Evidence map›Paper›PMID 27585742›Full record

ArticleNature communications2016

Retinal orientation and interactions in rhodopsin reveal a two-stage trigger mechanism for activation.

Naoki Kimata, Andreyah Pope, Markus Eilers, Chikwado A Opefi, Martine Ziliox, Amiram Hirshfeld, Ekaterina Zaitseva, Reiner Vogel, Mordechai Sheves, Philip J Reeves and 1 more

Abstract read
In one paragraph

Article in Nature communications, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers.

0numbers the graph read from it
0cells of the map it votes in
25citing papers in PubMed
–field-weighted citation impact
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

25 citing papers in PubMed.

  1. Article
  2. Article
  3. Article
  4. Review
  5. Coordination of bilayer properties by an inward-rectifier KJournal of structural biology: X · 2024
    Article
  6. Article
  7. Article
  8. Article
  9. Review
  10. Hydration-mediated G-protein-coupled receptor activation.Proceedings of the National Academy of Sciences of the United States of America · 2022
    Article
  11. Magic angle spinning NMR of G protein-coupled receptors.Progress in nuclear magnetic resonance spectroscopy · 2022
    Review
  12. Review
  13. Article
  14. Article
  15. Article
  16. Review
  17. Article
  18. Review
  19. Crystal structure of jumping spider rhodopsin-1 as a light sensitive GPCR.Proceedings of the National Academy of Sciences of the United States of America · 2019
    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

11 authors.

Naoki KimataDepartment of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, New York 11794-5215, USA.
Andreyah PopeDepartment of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, New York 11794-5215, USA.
Markus EilersDepartment of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, New York 11794-5215, USA.
Chikwado A OpefiSchool of Biological Sciences, University of Essex, Wivenhoe Park, Essex CO4 3SQ, UK.
Martine ZilioxDepartment of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, New York 11794-5215, USA.
Amiram HirshfeldDepartment of Organic Chemistry, Weizmann Institute, Rehovot 76100 Israel.
Ekaterina ZaitsevaUniversity of Freiburg, Institute of Physiology II, D79104 Freiburg Germany.
Reiner VogelBiophysics Section, Institute of Molecular Medicine and Cell Research, Albert-Ludwigs-University, D-79104 Freiburg, Germany.
Mordechai ShevesDepartment of Organic Chemistry, Weizmann Institute, Rehovot 76100 Israel.
Philip J ReevesSchool of Biological Sciences, University of Essex, Wivenhoe Park, Essex CO4 3SQ, UK.
Steven O SmithDepartment of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, New York 11794-5215, USA.ORCID 0000-0003-1861-7159

Funding

Structure and Activation Mechanism of the Visual Pigment RhodopsinR01GM041412 · NIGMS · YALE UNIVERSITY · PI SMITH, STEVEN OWEN · 1989 to 2014
$4.4M
NIGMS NIH HHS R01 GM041412
6 · The paper itself

Abstract

The 11-cis retinal chromophore is tightly packed within the interior of the visual receptor rhodopsin and isomerizes to the all-trans configuration following absorption of light. The mechanism by which this isomerization event drives the outward rotation of transmembrane helix H6, a hallmark of activated G protein-coupled receptors, is not well established. To address this question, we use solid-state NMR and FTIR spectroscopy to define the orientation and interactions of the retinal chromophore in the active metarhodopsin II intermediate. Here we show that isomerization of the 11-cis retinal chromophore generates strong steric interactions between its β-ionone ring and transmembrane helices H5 and H6, while deprotonation of its protonated Schiff's base triggers the rearrangement of the hydrogen-bonding network involving residues on H6 and within the second extracellular loop. We integrate these observations with previous structural and functional studies to propose a two-stage mechanism for rhodopsin activation.

Indexed as

Cell LineHEK293 CellsHumansModels, MolecularNuclear Magnetic Resonance, BiomolecularProtein Structure, TertiaryRetinaRetinaldehydeRhodopsinSpectroscopy, Fourier Transform InfraredmetarhodopsinsRetinaldehydeRhodopsin

Identifiers

PMID27585742
PMCPMC5025775

What OpenQuestion holds

Textmetadata
LicenceCC BY
Read underepoch 390

Registered trials

None linked

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.