(Q42171094)

17 October 2017

Generalized facilitated diffusion model for DNA-binding proteins with search and recognition states (English)

1 reference

17 October 2017

1 reference

17 October 2017

Maximilian Bauer

1 reference

PMC publication ID

3353100

17 October 2017

language of work or name

English

0 references

publication date

15 May 2012

1 reference

17 October 2017

1 reference

inferred from page(s)

published in

Biophysical Journal

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17 October 2017

102

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17 October 2017

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17 October 2017

2321-2330

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Effects of macromolecular crowding on genetic networks

17 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3353100

Theoretical and computational modeling of target-site search kinetics in vitro and in vivo

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3353100

Rapid search for specific sites on DNA through conformational switch of nonspecifically bound proteins

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3353100

Physics of protein–DNA interactions: mechanisms of facilitated target search

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3353100

Facilitated diffusion with DNA coiling.

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3353100

How DNA coiling enhances target localization by proteins

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3353100

Sliding and jumping of single EcoRV restriction enzymes on non-cognate DNA.

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3353100

Are DNA transcription factor proteins maxwellian demons?

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3353100

Probing transcription factor dynamics at the single-molecule level in a living cell

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3353100

How proteins search for their specific sites on DNA: the role of DNA conformation

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3353100

Target search of N sliding proteins on a DNA

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3353100

Kinetics of protein-DNA interaction: facilitated target location in sequence-dependent potential

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3353100

Kinetics of target site localization of a protein on DNA: a stochastic approach.

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3353100

How do site-specific DNA-binding proteins find their targets?

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3353100

Kinetic characterization of linear diffusion of the restriction endonuclease EcoRV on DNA.

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3353100

The lac repressor-operator interaction. 3. Kinetic studies

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3353100

Diffusion controlled reaction rates in spheroidal geometry. Application to repressor--operator association and membrane bound enzymes

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3353100

Diffusion in a rough potential

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3353100

Facilitated target location in biological systems

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3353100

Conformational transitions of the lac repressor from Escherichia coli

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3353100

Diffusion-driven mechanisms of protein translocation on nucleic acids. 3. The Escherichia coli lac repressor--operator interaction: kinetic measurements and conclusions.

26 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3353100

Association kinetics with coupled diffusional flows. Special application to the lac repressor--operator system.

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3353100

Association kinetics with coupled diffusion III. Ionic-strength dependence of the lac repressor-operator association

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3353100

Narrow escape for a stochastically gated Brownian ligand.

29 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3353100

Structure and flexibility adaptation in nonspecific and specific protein-DNA complexes.

17 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3353100

In vivo non-specific binding of lambda CI and Cro repressors is significant.

17 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3353100

Kinetic regulation of single DNA molecule denaturation by T4 gene 32 protein structural domains.

17 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3353100

Diffusion-driven mechanisms of protein translocation on nucleic acids. 1. Models and theory.

17 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3353100

Transcription factor search for a DNA promoter in a three-state model

17 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3353100

Facilitated Diffusion of DNA-Binding Proteins

1 December 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3353100

Bulk-mediated surface diffusion along a cylinder: Propagators and crossovers

1 December 2018

1 reference

12 December 2020

Single molecule measurements of repressor protein 1D diffusion on DNA

1 reference

12 December 2020

Optimal target search on a fast-folding polymer chain with volume exchange

1 reference

12 December 2020

Description of nonspecific DNA-protein interaction and facilitated diffusion with a dynamical model

1 reference

12 December 2020

Effective surface motion on a reactive cylinder of particles that perform intermittent bulk diffusion

1 reference

12 December 2020

10.1016/J.BPJ.2012.04.008

Identifiers

DOI

1 reference

17 October 2017

1 reference

PMC publication ID

3353100

17 October 2017

PubMed publication ID

22677385

1 reference

PMC publication ID

3353100