Facilitated diffusion of proteins through crumpled fractal DNA globules.
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.
Center for Soft Matter Research and Department of Physics, New York University, New York, New York 10003, USA.
Jan
J
Smrek
Center for Soft Matter Research and Department of Physics, New York University, New York, New York 10003, USA.
Alexander Y
AY
Grosberg
D003198:Computer Simulation; D004247:DNA / Q000737:chemistry*; D055459:Facilitated Diffusion; D017709:Fractals; D008956:Models, Chemical; D008957:Models, Genetic; D009010:Monte Carlo Method; D053770:Nanowires / Q000737:chemistry; D009690:Nucleic Acid Conformation; D011336:Probability; D011506:Proteins / Q000737:chemistry*
D011506:Proteins; D004247:DNA