  Using Monte-Carlo simulations, we deconvolved the sliding and hopping
kinetics of GFP-LacI proteins on elongated DNA from their experimentally
observed seconds-long diffusion trajectories. Our simulations suggest the
following results: (1) in each diffusion trajectory, a protein makes on average
hundreds of alternating slides and hops with a mean sliding time of several
tens of ms; (2) sliding dominates the root mean square displacement of fast
diffusion trajectories, whereas hopping dominates slow ones; (3) flow and
variations in salt concentration have limited effects on hopping kinetics,
while in vivo DNA configuration is not expected to influence sliding kinetics;
furthermore, (4) the rate of occurrence for hops longer than 200 nm agrees with
experimental data for EcoRV proteins.
