title: 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: (i) in each diffusion trajectory, a protein makes on average hundreds of alternating slides and hops with a mean sliding time of several tens of milliseconds; (ii) sliding dominates the root-mean-square displacement of fast diffusion trajectories, whereas hopping dominates slow ones; (iii) flow and variations in salt concentration have limited effects on hopping kinetics, while in vivo DNA configuration is not expected to influence sliding kinetics; and (iv) the rate of occurrence for hops longer than 200 nm agrees with experimental data for EcoRV proteins.
authors.affiliation: Department of Physics, Washington University in St. Louis, St. Louis, Missouri 63130, USA.
authors.forename: Michael C
authors.initials: MC
authors.lastname: DeSantis
authors.forename: Je-Luen
authors.initials: JL
authors.lastname: Li
authors.forename: Y M
authors.initials: YM
authors.lastname: Wang
mesh_terms: D001665:Binding Sites; D003198:Computer Simulation; D004247:DNA / Q000737:chemistry* / Q000648:ultrastructure*; D004268:DNA-Binding Proteins / Q000737:chemistry* / Q000648:ultrastructure*; D007700:Kinetics; D008956:Models, Chemical; D008958:Models, Molecular; D009038:Motion; D011485:Protein Binding
chemical_list: D004268:DNA-Binding Proteins; D004247:DNA