scholarly journals Simulation of Biochemical Reactions with ANN-Dependent Kinetic Parameter Extraction Method

Electronics ◽  
2022 ◽  
Vol 11 (2) ◽  
pp. 216
Author(s):  
Fei Tan ◽  
Jin Xu
Keyword(s):  
Thermodynamic Properties ◽  
Kinetic Parameter ◽  
Intermediate State ◽  
Rate Constants ◽  
Critical Role ◽  
Pso Algorithm ◽  
Parameter Extraction ◽  
Reaction Rates ◽  
Dissociation Rate ◽  
Time Curve

The measurement of thermodynamic properties of chemical or biological reactions were often confined to experimental means, which produced overall measurements of properties being investigated, but were usually susceptible to pitfalls of being too general. Among the thermodynamic properties that are of interest, reaction rates hold the greatest significance, as they play a critical role in reaction processes where speed is of essence, especially when fast association may enhance binding affinity of reaction molecules. Association reactions with high affinities often involve the formation of a intermediate state, which can be demonstrated by a hyperbolic reaction curve, but whose low abundance in reaction mixture often preclude the possibility of experimental measurement. Therefore, we resorted to computational methods using predefined reaction models that model the intermediate state as the reaction progresses. Here, we present a novel method called AKPE (ANN-Dependent Kinetic Parameter Extraction), our goal is to investigate the association/dissociation rate constants and the concentration dynamics of lowly-populated states (intermediate states) in the reaction landscape. To reach our goal, we simulated the chemical or biological reactions as system of differential equations, employed artificial neural networks (ANN) to model experimentally measured data, and utilized Particle Swarm Optimization (PSO) algorithm to obtain the globally optimum parameters in both the simulation and data fitting. In the Results section, we have successfully modeled a protein association reaction using AKPE, obtained the kinetic rate constants of the reaction, and constructed a full concentration versus reaction time curve of the intermediate state during the reaction. Furthermore, judging from the various validation methods that the method proposed in this paper has strong robustness and accuracy.

Calculation of anharmonic effect on the dissociation of ethylene glycol

2017 ◽  
Vol 16 (08) ◽  
pp. 1750077
Author(s):  
Qian Li ◽  
Li Yao ◽  
S. H. Lin
Keyword(s):  
Ethylene Glycol ◽  
Rate Constants ◽  
Critical Role ◽  
Canonical System ◽  
Dissociation Rate ◽  
Elimination Reaction ◽  
Anharmonic Effect ◽  
Bond Dissociation ◽  
Total Energies ◽  
Dissociation Rate Constants

The unimolecular dissociation rate constants of ethylene glycol were examined using the MP2/6-311[Formula: see text]G(d,p) method based on the Rice–Ramsperger–Kassel–Marcus (RRKM) theory. The effect of anharmonicity on the dissociation rate constants was evaluated at 500–4000[Formula: see text]K temperatures of the canonical system and 25,182–50,235[Formula: see text]cm[Formula: see text] total energies of the microcanonical system. The comparison of the results showed that the H2O elimination reaction played a critical role in the decomposition processes of ethylene glycol. The results of the rate constant calculations indicated that the H2O elimination reaction dominated at low temperatures, whereas the direct C–C bond dissociation reaction (CH2OHCH2OH [Formula: see text] CH2OH[Formula: see text][Formula: see text][Formula: see text]CH2OH) dominated at high temperatures. For channel 1, CH2OH[Formula: see text][Formula: see text][Formula: see text]CH2OH, the anharmonic effect of the canonical system was not observed, while it became more obvious with the increasing total energies in the microcanonical system. For channels 2–5, CH3CHO[Formula: see text][Formula: see text][Formula: see text]H2O, CH2CHOH[Formula: see text][Formula: see text][Formula: see text]H2O, CH3OH[Formula: see text][Formula: see text][Formula: see text]CHOH, and CH2OHCHO[Formula: see text][Formula: see text][Formula: see text]H2, the anharmonic effect of canonical and microcanonical systems became more obvious with increasing temperatures and total energies. The comparison showed that, for channels 1 and 4, C–C bond dissociation and the anharmonic effect of the microcanonical system were more evident, whereas the anharmonic effect of the canonical system was more predominant for channels 2 (CH3CHO[Formula: see text][Formula: see text][Formula: see text]H2O), 3 (CH2CHOH[Formula: see text][Formula: see text][Formula: see text]H2O), and 5 (CH2OHCHO[Formula: see text][Formula: see text][Formula: see text]H2).

