Facilitated diffusion of proteins on chromatin

TL;DR

This paper develops a theoretical model demonstrating that facilitated diffusion, considering protein-DNA binding/unbinding on fractal chromatin, efficiently accelerates target localization in the cell nucleus, optimizing search time through affinity tuning.

Contribution

It introduces a fractal-based model of facilitated diffusion that extends previous linear DNA models, showing robustness and efficiency in chromatin environments.

Findings

Facilitated diffusion speeds up target localization in the nucleus.

Tuning protein-DNA affinity minimizes search time.

The model applies to complex chromatin structures, not just linear DNA.

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.