Integrated function of a kinetic proofreading mechanism: steady-state analysis testing internal consistency of data obtained in vivo and in vitro and predicting parameter values

Abstract

Experimental measurements of the kinetic mechanism involving isoleucyl-tRNA synthetase proofreading valyl-tRNAIle in Escherichia coli were incorporated into the conventional Michaelis-Menten model for this system. The model was subjected to a detailed mathematical analysis in the steady-state. The results of the analysis provide an excellent illustration of the value of integrating fragmentary data into a model of the intact system. Such integration provides a rigorous test for consistency of the individual measurements. For the above synthetase system, the published experimental data were internally inconsistent. Such integration predicts which experimental data are most suspect. One questionable measurement, the isoleucine pool size in vivo, was in error by 10- to 15-fold. Correction of this error produced a self-consistent set of parameter values. The integrated analysis provides predictions for various parameter values. In many cases, these predictions provide estimates for parameter values that are difficult to determine directly or that have yet to be measured experimentally. A sensitivity analysis provides an indication of the relative importance of various parameter values and, hence, an indication of where future experimental effort might be focused most profitably.