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.

A Kinetic Model Describing the Interaction of Bovine Prothrombin Fragment 1 with Calcium Ions

1985 ◽  
Vol 53 (01) ◽  
pp. 019-023 ◽  
Author(s):  
Charles W Kabis ◽  
Martha M Sarasua ◽  
Karen E Gottschalk ◽  
Carolyn D Bourne ◽  
Lee G Pedersen ◽  
...  
Keyword(s):  
Kinetic Model ◽  
Calcium Ions ◽  
Rate Constants ◽  
Equilibrium Constants ◽  
Rate Equations ◽  
Differential Rate ◽  
Prothrombin Fragment ◽  
Fluorescence Change ◽  
Equilibrium Data ◽  
Best Fit

SummaryA kinetic model is derived for the interaction of bovine prothrombin fragment 1 with calcium ions. The model requires binding of a minimum of two calcium ions for induction of the observed biphasic fluorescence decrease as a function of time. The model is shown to be consistent with experimental kinetic and equilibrium data by fitting theoretical curves for the biphasic fluorescence change to the data through exact solution of the nonlinear differential rate equations derived from the model. The rate constants for the binding of these two required calcium ions are calculated from the solutions as best fit parameters. The thermodynamic equilibrium constants, K1 and K2, for the binding of these two calcium ions are calculated from ratios of the forward and reverse rate constants as 0.6 × 104 and 5.4 × 104, respectively. Thus, the model correctly predicts positively cooperative calcium ion binding for at least the two calcium ions required to induce fluorescence quenching.

FLUXY: a simple code for computing steady-state metal fluxes at consuming (bio)interfaces, in natural waters

2008 ◽  
Vol 5 (3) ◽  
pp. 204 ◽  
Author(s):  
Zeshi Zhang ◽  
Jacques Buffle ◽  
Konstantin Startchev ◽  
Davide Alemani
Keyword(s):  
Steady State ◽  
Rate Constants ◽  
Natural Waters ◽  
Equilibrium Constants ◽  
Computer Time ◽  
Rate Limiting Step ◽  
Broad Size Distribution ◽  
Metal Flux ◽  
User Friendly ◽  
Rate Limiting

Environmental context. Until now there was no user-friendly code for metal flux computations in natural mixtures of aquatic complexants, which are however essential for prediction of metal bioavailability. The present paper describes the capabilities and limitations of one of the only two such codes presently available, called FLUXY. The results of FLUXY are compared with those of another code, and it is shown that it enables quick computation and is applicable to natural ligands under many environmental conditions. Abstract. The computation of metal fluxes at consuming interfaces like microorganisms or bioanalogical sensors is of great importance in ecotoxicology. The present paper describes the application of a simple code, FLUXY, for the computation of steady-state metal fluxes in the presence of a very large number of complexes, with broadly varying values of equilibrium constants, rate constants and diffusion coefficients. This code includes two major limiting assumptions, namely, (i) the existence of excess of ligand (L) compared with metal (M), and (ii) the fact that in a series of successive MLn complexes, the reaction is the rate-limiting step in flux computation. The domains of rate constants for which these assumptions are valid are tested systematically, and the corresponding errors are evaluated by comparison with the exact results given by another code: MHEDYN. FLUXY is then applied and compared with MHEDYN for case studies typical of aquatic systems, namely (i) a culture medium containing simple ligands; (ii) solutions of fulvic compounds including a broad distribution of complex stability and rate constants; and (iii) suspensions of aggregates with a broad size distribution. It is shown that FLUXY gives good results for cases (i) and (iii). Application to case (ii) (fulvic compounds) is also feasible under conditions that are clearly described. Altogether, FLUXY and MHEDYN are complementary. In particular, FLUXY only computes steady-state fluxes and requires the fulfilment of a few conditions, but when these are met, computations require much less computer time than MHEDYN.

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>

Oxidation of (1-hydroxybenzyl)ferrocene and its derivatives substituted in phenyl ring with bis(triphenylsilyl) chromate

1982 ◽  
Vol 47 (12) ◽  
pp. 3375-3380 ◽  
Author(s):  
Jaroslav Holeček ◽  
Karel Handlíř ◽  
Milan Nádvorník ◽  
Milan Vlček
Keyword(s):  
Linear Dependence ◽  
Rate Constants ◽  
Oxidation Rate ◽  
Phenyl Ring ◽  
Equilibrium Constants ◽  
Aprotic Solvents ◽  
Protonation Equilibrium ◽  
Oxidation Of Alcohols ◽  
Hammett Σ Constants ◽  
Sulphuric Acid Medium

Kinetics have been studied of oxidation of (1-hydroxybenzyl)ferrocenes substituted in phenyl ring with bis(triphenylsilyl) chromate in benzene solutions as well as protonation of these alcohols in sulphuric acid medium. Logarithms of the oxidation rate constants (kobs, 20-40 °C) and those of the protonation equilibrium constants (KR+, 25 °C) show linear dependence on the Hammett σ constants, the ρ constant values being -0.86 to -0.40 and -2.50, respectively. These negative values suggest that the both processes are influenced by the same effects and confirm the mechanism proposed earlier for oxidation of alcohols with ferrocenyl substituent by action of bis(triphenylsilyl) chromate in aprotic solvents.

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 CHR: An Integrated Software Tool for chilling requirements

2020 ◽  
Author(s):  
Chen Chen ◽  
Wanyu Xu ◽  
Ningning Gou ◽  
Lasu Bai ◽  
Lin Wang ◽  
...  
Keyword(s):  
Statistical Analysis ◽  
Software Tool ◽  
Fruit Trees ◽  
Cold Weather ◽  
Chilling Requirements ◽  
Deciduous Fruit ◽  
Heat Requirement ◽  
Integrated Software ◽  
User Friendly ◽  
Analyze Data

Abstract Background Bud dormancy in deciduous fruit trees enables plants to survive cold weather. The buds adopt dormant state and resume growth after satisfying the chilling requirements. Chilling requirements play a key role in flowering time. So far, several chilling models, including ≤ 7.2 °C model, the 0–7.2 °C model, Utah model, and Dynamic Model, have been developed; however, it is still time-consuming to determine the chilling requirements employing any model. This calls for efficient tools that can analyze data. Results In this study, we developed novel software Chilling and Heat Requirement (CHR), by flexibly integrating data conversions, model selection, calculations, statistical analysis, and plotting. Conclusion CHR is a tool for chilling requirements estimation, which will be very useful to researchers. It is very simple, easy, and user-friendly.

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