scholarly journals Methods of determining rate constants in single-substrate–single-product enzyme reactions. Use of induced transport: limitations of product inhibition

1973 ◽  
Vol 133 (2) ◽  
pp. 255-261 ◽  
Author(s):  
H. G. Britton

1. The calculation of the rate constants from steady-state kinetics of a single-substrate–single-product enzyme reaction in which there is an isomerization of the enzyme is described. 2. It is shown that even with the use of isotopically labelled substrates a set of solutions for the constants is obtained rather than a unique solution. However, limits are derived within which they must lie. 3. The most appropriate observations to determine the rate constants are measurements of Vmax. and Km for both substrate and product, and measurement of the degree of countertransport in an induced-transport test. 4. Experimental procedures for induced-transport tests and the quantitative interpretation of the results obtained are discussed. 5. Product inhibition is shown to be an ambiguous and imprecise means of determining the rate constants. Further, the absence of a [substrate]×[product] term in the denominator of the steady-state rate equation does not necessarily mean that the isomerization of the enzyme is rapid, since the term also disappears when the isomerization is very slow. 6. Similar considerations apply to carrier mechanisms.

1975 ◽  
Vol 53 (4) ◽  
pp. 564-571
Author(s):  
Lewis J. Brubacher

Equations are developed for the pre-steady state kinetics of the proteolytic enzyme-catalyzed hydrolysis of a substrate A in the presence of a monitoring substrate (or covalent inhibitor) S of known properties. A two-intermediate acyl–enzyme mechanism is assumed in which the first intermediate is in instantaneous equilibrium with enzyme and substrate. The appearance of the first product of substrate S is characterized by two relaxation rate constants. From these constants it is possible to determine the dissociation constant and the acylation and deacylation rate constants of substrate A. Criteria are also developed for using the steady state rate parameters of A to establish conditions for which the slower relaxation process is equivalent to the deacylation rate constant of A. The technique of premixing enzyme with substrate A has certain advantages in this approach.


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.


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 161 (3) ◽  
pp. 517-526 ◽  
Author(s):  
H G Britton

1. Two methods are described for deriving the steady-state velocity of an enzyme reaction from a consideration of fluxes between enzyme intermediates. The equivalent-reaction technique, in which enzyme intermediates are systematically eliminated and replaced by equivalent reactions, appears the most generally useful. The methods are applicable to all enzyme mechanisms, including three-substrate and random Bi Bi Ping Pong mechanisms. Solutions are obtained in algebraic form and these are presented for the common random Bi Bi mechanisms. The steady-state quantities of the enzyme intermediates may also be calculated. Additional steps may be introduced into enzyme mechanisms for which the steady-state velocity equation is already known. 2. The calculation of fluxes between substrates and products in three-substrate and random Bi Bi Ping Pong mechanisms is described. 3. It is concluded that the new methods may offer advantages in ease of calculation and in the analysis of the effects of individual steps on the overall reaction. The methods are used to show that an ordered addition of two substrates to an enzyme which is activated by another ligand will not necessarily give hyperbolic steady-state-velocity kinetics or the flux ratios characteristic of an ordered addition, if the dissociation of the ligand from the enzyme is random.


2011 ◽  
Vol 10 (05) ◽  
pp. 659-678
Author(s):  
J. M. YAGO ◽  
C. GARRIDO-DEL SOLO ◽  
M. GARCIA-MORENO ◽  
R. VARON ◽  
F. GARCIA-SEVILLA ◽  
...  

The software WinStes, developed by our group, is used to derive the strict steady-state initial rate equation of the reaction mechanism of CTP:sn-glycerol-3-phosphate cytidylyltransferase [EC 2.7.7.39] from Bacillus subtilis. This enzyme catalyzes a reaction with two substrates and operates by a random ordered binding mechanism with two molecules of each substrate. The accuracy of the steady-state rate equation derived is checked by comparing the rate values it provides with those obtained from the simulated progress curves. To analyze the kinetics of this enzyme using the strict steady-state initial rate equation, several curves for different substrate concentrations and different rate constants are generated. A comparison of these curves with the curves obtained from the rapid equilibrium initial rate equation, with different substrate concentration values, serves to analyze how the strict steady-state rate equation values are closer to those of rapid equilibrium rate equations when rapid equilibrium conditions are fulfilled.


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.


1976 ◽  
Vol 155 (1) ◽  
pp. 61-70 ◽  
Author(s):  
K Brocklehurst ◽  
H B F Dixon

1. The pH-dependence is considered of a reaction between E and S that proceeds through an intermediate ES under “Briggs-Haldane” conditions, i.e. there is a steady state in ES and [S]o greater than [E]T, where [S]o is the initial concentration of S and [E]T is the total concentration of all forms of E. Reactants and intermediates are assumed to interconvert in three protonic states (E equilibrium ES; EH equilibrium EHS; EH2 equilibrium EH2S), but only EHS provides products by an irreversible reaction whose rate constant is kcat. Protonations are assumed to be so fast that they are all at equilibrium. 2. The rate equation for this model is shown to be v = d[P]/dt = (kcat.[E]T[S]o/A)/[(KmBC/DA) + [S]o], where Km is the usual assembly of rate constants around EHS and A-D are functions of the form (1 + [H]/K1 + K2/[H]), in which K1 and K2 are: in A, the molecular ionization constants of ES; in B, the analogous constants of E; in C and D, apparent ionization constants composed of molecular ionization constants (of E or ES) and assemblies of rate constants. 3. As in earlier treatments of this type of reaction which involve either the assumption that the reactants and intermediate are in equilibrium or the assumption of Peller & Alberty [(1959) J. Am. Chem. Soc. 81, 5907-5914] that only EH and EHS interconvert directly, the pH-dependence of kcat. is determined only by A. 4. The pH-dependence of Km is determined in general by B-C/A-D, but when reactants and intermediate are in equilibrium, C identical to D and this expression simplifies to B/A. 5. The pH-dependence of kcat./Km, i.e. of the rate when [S]o less than Km, is not necessarily a simple bell-shaped curve characterized only by the ionization constants of B, but is a complex curve characterized by D/B-C. 6. Various situations are discussed in which the pH-dependence of kcat./Km is determined by assemblies simpler than D/B-C. The special situation in which a kcat./Km-pH profile provides the molecular pKa values of the intermediate ES complex is delineated.


Sign in / Sign up

Export Citation Format

Share Document