54-65) fragment affects only the acylation rate, which is increased approx. 1.2-fold for all the substrates. Analysis of the dependence of acylation rate constants on hirudin-fragment concentration, allowed the determination of the equilibrium binding constant of C-terminal hir-(54-65) (Kd approximately 0.7 microM). In addition this peptide was found to competitively inhibit thrombin-fibrinogen interaction with a Ki which is in excellent agreement with the equilibrium constant derived from viscosity experiments. These results demonstrate that binding of hir-(54-65) to the fibrinogen recognition site of thrombin does not affect the equilibrium binding of amide substrates, but induces only a small increase in the acylation rate of the hydrolysis reaction.

PLATELET AGGREGATION DOES NOT CONFORM TO SIMPLE PARTICLE COLLISION THEORY

1987 ◽  
Author(s):  
Moideen P Jamaluddin
Keyword(s):  
Platelet Aggregation ◽  
Rate Equation ◽  
Rate Constants ◽  
Kinetic Scheme ◽  
Order Type ◽  
Second Order ◽  
Particle Collision ◽  
Collision Theory ◽  
Rate Law ◽  
First Order

Platelet aggregation kinetics, according to the particle collision theory, generally assumed to apply, ought to conform to a second order type of rate law. But published data on the time-course of ADP-induced single platelet recruitment into aggregates were found not to do so and to lead to abnormal second order rate constants much larger than even their theoretical upper bounds. The data were, instead, found to fit a first order type of rate law rather well with rate constants in the range of 0.04 - 0.27 s-1. These results were confirmed in our laboratory employing gelfiltered calf platelets. Thus a mechanism much more complex than hithertofore recognized, is operative. The following kinetic scheme was formulated on the basis of information gleaned from the literature.where P is the nonaggregable, discoid platelet, A the agonist, P* an aggregable platelet form with membranous protrusions, and P** another aggregable platelet form with pseudopods. Taking into account the relative magnitudes of the k*s and assuming aggregation to be driven by hydrophobic interaction between complementary surfaces of P* and P** species, a rate equation was derived for aggregation. The kinetic scheme and the rate equation could account for the apparent first order rate law and other empirical observations in the literature.

scholarly journals Isomerization of an enzyme-coenzyme complex in yeast alcohol dehydrogenase-catalysed reactions

2003 ◽  
Vol 68 (2) ◽  
pp. 77-84 ◽  
Author(s):  
Vladimir Leskovac ◽  
Svetlana Trivic ◽  
Draginja Pericin
Keyword(s):  
Alcohol Dehydrogenase ◽  
Rate Constants ◽  
Equilibrium Constants ◽  
Kinetic Mechanism ◽  
Yeast Alcohol Dehydrogenase ◽  
Catalyzed Reactions ◽  
The Individual ◽  
Individual Rate ◽  
Catalyzed Oxidation

In this work, all the rate constants in the kinetic mechanism of the yeast alcohol dehydrogenase-catalyzed oxidation of ethanol by NAD+, at pH 7.0, 25 ?C, have been estimated. The determination of the individual rate constants was achieved by fitting the reaction progress curves to the experimental data, using the procedures of the FITSIM and KINSIM software package of Carl Frieden. This work is the first report in the literature showing the internal equilibrium constants for the isomerization of the enzyme-NAD+ complex in yeast alcohol dehydrogenase-catalyzed reactions.

scholarly journals NmrLineGuru: Standalone and User-Friendly GUIs for Fast 1D NMR Lineshape Simulation and Analysis of Multi-State Equilibrium Binding Models

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Chao Feng ◽  
Evgenii L. Kovrigin ◽  
Carol Beth Post
Keyword(s):  
Kinetic Model ◽  
Molecular Interactions ◽  
Rate Constants ◽  
Nmr Spectra ◽  
Equilibrium Constants ◽  
Software Tool ◽  
Biological Interactions ◽  
Equilibrium Binding ◽  
Accurate Quantitative Analysis ◽  
User Friendly

