Facilitated diffusion on confined DNA

TL;DR

This paper investigates facilitated diffusion of proteins along confined DNA, revealing optimal conditions and robustness of the process in cellular environments, with implications for understanding intracellular reactions.

Contribution

It provides a detailed analysis of facilitated diffusion dynamics in confined geometries and highlights its robustness and efficiency in physiological conditions.

Findings

Facilitated diffusion is most efficient inside isotropic volumes and on flexible DNA.

The speedup from sliding is insensitive to parameter fine-tuning in vivo.

The results are relevant for in vitro systems and yeast chromatin.

Abstract

In living cells, proteins combine 3D bulk diffusion and 1D sliding along the DNA to reach a target faster. This process is known as facilitated diffusion, and we investigate its dynamics in the physiologically relevant case of confined DNA. The confining geometry and DNA elasticity are key parameters: we find that facilitated diffusion is most efficient inside an isotropic volume, and on a flexible polymer. By considering the typical copy numbers of proteins in vivo, we show that the speedup due to sliding becomes insensitive to fine tuning of parameters, rendering facilitated diffusion a robust mechanism to speed up intracellular diffusion-limited reactions. The parameter range we focus on is relevant for in vitro systems and for facilitated diffusion on yeast chromatin.