(Q40737258)

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Molecular dynamics simulation of the Escherichia coli NikR protein: equilibrium conformational fluctuations reveal interdomain allosteric communication pathways

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Europe PubMed Central

PMC publication ID

23 September 2017

Molecular dynamics simulation of the Escherichia coli NikR protein: equilibrium conformational fluctuations reveal interdomain allosteric communication pathways (English)

1 reference

Europe PubMed Central

PMC publication ID

23 September 2017

Escherichia coli

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3

1 reference

Europe PubMed Central

PMC publication ID

23 September 2017

Peter T Chivers

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Peter T Chivers

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author name string

Michael J Bradley

1

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Europe PubMed Central

PMC publication ID

23 September 2017

language of work or name

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publication date

14 March 2008

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Europe PubMed Central

PMC publication ID

23 September 2017

Journal of Molecular Biology

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Europe PubMed Central

PMC publication ID

23 September 2017

378

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Europe PubMed Central

PMC publication ID

23 September 2017

5

1 reference

Europe PubMed Central

PMC publication ID

23 September 2017

1155-1173

1 reference

Europe PubMed Central

PMC publication ID

23 September 2017

Large-scale allosteric conformational transitions of adenylate kinase appear to involve a population-shift mechanism

1 reference

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A study of communication pathways in methionyl- tRNA synthetase by molecular dynamics simulations and structure network analysis

1 reference

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Signal propagation in proteins and relation to equilibrium fluctuations

1 reference

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Nanosecond-timescale conformational dynamics of the human alpha7 nicotinic acetylcholine receptor

1 reference

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Computational protein design: structure, function and combinatorial diversity

1 reference

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A solution NMR study showing that active site ligands and nucleotides directly perturb the allosteric equilibrium in aspartate transcarbamoylase

1 reference

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

1 reference

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

1 reference

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Residues crucial for maintaining short paths in network communication mediate signaling in proteins

1 reference

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Common mechanism of pore opening shared by five different potassium channels

1 reference

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Determination of network of residues that regulate allostery in protein families using sequence analysis

1 reference

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The changing landscape of protein allostery

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Structural changes involved in protein binding correlate with intrinsic motions of proteins in the unbound state

1 reference

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1 reference

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Protease digestion analysis of Escherichia coli NikR: evidence for conformational stabilization with Ni(II).

1 reference

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WebLogo: A Sequence Logo Generator

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Multiconformational states in phosphoglycerate dehydrogenase

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ON THE NATURE OF ALLOSTERIC TRANSITIONS: A PLAUSIBLE MODEL

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Crystal structure of the nickel-responsive transcription factor NikR

1 reference

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Correlated motion and the effect of distal mutations in dihydrofolate reductase

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Classification and phylogeny of hydrogenases

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Analysis of a 10-ns molecular dynamics simulation of mouse acetylcholinesterase

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Structural determinants of MscL gating studied by molecular dynamics simulations

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Binding sites in Escherichia coli dihydrofolate reductase communicate by modulating the conformational ensemble

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A dynamic model for the allosteric mechanism of GroEL

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

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Exploring models of the influenza A M2 channel: MD simulations in a phospholipid bilayer

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Isolation and characterization of the nikR gene encoding a nickel-responsive regulator in Escherichia coli

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Essential dynamics of proteins

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

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1 reference

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1 reference

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1 reference

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1 reference

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1 reference

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

1 reference

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2478562

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

1 reference

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1 reference

https://pubmed.ncbi.nlm.nih.gov/18433769

12 December 2020

based on heuristic

inferred from PubMed ID database lookup

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

1 reference

https://pubmed.ncbi.nlm.nih.gov/18433769

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based on heuristic

inferred from PubMed ID database lookup

Scanning mutagenesis of the Arc represser as a functional probe of operator recognition

1 reference

https://pubmed.ncbi.nlm.nih.gov/18433769

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based on heuristic

inferred from PubMed ID database lookup

Dynamic Allostery in the Ring Protein TRAP

1 reference

https://pubmed.ncbi.nlm.nih.gov/18433769

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based on heuristic

inferred from PubMed ID database lookup

Sequence correlations between Cro recognition helices and cognate O(R) consensus half-sites suggest conserved rules of protein-DNA recognition

1 reference

https://pubmed.ncbi.nlm.nih.gov/18433769

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based on heuristic

inferred from PubMed ID database lookup

Fast and reliable analysis of molecular motion using proximity relations and dimensionality reduction

1 reference

https://pubmed.ncbi.nlm.nih.gov/18433769

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based on heuristic

inferred from PubMed ID database lookup

Large-amplitude nonlinear motions in proteins

1 reference

https://pubmed.ncbi.nlm.nih.gov/18433769

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based on heuristic

inferred from PubMed ID database lookup

Two-state allosteric behavior in a single-domain signaling protein

1 reference

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based on heuristic

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Identifiers

10.1016/J.JMB.2008.03.010

1 reference

Europe PubMed Central

PMC publication ID

23 September 2017

PMC publication ID

1 reference

Europe PubMed Central

PMC publication ID

23 September 2017

PubMed publication ID

1 reference

Europe PubMed Central

PMC publication ID

23 September 2017

ResearchGate publication ID

0 references

Sitelinks

Wikipedia(0 entries)

Wikibooks(0 entries)

Wikinews(0 entries)

Wikiquote(0 entries)

Wikisource(0 entries)

Wikiversity(0 entries)

Wikivoyage(0 entries)

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