title: Facilitated Diffusion of Transcription Factor Proteins with Anomalous Bulk Diffusion.
abstract: What are the physical laws of the diffusive search of proteins for their specific binding sites on DNA in the presence of the macromolecular crowding in cells? We performed extensive computer simulations to elucidate the protein target search on DNA. The novel feature is the viscoelastic non-Brownian protein bulk diffusion recently observed experimentally. We examine the influence of the protein-DNA binding affinity and the anomalous diffusion exponent on the target search time. In all cases an optimal search time is found. The relative contribution of intermittent three-dimensional bulk diffusion and one-dimensional sliding of proteins along the DNA is quantified. Our results are discussed in the light of recent single molecule tracking experiments, aiming at a better understanding of the influence of anomalous kinetics of proteins on the facilitated diffusion mechanism.
authors.affiliation: CAS Key Laboratory of Soft Matter Chemistry, Dept. of Polymer Science and Engineering, University of Science and Technology of China , Hefei, Anhui Province 230026, China.|Institute for Physics & Astronomy, University of Potsdam , 14476 Potsdam-Golm, Germany.
authors.forename: Lin
authors.initials: L
authors.lastname: Liu
authors.affiliation: Institute for Physics & Astronomy, University of Potsdam , 14476 Potsdam-Golm, Germany.
authors.forename: Andrey G
authors.identifier: 0000-0002-0516-9900
authors.initials: AG
authors.lastname: Cherstvy
authors.affiliation: Institute for Physics & Astronomy, University of Potsdam , 14476 Potsdam-Golm, Germany.
authors.forename: Ralf
authors.initials: R
authors.lastname: Metzler
mesh_terms: D004247:DNA / Q000737:chemistry; D004058:Diffusion; D056004:Molecular Dynamics Simulation; D014157:Transcription Factors / Q000737:chemistry*
chemical_list: D014157:Transcription Factors; D004247:DNA