Quantifying hopping and jumping in facilitated diffusion of DNA-binding proteins

Area of Science:

• Biophysics
• Molecular Biology
• Biochemistry

Background:

• Facilitated diffusion enhances DNA-binding protein target location.
• This process involves a combination of three-dimensional (3D) excursions and linear diffusion along DNA.

Purpose of the Study:

• To explicitly calculate the distribution of relocation lengths for 3D excursions of DNA-binding proteins.
• To quantify short-range correlated excursions (hops) and long-range uncorrelated jumps.
• To extend the analysis to anomalous 3D diffusion in crowded cellular media.

Main Methods:

• Theoretical calculation of relocation length distributions.
• Analysis of short-range (hops) and long-range (jumps) diffusion components.
• Modeling of anomalous 3D diffusion.

Main Results:

• The study provides explicit calculations for the distribution of 3D excursion relocation lengths.
• Quantification of both short-range hops and long-range jumps in protein diffusion.
• Results align with single-molecule experiments on EcoRV enzyme diffusion on DNA.

Conclusions:

• The findings support the model of facilitated diffusion involving 3D excursions and linear diffusion.
• The quantification of different diffusion types offers insights into protein-DNA interactions.
• The extension to anomalous diffusion addresses biologically relevant crowded cellular conditions.