DNA-binding-protein inhomogeneity in 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.