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We present a theoretical model of facilitated diffusion of proteins in the cell nucleus. This model, which takes into account the successive binding/unbinding events of proteins to DNA, relies on a fractal description of the chromatin which has been recently evidenced experimentally. Facilitated diffusion is shown quantitatively to be favorable for a fast localization of a target locus by a transcription factor, and even to enable the minimization of the search time by tuning the affinity of the transcription factor with DNA. This study shows the robustness of the facilitated diffusion mechanism, invoked so far only for linear conformations of DNA.
We study the impact of DNA coiling on the search rate of proteins moving along the DNA contour interspersed by three-dimensional (3D) bulk excursions. When the DNA is coiled proteins performing short 3D hops along a DNA segment can be captured by for
The diffusion-controlled limit of reaction times for site-specific DNA-binding proteins is derived from first principles. We follow the generally accepted concept that a protein propagates via two competitive modes, a three-dimensional diffusion in s
30% of the DNA in E. coli bacteria is covered by proteins. Such high degree of crowding affect the dynamics of generic biological processes (e.g. gene regulation, DNA repair, protein diffusion etc.) in ways that are not yet fully understood. In this
The recently introduced method of excess collisions (MEC) is modified to estimate diffusion-controlled reaction times inside systems of arbitrary size. The resulting MEC-E equations contain a set of empirical parameters, which have to be calibrated i
Experimental approaches have been applied to address questions in understanding three-dimensional chromatin organisation and function. As datasets increase in size and complexity, it becomes a challenge to reach a mechanistic interpretation of experi