Comparison of methods for analyzing kinetic data from mechanism-based enzyme inactivation: Application to nitric oxide synthase

Abstract

The goals of this study were (1) to investigate the performance of 2 classical methods of kinetic analysis when applied to data from enzyme systems in which mechanism-based inactivation and enzyme degradation are present, and (2) to develop and validate a nonlinear method of kinetic data analysis that may perform better under these situations. A composite equation was derived to link various parameters that govern the kinetics of mechanism-based inactivation, viz., enzyme activity, inhibitor-binding affinity (KI), inactivation rate (kinact), and enzyme degradation (kdeg). The relative accuracy and precision of parameter estimation by the Dixon and Kitz-Wilson methods and a new nonlinear method were evaluated by computer simulation. The behavior of these methods of analysis were validated experimentally, using the nitric oxide synthase enzyme, both in purified form and as expressed in murine macrophage cell cultures. We showed that the Dixon method, as expected, could not provide accurate estimates of KI in the presence of either enzyme inactivation or instability. The Kitz-Wilson method could provide accurate estimates of these parameters; however, the precisions of these estimates were poorer than those obtained using the nonlinear method of analysis. We conclude that the nonlinear approach is superior to classical methods of data analysis for enzyme inhibitor kinetics, based on better efficiency, accuracy, and precision.