(Q38626679)

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Late steps in the formation of E. coli RNA polymerase-lambda P R promoter open complexes: characterization of conformational changes by rapid [perturbant] upshift experiments

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scholarly article

1 reference

Europe PubMed Central

PMC publication ID

4 September 2017

Late steps in the formation of E. coli RNA polymerase-lambda P R promoter open complexes: characterization of conformational changes by rapid [perturbant] upshift experiments (English)

1 reference

Europe PubMed Central

PMC publication ID

4 September 2017

Escherichia coli

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author name string

Wayne S Kontur

1

1 reference

Europe PubMed Central

PMC publication ID

4 September 2017

Ruth M Saecker

2

1 reference

Europe PubMed Central

PMC publication ID

4 September 2017

Michael W Capp

3

1 reference

Europe PubMed Central

PMC publication ID

4 September 2017

M Thomas Record

4

1 reference

Europe PubMed Central

PMC publication ID

4 September 2017

language of work or name

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publication date

29 November 2007

1 reference

Europe PubMed Central

PMC publication ID

4 September 2017

Journal of Molecular Biology

1 reference

Europe PubMed Central

PMC publication ID

4 September 2017

376

1 reference

Europe PubMed Central

PMC publication ID

4 September 2017

4

1 reference

Europe PubMed Central

PMC publication ID

4 September 2017

1034-1047

1 reference

Europe PubMed Central

PMC publication ID

4 September 2017

Anatomy of energetic changes accompanying urea-induced protein denaturation.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2396949

6 September 2017

Urea-amide preferential interactions in water: quantitative comparison of model compound data with biopolymer results using water accessible surface areas

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2396949

6 September 2017

Real-time footprinting of DNA in the first kinetically significant intermediate in open complex formation by Escherichia coli RNA polymerase

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2396949

6 September 2017

DksA potentiates direct activation of amino acid promoters by ppGpp

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2396949

6 September 2017

Thermal and urea-induced unfolding of the marginally stable lac repressor DNA-binding domain: a model system for analysis of solute effects on protein processes

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2396949

6 September 2017

Thermodynamics of interactions of urea and guanidinium salts with protein surface: relationship between solute effects on protein processes and changes in water-accessible surface area

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2396949

6 September 2017

Bacterial RNA polymerase

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2396949

6 September 2017

Sequence complexity of disordered protein

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2396949

6 September 2017

The kinetics of sigma subunit directed promoter recognition by E. coli RNA polymerase

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2396949

6 September 2017

Quantitative analysis of multiple-hit footprinting studies to characterize DNA conformational changes in protein-DNA complexes: application to DNA opening by Esigma70 RNA polymerase

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2396949

6 September 2017

Contact order, transition state placement and the refolding rates of single domain proteins.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2396949

6 September 2017

A mutant RNA polymerase that forms unusual open promoter complexes

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2396949

6 September 2017

Coupling of local folding to site-specific binding of proteins to DNA

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2396949

6 September 2017

Urea unfolding of peptide helices as a model for interpreting protein unfolding

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2396949

6 September 2017

General method of analysis of kinetic equations for multistep reversible mechanisms in the single-exponential regime: application to kinetics of open complex formation between Esigma70 RNA polymerase and lambdaP(R) promoter DNA.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2396949

14 September 2017

Thermodynamic analysis of ion effects on the binding and conformational equilibria of proteins and nucleic acids: the roles of ion association or release, screening, and ion effects on water activity

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2396949

14 September 2017

Solute probes of conformational changes in open complex (RPo) formation by Escherichia coli RNA polymerase at the lambdaPR promoter: evidence for unmasking of the active site in the isomerization step and for large-scale coupled folding in the subse

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2396949

23 June 2018

Use of urea and glycine betaine to quantify coupled folding and probe the burial of DNA phosphates in lac repressor-lac operator binding

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2396949

23 June 2018

Kinetic studies and structural models of the association of E. coli sigma(70) RNA polymerase with the lambdaP(R) promoter: large scale conformational changes in forming the kinetically significant intermediates

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2396949

23 June 2018

Changes in the 17 bp spacer in the P(R) promoter of bacteriophage lambda affect steps in open complex formation that precede DNA strand separation

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2396949

23 June 2018

Promoter recognition by Escherichia coli RNA polymerase: effects of the UP element on open complex formation and promoter clearance

