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
    Volume92
    Issue number1
    DOIs
    StatePublished - Jul 1 2015

    Fingerprint

    globules
    Fractal
    fractals
    deoxyribonucleic acid
    Conformation
    proteins
    Protein
    eukaryotes
    chromatin
    Chromatin
    Smooth surface
    Nanowires
    Fractal Dimension
    Conductivity
    Affine transformation
    affinity
    nanowires
    Probability Distribution
    Polymers
    conductors

    ASJC Scopus subject areas

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

    Cite this

    Facilitated diffusion of proteins through crumpled fractal DNA globules. / Smrek, Jan; Grosberg, Alexander Y.

    In: Physical Review E, Vol. 92, No. 1, 012702, 01.07.2015.

    Research output: Contribution to journalArticle

    Smrek, Jan ; Grosberg, Alexander Y. / Facilitated diffusion of proteins through crumpled fractal DNA globules. In: Physical Review E. 2015 ; Vol. 92, No. 1.
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