Facilitated diffusion of proteins on chromatin

Abstract

We present a theoretical model of facilitated diffusion of proteins in the cell nucleus. This model, which takes into account the successive binding/unbinding events of proteins to DNA, relies on a fractal description of the chromatin which has been recently evidenced experimentally. Facilitated diffusion is shown quantitatively to be favorable for a fast localization of a target locus by a transcription factor, and even to enable the minimization of the search time by tuning the affinity of the transcription factor with DNA. This study shows the robustness of the facilitated diffusion mechanism, invoked so far only for linear conformations of DNA.

4 pages, 4 figures, accepted version

References in corpus (5)

• First-passage times in complex scale-invariant media
• Kinetics of protein-DNA interaction: facilitated target location in sequence-dependent potential
• Geometry-controlled kinetics
• Exact mean first-passage time on the T-graph
• Effects of intersegmental transfers on target location by proteins

Cited by in corpus (21)

• Intermittent search strategies
• Anomalous, non-Gaussian tracer diffusion in heterogeneously crowded environments
• Classes of fast and specific search mechanisms for proteins on DNA
• In vivo facilitated diffusion model
• Facilitated diffusion on mobile DNA: configurational traps and sequence heterogeneity
• Exit time distribution in spherically symmetric two-dimensional domains
• Optimization and universality of Brownian search in quenched heterogeneous media
• Physical constraints determine the logic of bacterial promoter architectures
• Optimality of spatially inhomogeneous search strategies
• Facilitated diffusion on confined DNA
• Facilitated diffusion buffers noise in gene expression
• Controlling Uncertainty of Empirical First-Passage Times in the Small-Sample Regime
• Fractal and knot-free chromosomes facilitate nucleoplasmic transport
• Target Searches of Interacting Brownian Particles
• Drift-diffusive resetting search process with stochastic returns: speed-up beyond optimal instantaneous return
• Potential evolutionary advantage of a dissociative search mechanism in DNA mismatch repair
• Fast solver for diffusive transport times on dynamic intracellular networks
• Concentration of Empirical First-Passage Times
• Variance-corrected Michaelis-Menten equation predicts transient rates of single-enzyme reactions and response times in bacterial gene-regulation
• Diffusive search and trajectories on spatial networks: a propagator approach
• Optimization of multisite reactions in complex compartmentalized media