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Facilitated diffusion of proteins through crumpled fractal DNA globules

Jan Smrek and Alexander Y. Grosberg
Phys. Rev. E 92, 012702 – Published 1 July 2015

Abstract

We explore how the specific fractal globule conformation, found for the chromatin fiber of higher eukaryotes and topologically constrained dense polymers, affects the facilitated diffusion of proteins in this environment. Using scaling arguments and supporting Monte Carlo simulations, we relate DNA looping probability distribution, fractal dimension, and protein nonspecific affinity for the DNA to the effective diffusion parameters of the proteins. We explicitly consider correlations between subsequent readsorption events of the proteins, and we find that facilitated diffusion is faster for the crumpled globule conformation with high intersegmental surface dimension than in the case of dense fractal conformations with smooth surfaces. As a byproduct, we obtain an expression for the macroscopic conductivity of a hypothetic material consisting of conducting fractal nanowires immersed in a weakly conducting medium.

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  • Received 23 February 2015

DOI:https://doi.org/10.1103/PhysRevE.92.012702

©2015 American Physical Society

Authors & Affiliations

Jan Smrek* and Alexander Y. Grosberg

  • Center for Soft Matter Research and Department of Physics, New York University, New York, New York 10003, USA

  • *Present address: Max Planck Institute for Polymer Research, Ackermannweg 10, D-55128 Mainz, Germany; js5013@nyu.edu

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Vol. 92, Iss. 1 — July 2015

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