Evidence map›Paper›PMID 25728261›Full record

ArticleScientific reports2015

Both piston-like and rotational motions are present in bacterial chemoreceptor signaling.

Daqi Yu, Xiaomin Ma, Yuhai Tu, Luhua Lai

Open access · goldAbstract read
In one paragraph

Article in Scientific reports, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.

0numbers the graph read from it
0cells of the map it votes in
20citing papers in PubMed
5.9field-weighted citation impact, top 4% of its field
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

20 citing papers in PubMed, 45 citations in OpenAlex.

  1. A chemoreceptor conformational equilibrium controlled by signaling inputs.Proceedings of the National Academy of Sciences of the United States of America · 2025
    Article
  2. Navigated range expansion promotes migratory culling.Proceedings of the National Academy of Sciences of the United States of America · 2024
    Article
  3. AlphaFold2 captures the conformational landscape of the HAMP signaling domain.Protein science : a publication of the Protein Society · 2024
    Article
  4. Article
  5. Discovery of a New Chemoeffector forACS bio & med chem Au · 2022
    Article
  6. Article
  7. Tasting the Terroir with Tsr.Biophysical journal · 2020
    Article
  8. Article
  9. Article
  10. Article
  11. Article
  12. Review
  13. Article
  14. Sensory Repertoire of Bacterial Chemoreceptors.Microbiology and molecular biology reviews : MMBR · 2017
    Review
  15. Article
  16. Article
  17. Identification of a Chemoreceptor inFrontiers in microbiology · 2016
    Article
  18. Article
  19. Article
  20. Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

4 authors at 2 institutions in 1 country.

Daqi Yu1] BNLMS, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, College of Chemistry and Molecular Engineering, Peking University, Beijing. 100871, China [2] Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing. 100871, China.
Xiaomin MaCenter for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing. 100871, China.
Yuhai Tu1] Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing. 100871, China [2] IBM T. J. Watson Research Center, Yorktown Heights, New York 10598, USA.
Luhua Lai1] BNLMS, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, College of Chemistry and Molecular Engineering, Peking University, Beijing. 100871, China [2] Center for Quantitative Biology, Academy for Advanced Interdisciplinary Studies, Peking University, Beijing. 100871, China [3] Peking-Tsinghua Center for Life Sciences, Peking University, Beijing. 100871, China.
Peking University · CNState Key Laboratory for Structural Chemistry of Unstable and Stable Species

Funding

Quantitative Modeling of Signal Transduction in Bacterial ChemotaxisR01GM081747 · NIGMS · IBM THOMAS J. WATSON RESEARCH CENTER · PI TU, YUHAI · 2007 to 2018
$2.6M
NIGMS NIH HHS GM081747NIGMS NIH HHS R01 GM081747
6 · The paper itself

Abstract

Bacterial chemotaxis signaling is triggered by binding of chemo-effectors to the membrane-bound chemoreceptor dimers. Though much is known about the structure of the chemoreceptors, details of the receptor dynamics and their effects on signaling are still unclear. Here, by using molecular dynamics simulations and principle component analysis, we study the dynamics of the periplasmic domain of aspartate chemoreceptor Tar dimer and its conformational changes when binding to different ligands (attractant, antagonist, and two attractant molecules). We found two dominant components (modes) in the receptor dynamics: a relative rotation of the two Tar monomers and a piston-like up-and-down sliding movement of the α4 helix. These two modes are highly correlated. Binding of one attractant molecule to the Tar dimer induced both significant piston-like downward movements of the α4 helix and strong relative rotations of the two Tar monomers, while binding of an antagonist or the symmetric binding of two attractant molecules to a Tar dimer suppresses both modes. The anti-symmetric effects of the relative rotation mode also explained the negative cooperativity between the two binding pockets. Our results suggest a mechanism of coupled rotation and piston-like motion for bacterial chemoreceptor signaling.

Indexed as

RotationSignal TransductionApoproteinsChemoreceptor CellsComputer SimulationEscherichia coliEscherichia coli ProteinsLigandsPrincipal Component AnalysisProtein BindingProtein Structure, SecondaryThermodynamicsApoproteinsEscherichia coli ProteinsLigands

Identifiers

PMID25728261
PMCPMC4345343
OpenAlexW1992677509

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Registered trials

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.