Protein sliding and hopping kinetics on DNA

Phys Rev E Stat Nonlin Soft Matter Phys. 2011 Feb;83(2 Pt 1):021907. doi: 10.1103/PhysRevE.83.021907. Epub 2011 Feb 16.

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.

Publication types

  • Research Support, N.I.H., Extramural

MeSH terms

  • Binding Sites
  • Computer Simulation
  • DNA / chemistry*
  • DNA / ultrastructure*
  • DNA-Binding Proteins / chemistry*
  • DNA-Binding Proteins / ultrastructure*
  • Kinetics
  • Models, Chemical*
  • Models, Molecular*
  • Motion
  • Protein Binding

Substances

  • DNA-Binding Proteins
  • DNA