title: Intracellular facilitated diffusion: searchers, crowders, and blockers.
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.
authors.affiliation: SUPA, School of Physics and Astronomy, University of Edinburgh, Mayfield Road, Edinburgh EH9 3JZ, United Kingdom.
authors.forename: C A
authors.initials: CA
authors.lastname: Brackley
authors.affiliation: SUPA, School of Physics and Astronomy, University of Edinburgh, Mayfield Road, Edinburgh EH9 3JZ, United Kingdom.
authors.forename: M E
authors.initials: ME
authors.lastname: Cates
authors.affiliation: SUPA, School of Physics and Astronomy, University of Edinburgh, Mayfield Road, Edinburgh EH9 3JZ, United Kingdom.
authors.forename: D
authors.initials: D
authors.lastname: Marenduzzo
mesh_terms: D001419:Bacteria / Q000235:genetics / Q000378:metabolism; D001665:Binding Sites; D003593:Cytoplasm / Q000378:metabolism*; D004247:DNA / Q000378:metabolism*; D004268:DNA-Binding Proteins / Q000378:metabolism*; D004058:Diffusion; D046911:Macromolecular Substances / Q000378:metabolism*; D008954:Models, Biological; D008958:Models, Molecular
chemical_list: D004268:DNA-Binding Proteins; D046911:Macromolecular Substances; D004247:DNA