Integrated function of a kinetic proofreading mechanism: dynamic analysis separating the effects of speed and substrate competition on accuracy

Abstract

All of the data relating to [Escherichia coli] isoleucyl-tRNA synthetase and its proofreading of valyl-tRNAIle were integrated into a single model, the dynamic behavior of which was determined by numerical solution of the relevant kinetic equations. The results indicate that the system normally operates in vivo with amino acid concentrations slightly above the apparent Km of the system, that increases in the displacement of reactants from thermodynamic equilibrium increase the net reaction velocity when the appropriate nominal parameter values are selected, that the cost of proofreading decreases with an increase in displacment of reactants from equilibrium, that accuracy and reaction velocity tend to be inversely related when substrate competition is unchanged but directly related or unrelated when substrate competition is altered, that changes in substrate competition are about twice as effective as changes in reaction velocity in altering the overall accuracy of aminoacylation, and that simultaneous changes in substrate competition and reaction velocity have a cumulative but not additive effect upon accuracy. With regard to the temporal development of errors and proofreading costs, 2 different patterns were seen. In one, errors or costs gradually change with time following an abrupt alteration; in the other, errors or costs change dramatically in one direction and then more slowly reverse themselves. In all cases, the system responds to change quickly (< 0.02-0.2 s) but shows no tendency to oscillate.