Comparison of kinetic and dynamical models of DNA-protein interaction and facilitated diffusion

Abstract

It has long been asserted that proteins like transcription factors may locate their target in DNA sequences at rates that surpass by several orders of magnitude the three-dimensional diffusion limit thank to facilitated diffusion, that is the combination of one-dimensional (sliding along the DNA) and three-dimensional diffusion. This claim has been supported along the years by several mass action kinetic models, while the dynamical model we proposed recently (J. Chem. Phys. 130, 015103 (2009)) suggests that acceleration of targeting due to facilitated diffusion cannot be large. In order to solve this apparent contradiction, we performed additional simulations to compare the results obtained with our model to those obtained with the kinetic model of Klenin et al (Phys. Rev. Letters 96, 018104 (2006)). We show in this paper that the two models actually support each other and agree in predicting a low efficiency for facilitated diffusion. Extrapolation of these results to real systems even indicates that facilitated diffusion necessarily slows down the targeting process compared to three-dimensional diffusion.

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• Preferential localization of the bacterial nucleoid
• Thermal and mechanical denaturation properties of a DNA model with three sites per nucleotide
• Role of salt valency in the switch of H-NS proteins between DNA-bridging and DNA-stiffening modes
• Coarse-Grained model of the demixing of DNA and non-binding globular macromolecules
• Impact of self-association on the architectural properties of bacterial nucleoid proteins
• Requirements for DNA-bridging proteins to act as topological barriers of the bacterial genome
• Equilibration of complexes of DNA and H-NS proteins on charged surfaces: A coarse-grained model point of view