Facilitated Diffusion of DNA-Binding Proteins
نویسندگان
چکیده
منابع مشابه
Facilitated diffusion of DNA-binding proteins.
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 space and a one-dimensional sliding along the DNA. However, our theoretical treatment of the problem is new. The accuracy of our analytical model is...
متن کاملFacilitated diffusion of DNA-binding proteins: Simulation of large systems.
The recently introduced method of excess collisions to estimate reaction times of protein-DNA systems in the presence of facilitated diffusion ("sliding") requires a cell of full system size. This bottleneck is avoided with a modification, by which a set of empirical parameters is calibrated using numerical simulations of a small test system. Once this is done, reaction times for systems of arb...
متن کاملFacilitated diffusion on confined DNA.
In living cells, proteins combine three-dimensional bulk diffusion and one-dimensional sliding along the DNA to reach a target faster. This process is known as facilitated diffusion and we investigate its dynamics in the physiologically relevant case of confined DNA. The confining geometry and DNA elasticity are key parameters: We find that facilitated diffusion is most efficient inside an isot...
متن کاملFacilitated diffusion with DNA coiling.
When DNA-binding proteins search for their specific binding site on a DNA molecule they alternate between linear 1-dimensional diffusion along the DNA molecule, mediated by nonspecific binding, and 3-dimensional volume excursion events between successive dissociation from and rebinding to DNA. If the DNA molecule is kept in a straight configuration, for instance, by optical tweezers, these 3-di...
متن کاملFacilitated diffusion of proteins on chromatin.
We present a theoretical model of facilitated diffusion of proteins in the cell nucleus. This model, which takes into account the successive binding and 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...
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ژورنال
عنوان ژورنال: Physical Review Letters
سال: 2006
ISSN: 0031-9007,1079-7114
DOI: 10.1103/physrevlett.96.018104