Intracellular Facilitated Diffusion: Searchers, Crowders, and Blockers

Chris Brackley*, M. E. Cates, D. Marenduzzo

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

Abstract

In bacteria, regulatory proteins search for a specific DNA-binding target via "facilitated diffusion": a series of rounds of three-dimensional diffusion in the cytoplasm, and one-dimensional (1D) linear diffusion along the DNA contour. Using large scale Brownian dynamics simulations we find that each of these steps is affected differently by crowding proteins, which can either be bound to the DNA acting as a road block to the 1D diffusion, or freely diffusing in the cytoplasm. Macromolecular crowding can strongly affect mechanistic features such as the balance between three-dimensional and 1D diffusion, but leads to surprising robustness of the total search time.

Original languageEnglish
Article number108101
Number of pages5
JournalPhysical Review Letters
Volume111
Issue number10
DOIs
Publication statusPublished - 3 Sep 2013

Keywords

  • PROTEIN-DNA INTERACTIONS
  • TARGET LOCATION
  • KINETICS
  • BINDING
  • ORGANIZATION
  • DYNAMICS
  • LATTICE
  • SYSTEMS
  • MODELS
  • CELLS

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