(Q41944092)

English

Formation of a wrapped DNA-protein interface: experimental characterization and analysis of the large contributions of ions and water to the thermodynamics of binding IHF to H' DNA.

scientific article published on 7 December 2007

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scholarly article

1 reference

Europe PubMed Central

PMC publication ID

14 October 2017

Formation of a wrapped DNA-protein interface: experimental characterization and analysis of the large contributions of ions and water to the thermodynamics of binding IHF to H' DNA. (English)

1 reference

Europe PubMed Central

PMC publication ID

14 October 2017

author name string

Kirk A Vander Meulen

1

1 reference

Europe PubMed Central

PMC publication ID

14 October 2017

Ruth M Saecker

2

1 reference

Europe PubMed Central

PMC publication ID

14 October 2017

M Thomas Record

3

1 reference

Europe PubMed Central

PMC publication ID

14 October 2017

language of work or name

0 references

publication date

7 December 2007

1 reference

Europe PubMed Central

PMC publication ID

14 October 2017

Journal of Molecular Biology

1 reference

Europe PubMed Central

PMC publication ID

14 October 2017

377

1 reference

Europe PubMed Central

PMC publication ID

14 October 2017

1

1 reference

Europe PubMed Central

PMC publication ID

14 October 2017

9-27

1 reference

Europe PubMed Central

PMC publication ID

14 October 2017

Direct observation of DNA bending/unbending kinetics in complex with DNA-bending protein IHF.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2336898

5 June 2018

Stepwise binding and bending of DNA by Escherichia coli integration host factor

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2336898

5 June 2018

Partitioning of atmospherically relevant ions between bulk water and the water/vapor interface

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2336898

5 June 2018

Structural basis for ATP-dependent DnaA assembly and replication-origin remodeling

1 reference

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5 June 2018

Interactions of cationic ligands and proteins with small nucleic acids: analytic treatment of the large coulombic end effect on binding free energy as a function of salt concentration

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2336898

5 June 2018

Effects of monovalent anions on a temperature-dependent heat capacity change for Escherichia coli SSB tetramer binding to single-stranded DNA

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2336898

5 June 2018

Bacteriophage lambda gpNu1 and Escherichia coli IHF proteins cooperatively bind and bend viral DNA: implications for the assembly of a genome-packaging motor.

1 reference

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5 June 2018

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

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5 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=2336898

5 June 2018

DNA-binding domain of GCN4 induces bending of both the ATF/CREB and AP-1 binding sites of DNA.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2336898

5 June 2018

Interactions of the KWK6 cationic peptide with short nucleic acid oligomers: demonstration of large Coulombic end effects on binding at 0.1-0.2 M salt

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2336898

5 June 2018

The C-terminal domain of DNA gyrase A adopts a DNA-bending beta-pinwheel fold

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2336898

5 June 2018

ModLoop: automated modeling of loops in protein structures

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2336898

5 June 2018

NEUTRAL SALTS: THE GENERALITY OF THEIR EFFECTS ON THE STABILITY OF MACROMOLECULAR CONFORMATIONS.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2336898

5 June 2018

Electrostatic interactions in a peptide--RNA complex.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2336898

5 June 2018

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=2336898

5 June 2018

Solvent mediated interactions in the structure of the nucleosome core particle at 1.9 a resolution

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2336898

5 June 2018

Stopped-flow studies of the kinetics of single-stranded DNA binding and wrapping around the Escherichia coli SSB tetramer

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2336898

5 June 2018

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=2336898

5 June 2018

Architecture of nucleotide excision repair complexes: DNA is wrapped by UvrB before and after damage recognition

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2336898

5 June 2018

Structure of the DNA binding domain of E. coli SSB bound to ssDNA

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2336898

5 June 2018

Global structure similarities of intact and nicked DNA complexed with IHF measured in solution by fluorescence resonance energy transfer

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2336898

5 June 2018

Wrapping of DNA around the E.coli RNA polymerase open promoter complex

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2336898

5 June 2018

A model for the mechanism of strand passage by DNA gyrase

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2336898

5 June 2018

In vitro selection of integration host factor binding sites

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2336898

5 June 2018

A quantitative UV laser footprinting analysis of the interaction of IHF with specific binding sites: re-evaluation of the effective concentration of IHF in the cell.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2336898

5 June 2018

Crystal structure of the nucleosome core particle at 2.8 A resolution

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2336898

5 June 2018

Electrostatic effects in homeodomain-DNA interactions.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2336898

5 June 2018

Crystal structure of an IHF-DNA complex: a protein-induced DNA U-turn

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2336898

5 June 2018

How Hofmeister ion interactions affect protein stability

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2336898

5 June 2018

The solution structure of the four-way DNA junction at low-salt conditions: a fluorescence resonance energy transfer analysis

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2336898

5 June 2018

On the magnitude of the electrostatic contribution to ligand-DNA interactions

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2336898

5 June 2018

The specific binding of Escherichia coli integration host factor involves both major and minor grooves of DNA.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2336898

5 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=2336898

5 June 2018

Interactions of bacteriophage T4-coded gene 32 protein with nucleic acids. I. Characterization of the binding interactions

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2336898

5 June 2018

Overproduction of Escherichia coli integration host factor, a protein with nonidentical subunits

