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What matters for lac repressor search in vivo--sliding, hopping, intersegment transfer, crowding on DNA or recognition?

Mahmutovic A, Berg OG, Elf J - Nucleic Acids Res. (2015)

Bottom Line: Including a mechanism of inter-segment transfer between distant DNA segments does not bring down the 1D diffusion to the expected fraction of the in vitro value.This suggests a mechanism where transcription factors can slide less hindered in vivo than what is given by a simple viscosity scaling argument or that a modification of the model is needed.For example, the estimated diffusion rate constant would be consistent with the expectation if parts of the chromosome, away from the operator site, were inaccessible for searching.

View Article: PubMed Central - PubMed

Affiliation: Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, 75124 Uppsala, Sweden.

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Related in: MedlinePlus

The figure depicts a cartoon of the search process and the fundamental parameters involved in our model. In the MC simulation scheme, following a dissociation the searching protein can associate with rate ka to a non-specific stretch of DNA given that no other proteins (roadblocks) are in the way. Given a successful non-specific association the protein may diffuse in 1D along the length of the DNA or perform intersegment transfer with rate kIST. After a number of non-specific association–sliding–dissociation iterations during the total time τ, the searching protein finds its way to the specific binding site and binds with rate constant ksp.
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Figure 1: The figure depicts a cartoon of the search process and the fundamental parameters involved in our model. In the MC simulation scheme, following a dissociation the searching protein can associate with rate ka to a non-specific stretch of DNA given that no other proteins (roadblocks) are in the way. Given a successful non-specific association the protein may diffuse in 1D along the length of the DNA or perform intersegment transfer with rate kIST. After a number of non-specific association–sliding–dissociation iterations during the total time τ, the searching protein finds its way to the specific binding site and binds with rate constant ksp.

Mentions: We build on the classical sliding model (2–5,8) (Figure 1), where the DNA is considered as a smooth cylinder and the protein is a fully reactive sphere. In the Supplementary material the classical model is extended to include roadblocks, i.e. non-specifically bound proteins to DNA, and a specific recognition step at the specific operator site. The reaction radius ρ is the sum of the radii of the cylinder and the sphere. Non-specific protein–DNA binding is described by the reaction radius ρ, a relative diffusion rate D3 and the extent of diffusion control, α (Equation (3)). All steric effects in the binding are assumed to be incorporated in the parameters α or ρ. Beyond the distance Rc from the DNA axis, where it is equally far to another DNA segment, the protein is assumed to have lost its correlations with a particular DNA segment and will be equally likely to bind anywhere on the DNA. If the number of accessible non-specific binding sites on DNA is Macc with each base pair having a length ℓ and where the genome is confined to a volume Vc, Rc can be determined from(1)\documentclass[12pt]{minimal}\usepackage{amsmath}\usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy}\usepackage{upgreek}\usepackage{mathrsfs}\setlength{\oddsidemargin}{-69pt}\begin{document}}{}\begin{equation*} M_{{\rm acc}} \ell \pi R_c^2 = V_c. \end{equation*}\end{document}


What matters for lac repressor search in vivo--sliding, hopping, intersegment transfer, crowding on DNA or recognition?

Mahmutovic A, Berg OG, Elf J - Nucleic Acids Res. (2015)

The figure depicts a cartoon of the search process and the fundamental parameters involved in our model. In the MC simulation scheme, following a dissociation the searching protein can associate with rate ka to a non-specific stretch of DNA given that no other proteins (roadblocks) are in the way. Given a successful non-specific association the protein may diffuse in 1D along the length of the DNA or perform intersegment transfer with rate kIST. After a number of non-specific association–sliding–dissociation iterations during the total time τ, the searching protein finds its way to the specific binding site and binds with rate constant ksp.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4402528&req=5

Figure 1: The figure depicts a cartoon of the search process and the fundamental parameters involved in our model. In the MC simulation scheme, following a dissociation the searching protein can associate with rate ka to a non-specific stretch of DNA given that no other proteins (roadblocks) are in the way. Given a successful non-specific association the protein may diffuse in 1D along the length of the DNA or perform intersegment transfer with rate kIST. After a number of non-specific association–sliding–dissociation iterations during the total time τ, the searching protein finds its way to the specific binding site and binds with rate constant ksp.
Mentions: We build on the classical sliding model (2–5,8) (Figure 1), where the DNA is considered as a smooth cylinder and the protein is a fully reactive sphere. In the Supplementary material the classical model is extended to include roadblocks, i.e. non-specifically bound proteins to DNA, and a specific recognition step at the specific operator site. The reaction radius ρ is the sum of the radii of the cylinder and the sphere. Non-specific protein–DNA binding is described by the reaction radius ρ, a relative diffusion rate D3 and the extent of diffusion control, α (Equation (3)). All steric effects in the binding are assumed to be incorporated in the parameters α or ρ. Beyond the distance Rc from the DNA axis, where it is equally far to another DNA segment, the protein is assumed to have lost its correlations with a particular DNA segment and will be equally likely to bind anywhere on the DNA. If the number of accessible non-specific binding sites on DNA is Macc with each base pair having a length ℓ and where the genome is confined to a volume Vc, Rc can be determined from(1)\documentclass[12pt]{minimal}\usepackage{amsmath}\usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy}\usepackage{upgreek}\usepackage{mathrsfs}\setlength{\oddsidemargin}{-69pt}\begin{document}}{}\begin{equation*} M_{{\rm acc}} \ell \pi R_c^2 = V_c. \end{equation*}\end{document}

Bottom Line: Including a mechanism of inter-segment transfer between distant DNA segments does not bring down the 1D diffusion to the expected fraction of the in vitro value.This suggests a mechanism where transcription factors can slide less hindered in vivo than what is given by a simple viscosity scaling argument or that a modification of the model is needed.For example, the estimated diffusion rate constant would be consistent with the expectation if parts of the chromosome, away from the operator site, were inaccessible for searching.

View Article: PubMed Central - PubMed

Affiliation: Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, 75124 Uppsala, Sweden.

Show MeSH
Related in: MedlinePlus