title: DNA-binding-protein inhomogeneity in E. coli modeled as biphasic facilitated diffusion.
abstract: We have recently shown that nonspecifically bound lac repressors are spatially inhomogeneous in E. coli cells and depends upon the location of its encoding gene and the DNA compaction state [Kuhlman and Cox, Mol. Syst. Biol. 8, 610 (2012)]. Here we model this inhomogeneity as a consequence of diffusion within and exchange between two distinct intracellular phases: the condensed chromosomal DNA and an extrachromosomal compartment, the cytoplasm. We discuss the consequences of this model for the target search process.
authors.affiliation: Department of Physics, Center for the Physics of Living Cells, and Center for Biophysics and Computational Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801-3080, USA.
authors.forename: Thomas E
authors.initials: TE
authors.lastname: Kuhlman
authors.forename: Edward C
authors.initials: EC
authors.lastname: Cox
mesh_terms: D002876:Chromosomes, Bacterial / Q000378:metabolism; D003593:Cytoplasm / Q000378:metabolism; D004269:DNA, Bacterial / Q000378:metabolism*; D004058:Diffusion; D004926:Escherichia coli / Q000166:cytology / Q000378:metabolism*; D029968:Escherichia coli Proteins / Q000378:metabolism*; D007700:Kinetics; D008954:Models, Biological; D011485:Protein Binding; D014157:Transcription Factors / Q000378:metabolism*
chemical_list: D004269:DNA, Bacterial; D029968:Escherichia coli Proteins; D014157:Transcription Factors