1 reference

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5 June 2018

Equilibrium binding of Escherichia coli single-strand binding protein to single-stranded nucleic acids in the (SSB)65 binding mode. Cation and anion effects and polynucleotide specificity.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2336898

5 June 2018

Integration host factor: a protein for all reasons.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2336898

5 June 2018

Monte Carlo description of oligoelectrolyte properties of DNA oligomers: range of the end effect and the approach of molecular and thermodynamic properties to the polyelectrolyte limits

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2336898

5 June 2018

Negative co-operativity in Escherichia coli single strand binding protein-oligonucleotide interactions. I. Evidence and a quantitative model

1 reference

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5 June 2018

Thermodynamic extent of counterion release upon binding oligolysines to single-stranded nucleic acids

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2336898

5 June 2018

Thermodynamic stoichiometries of participation of water, cations and anions in specific and non-specific binding of lac repressor to DNA. Possible thermodynamic origins of the "glutamate effect" on protein-DNA interactions

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2336898

5 June 2018

Fluorescence resonance energy transfer and nucleic acids

1 reference

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5 June 2018

Water as ligand: preferential binding and exclusion of denaturants in protein unfolding

1 reference

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5 June 2018

Electron microscopic study of (A)BC excinuclease. DNA is sharply bent in the UvrB-DNA complex

1 reference

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5 June 2018

Ion effects on ligand-nucleic acid interactions

1 reference

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5 June 2018

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

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5 June 2018

Nonspecific interactions of Escherichia coli RNA polymerase with native and denatured DNA: differences in the binding behavior of core and holoenzyme

1 reference

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5 June 2018

Direct measurement of association constants for the binding of Escherichia coli lac repressor to non-operator DNA

1 reference

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5 June 2018

Indirect recognition in sequence-specific DNA binding by Escherichia coli integration host factor: the role of DNA deformation energy

1 reference

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18 August 2018

Mutagenesis of PepA suggests a new model for the Xer/cer synaptic complex.

1 reference

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18 August 2018

The structural basis for substrate specificity in DNA topoisomerase IV.

1 reference

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18 August 2018

A superhelical spiral in the Escherichia coli DNA gyrase A C-terminal domain imparts unidirectional supercoiling bias.

1 reference

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18 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

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18 August 2018

The exclusion of glycine betaine from anionic biopolymer surface: why glycine betaine is an effective osmoprotectant but also a compatible solute

1 reference

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18 August 2018

Application of the local-bulk partitioning and competitive binding models to interpret preferential interactions of glycine betaine and urea with protein surface

1 reference

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18 August 2018

Binding of aminoglycoside antibiotics to the small ribosomal subunit: a continuum electrostatics investigation

1 reference

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18 August 2018

Concerted binding and bending of DNA by Escherichia coli integration host factor.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2336898

18 August 2018

Specific and non-specific interactions of integration host factor with DNA: thermodynamic evidence for disruption of multiple IHF surface salt-bridges coupled to DNA binding.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2336898

18 August 2018

Analysis of effects of salts and uncharged solutes on protein and nucleic acid equilibria and processes: a practical guide to recognizing and interpreting polyelectrolyte effects, Hofmeister effects, and osmotic effects of salts.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2336898

18 August 2018

Ion effects on the lac repressor-operator equilibrium

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2336898

18 August 2018

Extension of the theory of linked functions to incorporate the effects of protein hydration

1 reference

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18 August 2018

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

1 reference

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18 August 2018

The interaction of E. coli IHF protein with its specific binding sites.

1 reference

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18 August 2018

Salt effects on polyelectrolyte-ligand binding: comparison of Poisson-Boltzmann, and limiting law/counterion binding models

1 reference

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Thermodynamics of single-stranded RNA and DNA interactions with oligolysines containing tryptophan. Effects of base composition

1 reference

https://pubmed.ncbi.nlm.nih.gov/18237740

12 December 2020

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Thermodynamics of oligoarginines binding to RNA and DNA

1 reference

https://pubmed.ncbi.nlm.nih.gov/18237740

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Hofmeister salt effects on surface tension arise from partitioning of anions and cations between bulk water and the air-water interface

1 reference

https://pubmed.ncbi.nlm.nih.gov/18237740

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Wrapping of flanking non-operator DNA in lac repressor-operator complexes: implications for DNA looping

1 reference

https://pubmed.ncbi.nlm.nih.gov/18237740

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/18237740

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

DNA binding and bending by HMG boxes: energetic determinants of specificity

1 reference

https://pubmed.ncbi.nlm.nih.gov/18237740

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Calorimetric studies of E. coli SSB protein-single-stranded DNA interactions. Effects of monovalent salts on binding enthalpy

1 reference

https://pubmed.ncbi.nlm.nih.gov/18237740

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Equilibrium dialysis studies of polyamine binding to DNA

1 reference

https://pubmed.ncbi.nlm.nih.gov/18237740

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Thermodynamics of single-stranded RNA binding to oligolysines containing tryptophan

1 reference

https://pubmed.ncbi.nlm.nih.gov/18237740

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

Identifiers

10.1016/J.JMB.2007.11.104

1 reference

Europe PubMed Central

PMC publication ID

14 October 2017

PMC publication ID

1 reference

Europe PubMed Central

PMC publication ID

14 October 2017

PubMed publication ID

1 reference

Europe PubMed Central

PMC publication ID

14 October 2017

ResearchGate publication ID

0 references

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