Integrated function of a kinetic proofreading mechanism: dynamic analysis separating the effects of speed and...

All of the data relating to isoleucyl-tRNA synthetase and its proofreading of valyl-tRNAIle have been integrated into a single model whose dynamic behavior has been determined by numerical solution of the relevant kinetic equations. The results indicate that (1) the system normally operates in vivo with amino acid concentrations slightly above the apparent Km of the system, (2) increases in the displacement of reactants from thermodynamic equilibrium increase the net reaction velocity when the appropriate nominal parameter values are selected, (3) the cost of proofreading decreases with an increase in displacement of reactants from equilibrium, (4) accuracy and reaction velocity tend to be inversely related when substrate competition is unchanged but directly related or unrelated when substrate competition is altered, (5) changes in substrate competition are about twice as effective as changes in reaction velocity in altering the overall accuracy of aminoacylation, and (6) 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, we have seen two different patterns. 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 (less than 0.02-0.2 s) but shows no tendency to oscillate.