Facilitated diffusion of proteins through crumpled fractal DNA globules

Jan Smrek, Alexander Y. Grosberg

    Research output: Contribution to journalArticle

    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.

    Original languageEnglish (US)
    Article number012702
    JournalPhysical Review E - Statistical, Nonlinear, and Soft Matter Physics
    Volume92
    Issue number1
    DOIs
    StatePublished - Jul 1 2015

    ASJC Scopus subject areas

    • Statistical and Nonlinear Physics
    • Statistics and Probability
    • Condensed Matter Physics

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