(Q30367987)

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An integrated model of transcription factor diffusion shows the importance of intersegmental transfer and quaternary protein structure for target site finding.

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scholarly article

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Europe PubMed Central

11 November 2017

An integrated model of transcription factor diffusion shows the importance of intersegmental transfer and quaternary protein structure for target site finding. (English)

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Europe PubMed Central

11 November 2017

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Sven Sewitz

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Hugo G Schmidt

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Europe PubMed Central

11 November 2017

Steven S Andrews

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Europe PubMed Central

11 November 2017

Karen Lipkow

4

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Europe PubMed Central

11 November 2017

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publication date

21 October 2014

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Europe PubMed Central

11 November 2017

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Europe PubMed Central

11 November 2017

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Europe PubMed Central

11 November 2017

10

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Europe PubMed Central

11 November 2017

e108575

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Europe PubMed Central

11 November 2017

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Creative Commons Attribution 4.0 International

21 October 2014

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April 2022 Public Data File from Crossref

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Single-molecule dynamics of enhanceosome assembly in embryonic stem cells

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DNA concentration-dependent dissociation of EcoRI: direct transfer or reaction during hopping.

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In vivo facilitated diffusion model

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Timing facilitated site transfer of an enzyme on DNA

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Toward convergence of experimental studies and theoretical modeling of the chromatin fiber

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

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Nucleosome-mediated cooperativity between transcription factors

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

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Chromatin remodeling around nucleosome-free regions leads to repression of noncoding RNA transcription

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3 June 2018

Dynamic strategies for target-site search by DNA-binding proteins

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Hi-C: a method to study the three-dimensional architecture of genomes

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Characterisation of Bacillus subtilis transcriptional regulators involved in metabolic processes

1 reference

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3 June 2018

Detailed simulations of cell biology with Smoldyn 2.1

1 reference

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Spatial and topological organization of DNA chains induced by gene co-localization

1 reference

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Thioredoxin suppresses microscopic hopping of T7 DNA polymerase on duplex DNA.

1 reference

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1 reference

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Comprehensive mapping of long-range interactions reveals folding principles of the human genome

1 reference

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Introducing simulated cellular architecture to the quantitative analysis of fluorescent microscopy

1 reference

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3 June 2018

Facilitated diffusion with DNA coiling.

1 reference

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Tracking of single quantum dot labeled EcoRV sliding along DNA manipulated by double optical tweezers.

1 reference

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Mapping eGFP oligomer mobility in living cell nuclei

1 reference

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An end to 40 years of mistakes in DNA-protein association kinetics?

1 reference

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3 June 2018

Dissecting nucleosome free regions by a segmental semi-Markov model

1 reference

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3 June 2018

How DNA coiling enhances target localization by proteins

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4204827

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Global jumping and domain-specific intersegment transfer between DNA cognate sites of the multidomain transcription factor Oct-1.

1 reference

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3 June 2018

A barrier nucleosome model for statistical positioning of nucleosomes throughout the yeast genome

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4204827

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Are DNA transcription factor proteins maxwellian demons?

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4204827

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Spatial effects on the speed and reliability of protein-DNA search

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4204827

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Tumor suppressor p53 slides on DNA with low friction and high stability

1 reference

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Dynamic remodeling of individual nucleosomes across a eukaryotic genome in response to transcriptional perturbation

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4204827

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1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4204827

3 June 2018

Chromatin remodelling at promoters suppresses antisense transcription

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4204827

3 June 2018

Dynamic basis for one-dimensional DNA scanning by the mismatch repair complex Msh2-Msh6.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4204827

3 June 2018

A high-resolution atlas of nucleosome occupancy in yeast

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4204827

3 June 2018

The size of the nucleus increases as yeast cells grow

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4204827

3 June 2018

Single-molecule analysis of 1D diffusion and transcription elongation of T7 RNA polymerase along individual stretched DNA molecules

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4204827

3 June 2018

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4204827

3 June 2018

Rules and regulation in the primary structure of chromatin

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4204827

3 June 2018

Analysis of protein-DNA interactions using surface plasmon resonance

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4204827

3 June 2018

3D complex: a structural classification of protein complexes

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4204827

3 June 2018

Electrostatic design of protein-protein association rates

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4204827

3 June 2018

Chromosome Conformation Capture Carbon Copy (5C): a massively parallel solution for mapping interactions between genomic elements

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4204827

3 June 2018

Antagonistic forces that position nucleosomes in vivo.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4204827

3 June 2018

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1 reference

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RshA mimetic peptides inhibiting the transcription driven by a Mycobacterium tuberculosis sigma factor SigH

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1 reference

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3 June 2018

Genome-scale identification of nucleosome positions in S. cerevisiae

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3 June 2018

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Simulated diffusion of phosphorylated CheY through the cytoplasm of Escherichia coli.