Kinetics of esterification of monoisopropylphenols with phosphoryl trichloride

1989 ◽  
Vol 54 (5) ◽  
pp. 1311-1317
Author(s):  
Miroslav Magura ◽  
Ján Vojtko ◽  
Ján Ilavský
Keyword(s):  
Liquid Phase ◽  
Rate Constants ◽  
Reaction Rates ◽  
Activation Energies ◽  
The Individual ◽  
Kinetics Of

The kinetics of liquid-phase isothermal esterification of POCl3 with 2-isopropylphenol and 4-isopropylphenol have been studied within the temperature intervals of 110 to 130 and 90 to 110 °C, respectively. The rate constants and activation energies of the individual steps of this three-step reaction have been calculated from the values measured. The reaction rates of the two isomers markedly differ: at 110 °C 4-isopropylphenol reacts faster by the factors of about 7 and 20 for k1 and k3, respectively. This finding can be utilized in preparation of mixed triaryl phosphates, since the alkylation mixture after reaction of phenol with propene contains an excess of 2-isopropylphenol over 4-isopropylphenol.

scholarly journals Dissociation Rate Constants of Human Fibronectin Binding to Fibronectin-binding Proteins on LivingStaphylococcus aureusIsolated from Clinical Patients

2012 ◽  
Vol 287 (9) ◽  
pp. 6693-6701 ◽  
Author(s):  
Nadia N. Casillas-Ituarte ◽  
Brian H. Lower ◽  
Supaporn Lamlertthon ◽  
Vance G. Fowler ◽  
Steven K. Lower
Keyword(s):  
Rate Constants ◽  
Binding Proteins ◽  
Dissociation Rate ◽  
Human Fibronectin ◽  
Fibronectin Binding ◽  
Dissociation Rate Constants

scholarly journals Head-to-tail polymerization of microtubules in vitro. Electron microscope analysis of seeded assembly.

1980 ◽  
Vol 84 (1) ◽  
pp. 141-150 ◽  
Author(s):  
L G Bergen ◽  
G G Borisy
Keyword(s):  
Electron Microscope ◽  
Rate Constants ◽  
Dissociation Constants ◽  
Dissociation Rate ◽  
Association Constants ◽  
Directional Growth ◽  
Microtubule Protein ◽  
Electron Microscope Analysis ◽  
Dissociation Rate Constants

Microtubules are polar structures, and this polarity is reflected in their biased directional growth. Following a convention established previously (G. G. Borisy, 1978, J. Mol. Biol. 124:565--570), we define the plus (+) and minus (-) ends of a microtubule as those equivalent in structural orientation to the distal and proximal ends, respectively, of the A subfiber of flagellar outer doublets. Rates of elongation were obtained for both ends using flagellar axonemes as seeds and porcine brain microtubule protein as subunits. Since the two ends of a flagellar seed are distinguishable morphologically, elongation of each end may be analyzed separately. By plotting rates of elongation at various concentrations of subunit protein, we have determined the association and dissociation rate constants for the plus and minus ends. Under our conditions at 30 degrees C, the association constants were 7.2 X 10(6) M-1 s-1 and 2.25 X 10(6) M-1 s-1 for the plus and minus ends, respectively, and the dissociation constants were 17 s-1 and 7 s-1. From these values and Wegner's equations (1976, J. Mol. Biol. 108:139--150), we identified the plus end of the microtubule as its head and calculated "s," the head-to-tail polymerization parameter. Surprisingly small values (s = 0.07 +/- 0.02) were found. The validity of models of mitosis based upon head-to-tail polymerization (Margolis et al., 1978, Nature (Lond.) 272:450--452) are discussed in light of a small value for s.

