• Corpus ID: 17870502

Theory on the mechanism of rapid binding of transcription factor proteins at specific-sites on DNA

@article{Murugan2014TheoryOT,
  title={Theory on the mechanism of rapid binding of transcription factor proteins at specific-sites on DNA},
  author={Rajamanickam Murugan},
  journal={arXiv: Biological Physics},
  year={2014}
}
  • R. Murugan
  • Published 3 July 2014
  • Biology
  • arXiv: Biological Physics
We develop revised theoretical ideas on the mechanism by which the transcription factor proteins locate their specific binding sites on DNA faster than the three-dimensional (3D) diffusion controlled rate limit. We demonstrate that the 3D-diffusion controlled rate limit can be enhanced when the protein molecule reads several possible binding stretches of the template DNA via one-dimensional (1D) diffusion upon each 3D-diffusion mediated collision or nonspecific binding event. The overall… 

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References

SHOWING 1-10 OF 39 REFERENCES
Kinetics of protein-DNA interaction: facilitated target location in sequence-dependent potential.
TLDR
A search-and-fold mechanism that involves the coupling of protein binding and partial protein folding is proposed that has several important biological implications for search in the presence of other proteins and nucleosomes, simultaneous search by several proteins, etc.
Diffusion-driven mechanisms of protein translocation on nucleic acids. 1. Models and theory.
TLDR
Four types of processes that may be involved in protein translocation events between DNA sites are defined, and the consequences of each for the overall rate of target location are worked out as a function of both the nonspecific binding affinity between protein and DNA and the length of the DNA molecule containing the target sequence.
Packaging effects on site-specific DNA-protein interactions.
  • R. Murugan
  • Biology
    Physical review. E, Statistical, nonlinear, and soft matter physics
  • 2009
TLDR
The extent of packaging and volume compression of the genomic DNA inside the living cell is designed in such a way that the efficiency of the protein molecule in the process of searching for its specific site on the genomicDNA is a maximum.
Theory on thermodynamic coupling of site-specific DNA–protein interactions with fluctuations in DNA-binding domains
TLDR
There exists an optimum barrier height (∼kBT ln2) that separates these fast- and slow-moving states of DNA-binding domains, at which the efficiency associated with the thermodynamic coupling of thermally driven flipping and the overall search dynamics is the maximum.
Generalized theory of site-specific DNA-protein interactions.
  • R. Murugan
  • Mathematics
    Physical review. E, Statistical, nonlinear, and soft matter physics
  • 2007
We develop a generalized theory of the site-specific DNA-protein interactions, which includes both the static as well as the dynamical factors influencing the one-dimensional diffusion of the
An end to 40 years of mistakes in DNA-protein association kinetics?
  • S. Halford
  • Biology
    Biochemical Society transactions
  • 2009
TLDR
There is, in fact, no known example of a protein binding to a specific DNA site at a rate above the diffusion limit, and it will be shown that reduced dimensionality does not, in general, increase the rate of target-site location but instead reduces it.
Kinetics of target site localization of a protein on DNA: a stochastic approach.
TLDR
A stochastic model is proposed which comprises a series of one-dimensional diffusions of a restriction enzyme on nonspecific DNA sequences interrupted by three-dimensional excursions in the solution until the target sequence is reached and provides an optimal finding strategy which explains the fast association rate.
How DNA coiling enhances target localization by proteins
TLDR
Direct evidence that DNA coiling influences the specific association rate of EcoRV restriction enzymes is shown, and a major impact of intersegmental jumps on target localization speed on DNA is predicted.
Probing Transcription Factor Dynamics at the Single-Molecule Level in a Living Cell
TLDR
In a living Escherichia coli cell, specific binding of a lac repressor, labeled with a fluorescent protein, to a chromosomal lac operator is observed and the kinetics of binding and dissociation of the repressor in response to metabolic signals are measured using single-molecule detection techniques.
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