Kinlsq: a program for fitting kinetics data with numerically integrated rate equations and its application to the...

Kinlsq, a Matlab-based computer program for the least-squares fitting of parameters to kinetics data described by numerically integrated rate equations, is described, and three applications to the analysis of enzyme kinetics data are given. The first application was to the analysis of a simple bimolecular enzyme plus inhibitor binding curve. The kinlsq fit to these data was essentially identical to that obtained with the corresponding analytically integrated rate equation, validating kinlsq. The second application was to the fit of a numerically integrated Michaelis-Menten model to the progress curve for dipeptidyl peptidase IV-catalyzed hydrolysis of Ala-Pro-p-nitroanilide as a demonstration of the analysis of steady-state enzyme kinetics data. The results obtained with kinlsq were compared with the results obtained by fitting this time course with the integrated Michaelis-Menten equation, and with the results obtained by fitting the (S,dP/dt) transform of the data with the Michaelis-Menten equation. The third application was to the analysis of the inhibition of chymotrypsin by the slow, tight-binding inhibitor MeOSuc-Ala-Ala-Pro-boroPhe, data not readily amenable to other methods of analysis. These applications demonstrate how kinlsq can be used to fit rate constants, equilibrium constants, steady-state constants, and the stoichiometric relationships between components.