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3 June 2018

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3 June 2018

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

1 reference

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3 June 2018

Global nucleosome occupancy in yeast

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4204827

3 June 2018

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1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4204827

3 June 2018

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

1 reference

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3 June 2018

Structural characterization of the Fpg family of DNA glycosylases

1 reference

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3 June 2018

Protein motion from non-specific to specific DNA by three-dimensional routes aided by supercoiling

1 reference

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3 June 2018

How to get from A to B: strategies for analysing protein motion on DNA.

1 reference

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The influence of macromolecular crowding and macromolecular confinement on biochemical reactions in physiological media

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Roles of glucitol in the GutR-mediated transcription activation process in Bacillus subtilis: tight binding of GutR to tis binding site

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3 June 2018

The Protein Data Bank

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3 June 2018

Steroidogenic factor 1-DNA binding: a kinetic analysis using surface plasmon resonance

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3 June 2018

Crystal structure of the nucleosome core particle at 2.8 A resolution

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3 June 2018

Comparison of the DNA association kinetics of the Lac repressor tetramer, its dimeric mutant LacIadi, and the native dimeric Gal repressor

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3 June 2018

Eukaryotic transcription factor-DNA complexes.

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3 June 2018

Translational diffusion of macromolecule-sized solutes in cytoplasm and nucleus

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3 June 2018

Recognition and cleavage of DNA by type-II restriction endonucleases

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3 June 2018

Recycling of the general transcription factors during RNA polymerase II transcription

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3 June 2018

The dimensions of DNA in solution

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3 June 2018

The lac repressor-operator interaction. 3. Kinetic studies

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3 June 2018

Lac repressor-operator interaction. I. Equilibrium studies.

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3 June 2018

Diffusion-controlled macromolecular interactions

1 reference

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3 June 2018

One-dimensional diffusion of Escherichia coli DNA-dependent RNA polymerase: a mechanism to facilitate promoter location

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3 June 2018

Facilitated target location in biological systems

1 reference

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3 June 2018

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

1 reference

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3 June 2018

The one-dimensional diffusion coefficient of proteins absorbed on DNA. Hydrodynamic considerations

1 reference

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3 June 2018

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

1 reference

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21 January 2018

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

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0108575

21 January 2018

Stopped-flow fluorescence kinetic study of protein sliding and intersegment transfer in the target DNA search process

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0108575

21 January 2018

Periodic epi-organization of the yeast genome revealed by the distribution of promoter sites.

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0108575

21 January 2018

Periodic transcriptional organization of the E.coli genome

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0108575

21 January 2018

Sequestration of CaMKII in dendritic spines in silico.

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0108575

21 January 2018

Silencing c-MYC expression by targeting quadruplex in P1 promoter using locked nucleic acid trap

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0108575

21 January 2018

Modeling transcription factor binding events to DNA using a random walker/jumper representation on a 1D/2D lattice with different affinity sites.

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0108575

21 January 2018

Stochastic simulation of chemical reactions with spatial resolution and single molecule detail.

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0108575

21 January 2018

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

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0108575

21 January 2018

Contribution of facilitated diffusion and processive catalysis to enzyme efficiency: implications for the EcoRI restriction-modification system

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0108575

21 January 2018

DNA sequence plays a major role in determining nucleosome positions in yeast CUP1 chromatin.

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0108575

21 January 2018

The Crystal Structure of the Transcriptional Regulator HucR from Deinococcus radiodurans Reveals a Repressor Preconfigured for DNA Binding

1 reference

https://pubmed.ncbi.nlm.nih.gov/25333780

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Nucleosome positions predicted through comparative genomics

1 reference

https://pubmed.ncbi.nlm.nih.gov/25333780

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

The study of the interaction of (cytosine-5)-DNA methyltransferase SsoII with DNA by acoustic method

1 reference

https://pubmed.ncbi.nlm.nih.gov/25333780

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Single molecule measurements of repressor protein 1D diffusion on DNA

1 reference

https://pubmed.ncbi.nlm.nih.gov/25333780

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Thermodynamic and kinetic measurements of promoter binding by T7 RNA polymerase

1 reference

https://pubmed.ncbi.nlm.nih.gov/25333780

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

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

1 reference

https://pubmed.ncbi.nlm.nih.gov/25333780

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Facilitated search of proteins on DNA: correlations are important

1 reference

https://pubmed.ncbi.nlm.nih.gov/25333780

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

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

1 reference

https://pubmed.ncbi.nlm.nih.gov/25333780

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Protein sliding along DNA: dynamics and structural characterization

1 reference

https://pubmed.ncbi.nlm.nih.gov/25333780

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Modulating protein-DNA interactions by post-translational modifications at disordered regions

1 reference

https://pubmed.ncbi.nlm.nih.gov/25333780

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Identifiers

10.1371/JOURNAL.PONE.0108575

1 reference

Europe PubMed Central

11 November 2017

2014PLoSO...9j8575S

0 references

1 reference

Europe PubMed Central

11 November 2017

1 reference

Europe PubMed Central

11 November 2017

ResearchGate publication ID

0 references

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