Evidence map›Paper›PMID 26061742›Full record

ArticleScientific reports2015

Origin of the low thermal isomerization rate of rhodopsin chromophore.

Masataka Yanagawa, Keiichi Kojima, Takahiro Yamashita, Yasushi Imamoto, Take Matsuyama, Koji Nakanishi, Yumiko Yamano, Akimori Wada, Yasushi Sako, Yoshinori Shichida

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 26 papers.

0numbers the graph read from it
0cells of the map it votes in
26citing papers in PubMed
2.2field-weighted citation impact, top 13% 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

26 citing papers in PubMed, 55 citations in OpenAlex.

  1. Article
  2. Article
  3. Structure of human green cone opsin yields insights into mechanisms underlying the rapid decay of its active, signaling state.Proceedings of the National Academy of Sciences of the United States of America · 2025
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  5. Thermosensory Roles of G Protein-Coupled Receptors and Other Cellular Factors in Animals.BioEssays : news and reviews in molecular, cellular and developmental biology · 2025
    Review
  6. Article
  7. Whale shark rhodopsin adapted to deep-sea lifestyle by a substitution associated with human disease.Proceedings of the National Academy of Sciences of the United States of America · 2023
    Article
  8. Review
  9. Article
  10. Phototransduction in Anuran Green Rods: Origins of Extra-Sensitivity.International journal of molecular sciences · 2021
    Article
  11. Article
  12. Article
  13. Visual cells and visual pigments of the river lamprey revisited.Journal of comparative physiology. A, Neuroethology, sensory, neural, and behavioral physiology · 2020
    Article
  14. Article
  15. Article
  16. Article
  17. Apo-Opsin Exists in Equilibrium Between a Predominant Inactive and a Rare Highly Active State.The Journal of neuroscience : the official journal of the Society for Neuroscience · 2019
    Article
  18. Article
  19. Adaptation of cone pigments found in green rods for scotopic vision through a single amino acid mutation.Proceedings of the National Academy of Sciences of the United States of America · 2017
    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

10 authors at 4 institutions in 2 countries.

Masataka YanagawaCellular Informatics Laboratory, RIKEN, 2-1 Hirosawa, Wako 351-0198, Japan.
Keiichi KojimaDepartment of Biophysics, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan.
Takahiro YamashitaDepartment of Biophysics, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan.
Yasushi ImamotoDepartment of Biophysics, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan.
Take MatsuyamaDepartment of Biophysics, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan.
Koji NakanishiDepartment of Chemistry, Columbia University, New York, NY 10027, USA.
Yumiko YamanoDepartment of Organic Chemistry for Life Science, Kobe Pharmaceutical University, Kobe 658-8558, Japan.
Akimori WadaDepartment of Organic Chemistry for Life Science, Kobe Pharmaceutical University, Kobe 658-8558, Japan.
Yasushi SakoCellular Informatics Laboratory, RIKEN, 2-1 Hirosawa, Wako 351-0198, Japan.
Yoshinori ShichidaDepartment of Biophysics, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan.
Kyoto University · JPKobe Pharmaceutical University · JPRIKEN Advanced Science Institute · JPColumbia University · US

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Low dark noise is a prerequisite for rod cells, which mediate our dim-light vision. The low dark noise is achieved by the extremely stable character of the rod visual pigment, rhodopsin, which evolved from less stable cone visual pigments. We have developed a biochemical method to quickly evaluate the thermal activation rate of visual pigments. Using an isomerization locked chromophore, we confirmed that thermal isomerization of the chromophore is the sole cause of thermal activation. Interestingly, we revealed an unexpected correlation between the thermal stability of the dark state and that of the active intermediate MetaII. Furthermore, we assessed key residues in rhodopsin and cone visual pigments by mutation analysis and identified two critical residues (E122 and I189) in the retinal binding pocket which account for the extremely low thermal activation rate of rhodopsin.

Indexed as

Protein MultimerizationThermodynamicsAmino AcidsModels, MolecularProtein BindingProtein ConformationRetinaRhodopsinAmino AcidsRhodopsin

Identifiers

PMID26061742
PMCPMC4462023
OpenAlexW2200929956

What OpenQuestion holds

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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.