scholarly journals Reactivity of cyclohex-1-enylcarboxylic and 2-methylcyclohex-1-enylcarboxylic acids with diazodiphenylmethane in aprotic solvents

2000 ◽  
Vol 65 (12) ◽  
pp. 839-846
Author(s):  
Jasmina Nikolic ◽  
Gordana Uscumlic ◽  
Vera Krstic
Keyword(s):  
Hydrogen Bond ◽  
Rate Constants ◽  
Kinetic Data ◽  
Linear Regression Analysis ◽  
Spectroscopic Method ◽  
Reaction Rates ◽  
Aprotic Solvents ◽  
Experimental Conditions ◽  
Hydrogen Bond Acceptor ◽  
Protic Solvents

Rate constants for the reaction of diazodiphenylmethane with cyclohex-1-enylcarboxylic acid and 2-methylcyclohex-1-enylcarboxylic acid were determined in nine aprotic solvents, as well as in seven protic solvents, at 30?C using the appropriate UV-spectroscopic method. In protic solvents the unsubsituted acid displayed higher reaction rates than the methyl-substituted one. The results in aprotic solvents showed quite the opposite, and the reaction rates were considerably lower. In order to explain the obtained results through solvent effects, reaction rate constants (k) of the examined acids were correlated using the total solvatochromic equation of the form: log k=logk0+s?*+a?+b?, where ?* is the measure of the solvent polarity, a represents the scale of the solvent hydrogen bond donor acidities (HBD) and b represents the scale of the solvent hydrogen bond acceptor basicities (HBA). The correlation of the kinetic data were carried out by means of multiple linear regression analysis and the opposite effects of aprotic solvents, as well as the difference in the influence of protic and aprotic solvents on the reaction of the two examined acids with DDM were discussed. The results presented in this paper for cyclohex-1-enylcarboxylic and 2-methylcyclohex-1-enylcarboxylic acids were compared with the kinetic data for benzoic acid obtained in the same chemical reaction, under the same experimental conditions.

scholarly journals Mechanism of a Disassembly Driven Sensing System Studied by Stopped-Flow Kinetics

2021 ◽  
Author(s):  
Cara Gallo ◽  
Suma S. Thomas ◽  
Allison Selinger ◽  
Fraser Hof ◽  
Cornelia Bohne
Keyword(s):  
Steady State ◽  
Rate Constants ◽  
Artificial Saliva ◽  
Global Analysis ◽  
Dissociation Rate ◽  
Stopped Flow ◽  
Steady State Fluorescence ◽  
Saliva Analysis ◽  
Binding Isotherms ◽  
Dissociation Rate Constants

<div> Mechanistic studies were carried out on the kinetics for the assembly of a DimerDye (DD12) and the binding of the monomeric DimerDye (DD1) with nicotine in aqueous buffer and artificial saliva. DD12 is non-fluorescent, while monomeric DD1 and DD1-nicotine fluoresce. Binding isotherms were determined from steady-state fluorescence experiments. The report includes measurements of the steady-state fluorescence at pHs 2.2, 6.3 and 12.1, and stopped-flow kinetic data for the homodimerization forming DD12 and DD1-nicotine formation in buffer and artificial saliva. Analysis of the homodimerization kinetics led to the recovery of the association and dissociation rate constants for DD12. These rate constants were used in the global analysis for the coupled kinetics for DD1-nicotine formation, which led to the determination of the association and dissociation rate constants for nicotine binding to DD1.</div>

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