Application of the median method to estimate the kinetic constants of the substrate uncompetitive inhibition equation

Abstract

In 1974, Eisenthal and Cornish-Bowden published the direct linear plot method, which used the median to estimate the V_max and K_m from a set of initial rates as a function of substrate concentrations. The robustness of this non-parametric method was clearly demonstrated by comparing it with the least-squares method. The authors commented that the method cannot readily be generalized to equations of more than two parameters. Unfortunately, this comment has been misread by other authors. Comments such as "this method cannot be extended directly to equations with more than two parameters" were found in some publications. In addition, recently, the most drastic comment was published: "this method cannot be applied for the analysis of substrate inhibition." Given all of these presumptions, we have been motivated to publish a demonstration of the contrary: the median method can be applied to more than two-parameter equations, using as an example, the substrate uncompetitive inhibition equation. A computer algorithm was written to evaluate the effect of simulated experimental error of the initial rates on the estimation of V_max, K_m and K_S. The error was assigned to different points of the experimental design. Four different K_S/K_m ratios were analyzed with the values 10, 100, 1000 and 10,000. The results indicated that the least-squares method was slightly better than the median method in terms of accuracy and variance. However, the presence of outliers affected the estimation of kinetic constants using the least-squares method more severely than the median method. The estimation of K_S using the median method to estimate 1/K_S was much better than the direct estimation of K_S, causing a negative effect of non-linearity of K_S in the kinetic equation. Considering that the median method is free from the assumptions of the least-squares method and the arbitrary assumptions implicit in the linearization methods to estimate the kinetic constants V_max, K_m and K_S from the substrate uncompetitive inhibition equation, the median method is highly superior to all published methods, including the non-linear regression by least squares. We concluded that the median method can be applied to the substrate uncompetitive inhibition equation and other equations with more than two parameters. In addition, as we can project, the median method is the most reliable and robust method for the estimation of kinetic parameters from enzyme kinetic models.

Keywords: Direct linear plot; Kinetic constants estimation; Median method; Substrate inhibition.