(Q39771675)

14 September 2017

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

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14 September 2017

3

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14 September 2017

Anel Mahmutovic

1

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14 September 2017

Otto G Berg

series ordinal

2

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14 September 2017

language of work or name

English

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publication date

16 March 2015

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14 September 2017

Nucleic Acids Research

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14 September 2017

43

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14 September 2017

7

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14 September 2017

3454-3464

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Creative Commons Attribution 4.0 International

14 September 2017

start time

7 November 2016

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April 2022 Public Data File from Crossref

copyright status

copyrighted

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cites work

Sliding of proteins non-specifically bound to DNA: Brownian dynamics studies with coarse-grained protein and DNA models

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Probing the rate-limiting step for intramolecular transfer of a transcription factor between specific sites on the same DNA molecule by (15)Nz-exchange NMR spectroscopy.

22 September 2017

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Quantifying absolute protein synthesis rates reveals principles underlying allocation of cellular resources

22 September 2017

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4402528

Transcription-factor binding and sliding on DNA studied using micro- and macroscopic models

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4402528

How do proteins locate specific targets in DNA?

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4402528

Quantitative influence of macromolecular crowding on gene regulation kinetics.

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4402528

Obstacles may facilitate and direct DNA search by proteins

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4402528

Effect of DNA conformation on facilitated diffusion.

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4402528

In vivo facilitated diffusion model

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4402528

Computational models for large-scale simulations of facilitated diffusion

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4402528

Intrinsically disordered regions as affinity tuners in protein-DNA interactions

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4402528

Dancing on DNA: kinetic aspects of search processes on DNA

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4402528

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

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4402528

DNA search efficiency is modulated by charge composition and distribution in the intrinsically disordered tail

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4402528

Bacterial nucleoid-associated proteins, nucleoid structure and gene expression

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4402528

Nonspecifically bound proteins spin while diffusing along DNA.

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4402528

Facilitated diffusion with DNA coiling.

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4402528

How DNA coiling enhances target localization by proteins

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4402528

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

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4402528

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

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4402528

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

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4402528

The lac repressor-operator interaction. 3. Kinetic studies

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4402528

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

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4402528

Diffusion in a rough potential

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4402528

Sliding and intermolecular transfer of the lac repressor: kinetic perturbation of a reaction intermediate by a distant DNA sequence

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4402528

Association kinetics with coupled diffusion. An extension to coiled-chain macromolecules applied to the LAC repressor-operator system

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4402528

Comparison of protein binding to DNA in vivo and in vitro: defining an effective intracellular target.

22 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4402528

Facilitated DNA search by multidomain transcription factors: cross talk via a flexible linker

25 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4402528

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

17 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4402528

Proteins from the prokaryotic nucleoid. Interaction of nucleic acids with the 15 kDa Escherichia coli histone-like protein H-NS.

17 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4402528

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

17 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4402528

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

17 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4402528

Facilitated diffusion buffers noise in gene expression

17 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4402528

Protein-DNA electrostatics: toward a new paradigm for protein sliding

20 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4402528

Asymmetric DNA-search dynamics by symmetric dimeric proteins

20 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4402528

Speed-selectivity paradox in the protein search for targets on DNA: is it real or not?

20 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4402528

The lac repressor displays facilitated diffusion in living cells.

20 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4402528

Insights into the sliding movement of the lac repressor nonspecifically bound to DNA.

20 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4402528

Quantifying hopping and jumping in facilitated diffusion of DNA-binding proteins.

20 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4402528

Facilitated diffusion of DNA-binding proteins: Simulation of large systems.

20 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4402528

Interaction of Fis protein with DNA: bending and specificity of binding.

20 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4402528

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

20 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4402528

Facilitated Diffusion of Proteins on Chromatin

20 August 2018

1 reference

Crossref

https://api.crossref.org/works/10.1093%2FNAR%2FGKV207

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

21 January 2018

1 reference

12 December 2020

Salt dependence of the kinetics of the lac repressor-operator interaction: role of nonoperator deoxyribonucleic acid in the association reaction

1 reference

12 December 2020

Differential binding of the Escherichia coli HU, homodimeric forms and heterodimeric form to linear, gapped and cruciform DNA

1 reference

12 December 2020

Twelve species of the nucleoid-associated protein from Escherichia coli. Sequence recognition specificity and DNA binding affinity

1 reference

12 December 2020

Facilitated diffusion on confined DNA

1 reference

12 December 2020

One-dimensional diffusion of proteins along DNA. Its biological and chemical significance revealed by single-molecule measurements

1 reference

12 December 2020

How a protein searches for its specific site on DNA: the role of intersegment transfer

1 reference

12 December 2020

Facilitated search of proteins on DNA: correlations are important

1 reference

12 December 2020

Searching DNA via a "Monkey Bar" mechanism: the significance of disordered tails

1 reference

12 December 2020

Protein sliding along DNA: dynamics and structural characterization

1 reference

12 December 2020

Identifiers

DOI

10.1093/NAR/GKV207

1 reference

14 September 2017

1 reference

14 September 2017

PubMed publication ID

25779051

1 reference