Protein sliding and hopping kinetics on DNA
Abstract
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.
Keywords
Cite
@article{arxiv.1010.3247,
title = {Protein sliding and hopping kinetics on DNA},
author = {Michael C. DeSantis and Je-Luen Li and Y. M. Wang},
journal= {arXiv preprint arXiv:1010.3247},
year = {2015}
}