Physical basis of metal-binding specificity in Escherichia coli NikR (Q41893966)

13 October 2017

Physical basis of metal-binding specificity in Escherichia coli NikR (English)

1 reference

13 October 2017

Escherichia coli

1 reference

Christine M Phillips

1

1 reference

13 October 2017

Paul S Nerenberg

series ordinal

2

1 reference

13 October 2017

Catherine L Drennan

series ordinal

3

1 reference

13 October 2017

Collin M Stultz

series ordinal

4

1 reference

13 October 2017

language of work or name

English

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publication date

1 July 2009

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13 October 2017

9

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Journal of the American Chemical Society

inferred from page(s)

published in

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13 October 2017

131

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13 October 2017

29

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13 October 2017

10220-10228

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Helicobacter pylori NikR's interaction with DNA: a two-tiered mode of recognition

13 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3579654

Molecular dynamics simulations of nucleic acid-protein 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=3579654

Structural basis of the metal specificity for nickel regulatory protein NikR

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3579654

Continuum molecular electrostatics, salt effects, and counterion binding--a review of the Poisson-Boltzmann theory and its modifications

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3579654

Nickel-specific response in the transcriptional regulator, Escherichia coli NikR.

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3579654

Characterization of the Helicobacter pylori NikR-P(ureA) DNA interaction: metal ion requirements and sequence specificity

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3579654

Helicobacter pylori HP1512 is a nickel-responsive NikR-regulated outer membrane protein

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3579654

NikR-operator complex structure and the mechanism of repressor activation by metal ions

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3579654

Crystallization and preliminary crystallographic analysis of the nickel-responsive regulator NikR from Pyrococcus horikoshii

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3579654

Microbial nickel metalloregulation: NikRs for nickel ions

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3579654

Structure of Pyrococcus horikoshii NikR: nickel sensing and implications for the regulation of DNA 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=3579654

Coot: model-building tools for molecular graphics

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3579654

Computational and experimental probes of symmetry mismatches in the Arc repressor-DNA complex.

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3579654

Announcing the worldwide Protein Data Bank

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3579654

A Structural Model that Explains the Effects of Hyperglycemia on Collagenolysis

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3579654

Crystal structure of the nickel-responsive transcription factor NikR

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3579654

Nickel uptake and utilization by microorganisms

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3579654

Structure, dynamics and electrostatics of the active site of glutaredoxin 3 from Escherichia coli: comparison with functionally related 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=3579654

NMR and molecular dynamics studies of the hydration of a zinc finger-DNA complex

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3579654

Calculating structures and free energies of complex molecules: combining molecular mechanics and continuum 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=3579654

Regulation of high affinity nickel uptake in bacteria. Ni2 -Dependent interaction of NikR with wild-type and mutant operator sites

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3579654

Canonical dynamics: Equilibrium phase-space distributions

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3579654

A 5-nanosecond molecular dynamics trajectory for B-DNA: analysis of structure, motions, and solvation

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3579654

Alternative respiratory pathways of Escherichia coli: energetics and transcriptional regulation in response to electron acceptors

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3579654

Structural changes at the metal ion binding site during the phosphoglucomutase reaction

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3579654

Antagonistic effect of nickel on the fermentative growth of Escherichia coli K-12 and comparison of nickel and cobalt toxicity on the aerobic and anaerobic growth

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3579654

Cation transport in Escherichia coli. VI. K exchange

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3579654

Active site dynamics in protein molecules: a stochastic boundary molecular-dynamics approach.

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3579654

Extracting hydrophobic free energies from experimental data: relationship to protein folding and theoretical 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=3579654

Protein folding and association: insights from the interfacial and thermodynamic properties of hydrocarbons

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3579654

Detailed microscopic study of the full zipA:FtsZ interface.

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3579654

Structure of the azurin mutant nickel-Trp48Met from Pseudomonas aeruginosa at 2.2 A resolution

18 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3579654

Metal-selective DNA-binding response of Escherichia coli NikR.

18 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3579654

Selectivity of metal binding and metal-induced stability of Escherichia coli NikR.

18 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3579654

Nickel coordination is regulated by the DNA-bound state of NikR.

18 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3579654

NikR repressor: high-affinity nickel binding to the C-terminal domain regulates binding to operator DNA.

18 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3579654

Dynamic ligand design and combinatorial optimization: designing inhibitors to endothiapepsin

18 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3579654

Free energy simulations: the meaning of the individual contributions from a component analysis.

18 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3579654

Structural basis of the nickel response in Helicobacter pylori: crystal structures of HpNikR in Apo and nickel-bound states

18 August 2018

1 reference

12 December 2020

Molecular dynamics study of a hyperthermophilic and a mesophilic rubredoxin

1 reference

12 December 2020

Coordination geometries of selected transition metal ions (Co2 , Ni2 , Cu2 , Zn2 , Cd2 , and Hg2 ) in metalloproteins

1 reference

12 December 2020

Metal-ligand geometry relevant to proteins and in proteins: sodium and potassium

1 reference

12 December 2020

Zinc binding in proteins and solution: a simple but accurate nonbonded representation

1 reference

12 December 2020

Identifiers

DOI

10.1021/JA9026314

1 reference

13 October 2017

1 reference

13 October 2017

PubMed publication ID

19621966

1 reference