Arc-repressor dimerization on DNA: folding rate enhancement by colocalization (Q42066088)

15 October 2017

Arc-repressor dimerization on DNA: folding rate enhancement by colocalization (English)

1 reference

15 October 2017

Amir Marcovitz

1

1 reference

PMCID

2712150

15 October 2017

Yaakov Levy

series ordinal

2

1 reference

PMCID

2712150

15 October 2017

language of work or name

English

0 references

publication date

1 May 2009

1 reference

15 October 2017

1 reference

15 October 2017

96

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15 October 2017

10

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15 October 2017

4212-4220

1 reference

Dynamic energy landscape view of coupled binding and protein conformational change: induced-fit versus population-shift mechanisms

15 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2712150

Binding-induced folding of a natively unstructured transcription factor.

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2712150

The origin of protein interactions and allostery in colocalization

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2712150

Folding of a DNA hairpin loop structure in explicit solvent using replica-exchange molecular dynamics simulations

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2712150

Electrostatic, steric, and hydration interactions favor Na(+) condensation around DNA compared with K(+).

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2712150

Single-molecule dynamics reveals cooperative binding-folding in protein recognition

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2712150

Mechanisms of protein assembly: lessons from minimalist models

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2712150

Mechanical unfolding of RNA hairpins

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2712150

Single-Stranded Adenine-Rich DNA and RNA Retain Structural Characteristics of Their Respective Double-Stranded Conformations and Show Directional Differences in Stacking Pattern †

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2712150

The power of two: protein dimerization in biology

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2712150

DNA-mediated assembly of weakly interacting DNA-binding protein subunits: in vitro recruitment of phage 434 repressor and yeast GCN4 DNA-binding domains

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2712150

Combinatorial control of gene expression.

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2712150

Reassessing random-coil statistics in unfolded proteins

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2712150

Random-coil behavior and the dimensions of chemically unfolded proteins

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2712150

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

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2712150

Theory of protein folding

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2712150

Protein topology determines binding mechanism

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2712150

On schemes of combinatorial transcription logic

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2712150

From folding theories to folding proteins: a review and assessment of simulation studies of protein folding and unfolding

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2712150

Hepatitis B virus protein pX enhances the monomer assembly pathway of bZIP.DNA complexes

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2712150

Speeding molecular recognition by using the folding funnel: the fly-casting mechanism

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2712150

How native-state topology affects the folding of dihydrofolate reductase and interleukin-1beta

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2712150

Topological and energetic factors: what determines the structural details of the transition state ensemble and "en-route" intermediates for protein folding? An investigation for small globular proteins

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2712150

Gene regulation: protein escorts to the transcription ball

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2712150

Exploring the origins of topological frustration: design of a minimally frustrated model of fragment B of protein A.

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2712150

DNA specificity enhanced by sequential binding of protein monomers.

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2712150

Multiprotein-DNA complexes in transcriptional regulation

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2712150

cAMP response element-binding protein monomers cooperatively assemble to form dimers on DNA.

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2712150

Theory of protein folding: the energy landscape perspective

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2712150

Transcriptional activation by recruitment

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2712150

DNA recognition by beta-sheets in the Arc repressor-operator crystal structure

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2712150

Nuclear magnetic resonance solution structure of the Arc repressor using relaxation matrix calculations

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2712150

The influence of salt on the structure and energetics of supercoiled DNA

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2712150

Equilibrium dissociation and unfolding of the Arc repressor dimer

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2712150

Diversity and specificity in transcriptional regulation: the benefits of heterotypic dimerization

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2712150

Fly-casting in protein-DNA binding: frustration between protein folding and electrostatics facilitates target recognition

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2712150

Effect of finite size on cooperativity and rates of protein folding.

17 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2712150

Thermodynamics of Go-type models for protein folding.

17 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2712150

A survey of flexible protein binding mechanisms and their transition states using native topology based energy landscapes

17 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2712150

Monomeric and dimeric bZIP transcription factor GCN4 bind at the same rate to their target DNA site

17 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2712150

The physics and bioinformatics of binding and folding-an energy landscape perspective

17 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2712150

Roles of native topology and chain-length scaling in protein folding: a simulation study with a Go-like 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=2712150

Reversible unfolding of single RNA molecules by mechanical force

17 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2712150

Computational modeling predicts the structure and dynamics of chromatin fiber

17 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2712150

Modeling salt-mediated electrostatics of macromolecules: the discrete surface charge optimization algorithm and its application to the nucleosome

17 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2712150

Acceleration of the refolding of Arc repressor by nucleic acids and other polyanions

17 August 2018

1 reference

12 December 2020

Effects of nucleic acids and polyanions on dimer formation and DNA binding by bZIP and bHLHZip transcription factors

1 reference

12 December 2020

Sequence dependent rigidity of single stranded DNA

1 reference

12 December 2020

Kinetic mechanism of DNA binding and DNA-induced dimerization of the Escherichia coli Rep helicase

1 reference

12 December 2020

Certain bZIP peptides bind DNA sequentially as monomers and dimerize on the DNA

1 reference

12 December 2020

Dominant kinetic paths on biomolecular binding-folding energy landscape

1 reference

12 December 2020

Inter-DNA electrostatics from explicit solvent molecular dynamics simulations

1 reference

12 December 2020

Exploring the mechanism of flexible biomolecular recognition with single molecule dynamics

1 reference

12 December 2020

Protein sliding along DNA: dynamics and structural characterization

1 reference

12 December 2020

DNA-mediated folding and assembly of MyoD-E47 heterodimers

1 reference

12 December 2020

Diffusion-controlled DNA recognition by an unfolded, monomeric bZIP transcription factor

1 reference

12 December 2020

Kinetic Studies of Fos·Jun·DNA Complex Formation: DNA Binding Prior to Dimerization†

1 reference

12 December 2020

10.1016/J.BPJ.2009.01.057

Identifiers

DOI

1 reference

15 October 2017

1 reference

15 October 2017

1 reference

PMCID

2712150