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2396949

23 June 2018

DNA footprints of the two kinetically significant intermediates in formation of an RNA polymerase-promoter open complex: evidence that interactions with start site and downstream DNA induce sequential conformational changes in polymerase and DNA.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2396949

23 June 2018

Influence of Mg2+ and temperature on formation of the transcription bubble

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2396949

23 June 2018

Two open complexes and a requirement for Mg2+ to open the lambda PR transcription start site

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2396949

23 June 2018

HO. and DNase I probing of E sigma 70 RNA polymerase--lambda PR promoter open complexes: Mg2+ binding and its structural consequences at the transcription start site

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2396949

23 June 2018

Kinetics and mechanism of the interaction of Escherichia coli RNA polymerase with the λPR promoter

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2396949

23 June 2018

Temperature dependence of the rate constants of the Escherichia coli RNA polymerase-lambda PR promoter interaction. Assignment of the kinetic steps corresponding to protein conformational change and DNA opening

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2396949

23 June 2018

Changes in the DNA structure of the lac UV5 promoter during formation of an open complex with Escherichia coli RNA polymerase

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2396949

23 June 2018

Kinetics of open complex formation between Escherichia coli RNA polymerase and the lac UV5 promoter. Evidence for a sequential mechanism involving three steps

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2396949

23 June 2018

Roles of Mg2+ in the mechanism of formation and dissociation of open complexes between Escherichia coli RNA polymerase and the lambda PR promoter: kinetic evidence for a second open complex requiring Mg2+

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2396949

23 June 2018

Procedure for the rapid, large-scale purification of Escherichia coli DNA-dependent RNA polymerase involving polymin P precipitation and DNA-cellulose chromatography

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2396949

23 June 2018

Remodeling of the sigma70 subunit non-template DNA strand contacts during the final step of transcription initiation.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2396949

31 August 2018

TFIIH XPB mutants suggest a unified bacterial-like mechanism for promoter opening but not escape

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2396949

31 August 2018

Preferential interactions of glycine betaine and of urea with DNA: implications for DNA hydration and for effects of these solutes on DNA stability

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2396949

31 August 2018

Differential melting of the transcription start site associated with changes in RNA polymerase-promoter contacts in initiating transcription complexes.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2396949

31 August 2018

DNA-melting at the Bacillus subtilis flagellin promoter nucleates near -10 and expands unidirectionally.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2396949

31 August 2018

Pathway of promoter melting by Bacillus subtilis RNA polymerase at a stable RNA promoter: effects of temperature, delta protein, and sigma factor mutations.

1 reference

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31 August 2018

Regulation of the kinetics of the interaction of Escherichia coli RNA polymerase with the lambda PR promoter by salt concentration

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2396949

31 August 2018

DksA: a critical component of the transcription initiation machinery that potentiates the regulation of rRNA promoters by ppGpp and the initiating NTP

1 reference

https://pubmed.ncbi.nlm.nih.gov/18191943

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Helix-random coil transitions in synthetic DNAs of alternating sequence

1 reference

https://pubmed.ncbi.nlm.nih.gov/18191943

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Enthalpy and heat capacity changes for formation of an oligomeric DNA duplex: interpretation in terms of coupled processes of formation and association of single-stranded helices

1 reference

https://pubmed.ncbi.nlm.nih.gov/18191943

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Thermodynamic analysis of interactions between denaturants and protein surface exposed on unfolding: interpretation of urea and guanidinium chloride m-values and their correlation with changes in accessible surface area (ASA) using preferential inte

1 reference

https://pubmed.ncbi.nlm.nih.gov/18191943

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Physical studies on ribonucleic acid polymerase from Escherichia coli B

1 reference

https://pubmed.ncbi.nlm.nih.gov/18191943

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Analysis of ion concentration effects of the kinetics of protein-nucleic acid interactions. Application to lac repressor-operator interactions

1 reference

https://pubmed.ncbi.nlm.nih.gov/18191943

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Predicting Protein Disorder for N-, C-, and Internal Regions

1 reference

https://pubmed.ncbi.nlm.nih.gov/18191943

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Identifiers

10.1016/J.JMB.2007.11.064

1 reference

Europe PubMed Central

PMC publication ID

4 September 2017

PMC publication ID

1 reference

Europe PubMed Central

PMC publication ID

4 September 2017

PubMed publication ID

1 reference

Europe PubMed Central

PMC publication ID

4 September 2017

ResearchGate publication ID

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