Abstract The ability of high-resolution NMR spectroscopy to readout the response of molecular interactions at multiple atomic sites presents a unique capability to define thermodynamic equilibrium constants and kinetic rate constants for complex, multiple-step biological interactions. Nonetheless, the extraction of the relevant equilibrium binding and rate constants requires the appropriate analysis of not only a readout that follows the equilibrium concentrations of typical binding titration curves, but also the lineshapes of NMR spectra. To best take advantage of NMR data for characterizing molecular interactions, we developed NmrLineGuru, a software tool with a user-friendly graphical user interface (GUI) to model two-state, three-state, and four-state binding processes. Application of NmrLineGuru is through stand-alone GUIs, with no dependency on other software and no scripted input. NMR spectra can be fitted or simulated starting with user-specified input parameters and a chosen kinetic model. The ability to both simulate and fit NMR spectra provides the user the opportunity to not only determine the binding parameters that best reproduce the measured NMR spectra for the selected kinetic model, but to also query the possibility that alternative models agree with the data. NmrLineGuru is shown to provide an accurate, quantitative analysis of complex molecular interactions.

The Kinetics of Isotope Effects in a Model Solvolysis System Involving One Optically Active Ion Pair Intermediate

1974 ◽  
Vol 52 (10) ◽  
pp. 1937-1941 ◽  
Author(s):  
P. Christian Vogel
Keyword(s):  
Rate Constant ◽  
Rate Constants ◽  
Isotope Effects ◽  
Kinetic Scheme ◽  
Ion Pair ◽  
Rate Equations ◽  
Differential Analysis ◽  
First Order ◽  
Order Rate ◽  
Special Cases

The derivation of the observed first-order rate constants from the "exact" integrated rate equations for the kinetic scheme of reaction 1 is presented. It is shown that the solvolytic exponential first-order rate constant is a special case of the polarimetric rate constant and that the optical activity of the product is determined by a multiplicative ratio of rate constants for the optically important reactions of the ion pair intermediate. A form of the integrated first-order polarimetric rate equation with a linearly independent parameter set is presented. The functions for the first-order rate constants derived using the steady state approximation are special cases of the functions derived from the exact equations, as are the functions for the first-order rate constants for two systems which involve pre-equilibria followed by a slow product forming step. These functions cannot all be derived one from the other. A differential analysis of observed isotope effects as functions of isotope effects on the rate constants for reactions involving the intermediates is presented.

The retroaldol reaction of 3-methyl-2-butenal

1983 ◽  
Vol 61 (1) ◽  
pp. 171-178 ◽  
Author(s):  
J. Peter Guthrie ◽  
Brian A. Dawson
Keyword(s):  
Sodium Hydroxide ◽  
Equilibrium Constant ◽  
Rate Constants ◽  
Equilibrium Constants ◽  
Aqueous Sodium Hydroxide ◽  
Initial Increase ◽  
Aqueous Sodium ◽  
Rate Determining Step ◽  
Kinetics Of

In aqueous sodium hydroxide solutions at 25 °C, 3-methyl-2-butenal, 1c, undergoes retroaldol cleavage to acetone and acetaldehyde. The kinetics of the retroaldol reaction were followed spectrophotometrically at 242 nm and showed simple first order behavior. When 3-methyl-3-hydroxybutanal, 2c, was added to aqueous sodium hydroxide solutions at 25 °C, there was an initial increase in absorbance at 242 nm, attributed to formation of 1c, followed by a 20-fold slower decrease; the rate of the slow decrease matches the rate of disappearance of 1c under the same conditions. Analysis of the kinetics allows determination of the three rate constants needed to describe the system: khyd = 0.00342; kdehyd = 0.00832; kretro = 0.0564; all M−1 s−1. The equilibrium constant for enone hydration is 0.41. Rate constants for the analogous reactions for acrolein and crotonaldehyde could be obtained from the literature. There is a reasonable rate–equilibrium correlation for the retroaldol step. For the enone hydration step, rate and equilibrium constants respond differently to replacement of hydrogen by methyl. It is proposed that this results from release of strain after the rate-determining step by rotation about a single bond; this decrease in strain is reflected in the equilibrium constant but not in the rate constant.

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