scholarly journals The computerized derivation of steady-state rate equations for enzyme kinetics

1984 ◽  
Vol 223 (2) ◽  
pp. 551-553 ◽  
Author(s):  
D G Herries

A FORTRAN 77 program is described for the derivation of steady-state rate equations for enzyme kinetics. Input is very simple and consists of the two enzyme forms and the two rate constants for each step in the mechanism. The program may be run interactively or off-line. The results are produced after collecting together the algebraic coefficients of like concentration terms, taking account of sign. A fully interactive BASIC version running on a BBC Microcomputer is also available. Details of the programs have been deposited as Supplementary Publication SUP 50126 (45 pages) with the British Library Lending Division, Boston Spa, Wetherby, West Yorkshire LS23 7BQ, U.K., from whom copies may be obtained as indicated in Biochem. J. (1984) 217, 5.

1977 ◽  
Vol 163 (3) ◽  
pp. 633-634
Author(s):  
K J Indge

A criticism [Cornish-Bowden (1976) Biochem. J. 159, 167] of an algebraic method for deriving steady-state rate equations [Indge & Childs (1976) Biochem. J. 155, 567-570] is theoretically founded.


1976 ◽  
Vol 155 (3) ◽  
pp. 567-570 ◽  
Author(s):  
K J Indge ◽  
R E Childs

A schematic method for the derivation of steady-state enzyme rate equations by using the Wang algebra is described. The method is simple, easy to learn and offers a substantial decrease in analytical effort over previously published algorithms. Being essentially an algebraic procedure the method can be readily computerized. Computer programs in BASIC and ALGOL languages have been deposited as Supplementary Publication SUP 50065 (19 pages) at the British Library (Lending Division), Boston Spa, Wetherby, W. Yorkshire LS23 7BQ, U.K., from whom copies can be obtained on the terms indicated in Biochem. J. (1976). 153, 5.


1977 ◽  
Vol 165 (1) ◽  
pp. 55-59 ◽  
Author(s):  
A Cornish-Bowden

A method is described for systematically deriving steady-state rate equations. It is based on the schematic method of King & Altman [J. Phys. Chem. (1956) 60, 1375-1378], but is expressed in purely algebraic terms. It is suitable for implementation as a computer program, and a program has been written in FORTRAN IV and deposited as Supplementary Publication SUP 50078 (12 pages) at the British Library (Lending Division), Boston Spa, Wetherby, West Yorkshire LS23 7BQ, U.K., from whom copies can be obtained on the terms indicated in Biochem. J. (1977) 161, 1-2.


1976 ◽  
Vol 159 (1) ◽  
pp. 167-167 ◽  
Author(s):  
A Cornish-Bowden

Methods of deriving rate equations that rely on repetition of terms for identification of redundant or invalid terms give incorrect results if used with mechanisms in which some rate constants appear more than once.


Gas-phase dissociation of fluorine ( 1 Ʃ + g ) molecules in an agron bath at 3000 K was studied by using the 3D Monte Carlo classical trajectory (3DMCCT) method. To assess the importance of the potential energy surface (PES) in such calculations, three surfaces, with a fixed, experimentally determined F 2 dissociation energy, were constructed. These surfaces span the existing experimental uncertainties in the shape of the F 2 potential. The first potential was the widest and softest; in the second potential the anharmonicity was minimized. The intermediate potential was constructed to ‘localize’ anharmonicity in the energy range in which the collisions are most reactive. The remaining parameters for each PES were estimated from the best available data on interatomic potentials. By using the single uniform ensemble (SUE) method (Kutz, H. D. & Burns, G. J. chem. Phys . 72, 3652-3657 (1980)), large ensembles of trajectories (LET) were generated for the PES. Two such ensembles consisted of 30000 trajectories each and the third of 26200. It was found that the computed one-way-flux equilibrium rate coefficients (Widom, B. Science 148, 1555-1560 (1965)) depend in a systematic way upon the anharmonicity of the potential, with the most anharmonic potential yielding the largest rate coefficient. Steady-state reaction-rate constants, which correspond to experimentally observable rate constants, were calculated by the SUE method. It was determined that this method yields (for a given trajectory ensemble, PES and translational temperature) a unique steady-state rate constant, independent of the initial, arbitrarily chosen, state (Tolman, R. C. The principles of statistical mechanics , p. 17. Oxford University Press (1938)) of the LET, and consequently independent of the corresponding initial value of the reaction rate coefficient. For each initial state of the LET, the development of the steady-state rate constant from the equilibrium rate coefficient was smooth, monotonic, and consistent with the detailed properties of the PES. It was found that, although the increased anharmonicity of the F 2 potential enhanced the equilibrium rate coefficients, it also enhanced the non-equilibrium effects. As a result, the steady-state rate constants were found to be insensitive to the variation of the PES. Thus, the differences among the steady-state rate constants for the three potentials were of the order of their standard errors, which was about 15% or less. On the other hand, the calculated rate constants exceeded the experimental rate constant by a factor of five to six. Because within the limitations of classical mechanics the calculations were ab initio , it was tentatively concluded that the discrepancy of five to six is due to the use of classical mechanics rather than details of the PES structure.


1992 ◽  
Vol 286 (2) ◽  
pp. 357-359 ◽  
Author(s):  
S G Waley

The scope and limitations of a simple and satisfactory method of deducing steady-state rate equations is described. This method (called the Flux Method) consists in writing down the flux in successive steps of the reaction, and calculating the relative concentration of enzyme forms and thence the turnover time. Kinetic mechanisms for linear and branched pathways are used as examples of this method.


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