Stochastic single-enzyme kinetics: effect of substrate fluctuations
Abstract Book of the XXIII IUPAP International Conference on Statistical Physics, Genova, Italy, (9-13 July 2007)Abstract
Advances in single molecule spectroscopy have made it possible to watch turnovers of single enzyme molecules. One of the current issues in single-molecule enzymology is the interpretation of the dynamic heterogeneity observed in single-enzyme experiments. A suggested origin of this behavior is the conformational changes of a working enzyme. For proper interpretation of dynamic heterogeneity one needs to examine other possible sources for variations in the turnover rate.
Using Monte Carlo simulations of a model of stochastic single-enzyme kinetics, we have gauged the effect of substrate fluctuations on the Lineweaver-Burke plot, probability density functuin turnover time, $ p(\tau) $, correlation index $ r $, and correlation function of consecutive turnovers cm. We have explored a broad range of parameters and found that substrate fluctuations can be detected only when the substrate binding is rate limiting and long turnover time trajectories are analyzed. For reversible binding substrate fluctuations may not be experimentally detectable. We conclude that fluctuations in the local concentration of substrates around an enzyme molecule cannot explain the experimentally observed deviations from Michaelis-Menten kinetics.