Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Concept Videos

Ligand Binding Sites02:40

Ligand Binding Sites

15.9K
Proteins are dynamic macromolecules that carry out a wide variety of essential processes; however, the activities of most proteins depend on their interactions with other molecules or ions, known as ligands.
Protein-ligand interactions are quite specific; even though numerous potential ligands surround a cellular protein at any given time, only a particular ligand can bind to that protein. Moreover, a ligand binds only to a dedicated area on the surface of the protein, known as the...
15.9K
Channel Rhodopsins01:11

Channel Rhodopsins

3.5K
Most organisms use photoreceptors to sense and respond to light. Examples of photoreceptors include bacteriorhodopsins and bacteriophytochromes in some bacteria, phytochromes in plants, and rhodopsins in the photoreceptor cells of the vertebral retina. The light-sensitive property of these receptors is because of the bound chromophores, such as bilin in the phytochromes and retinal in the rhodopsins.
Rhodopsins belong to the family of cell surface proteins called G-protein coupled receptors,...
3.5K

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by
Same author

Characterization of Recombinant GMPR from <i>Pocillopora damicornis</i> and Potential Mechanisms of Cold-Induced Metabolic Adaptation.

Biology·2026
Same author

Drug design using unique conformations to preferentially target a specific site on collagen-bound MMP1.

bioRxiv : the preprint server for biology·2026
Same author

Author Correction: 7-Dehydrocholesterol is an endogenous suppressor of ferroptosis.

Nature·2026
Same author

Three Unrelated Children With Childhood Apraxia of Speech: Exome Sequencing and Functional Gene Analysis Imply a Role of Laminin-511 in Early Neurodevelopment.

Case reports in genetics·2026
Same author

Allostery-Driven Substrate Gating in the Chlorothalonil Dehalogenase from <i>Pseudomonas</i> sp. CTN-3.

Biology·2026
Same author

Speech and Language Development of Two Brothers With Bainbridge-Ropers Syndrome: Phenotypic and Bioinformatic Support for a Cerebellar ASXL3 Hypothesis.

American journal of medical genetics. Part A·2025

Related Experiment Video

Updated: Apr 11, 2026

Author Spotlight: Unraveling Vitamin A Transport Mechanisms &#8212; Linking Liver Receptors to Vision Health Through RBPR2 and RBP4 Interactions
08:18

Author Spotlight: Unraveling Vitamin A Transport Mechanisms — Linking Liver Receptors to Vision Health Through RBPR2 and RBP4 Interactions

Published on: October 4, 2024

1.6K

Comprehensive and quantitative molecular docking analysis of rhodopsin-retinal interactions.

Aditya Lakshminarasimhan1, Chase Harms1, Judith Klein-Seetharaman1

  • 1School of Molecular Sciences and College of Health Solutions, Arizona State University, Phoenix, Arizona.

Biophysical Journal
|April 10, 2026
PubMed
Summary

This study quantifies retinal binding to various rhodopsin structures, revealing that photo-intermediate states exhibit higher affinity for both retinal forms, offering new insights into vision protein activation.

More Related Videos

A Rhodopsin Transport Assay by High-Content Imaging Analysis
12:11

A Rhodopsin Transport Assay by High-Content Imaging Analysis

Published on: January 16, 2019

7.0K
Strategic Screening and Characterization of the Visual GPCR-mini-G Protein Signaling Complex for Successful Crystallization
09:19

Strategic Screening and Characterization of the Visual GPCR-mini-G Protein Signaling Complex for Successful Crystallization

Published on: March 16, 2020

7.7K

Related Experiment Videos

Last Updated: Apr 11, 2026

Author Spotlight: Unraveling Vitamin A Transport Mechanisms &#8212; Linking Liver Receptors to Vision Health Through RBPR2 and RBP4 Interactions
08:18

Author Spotlight: Unraveling Vitamin A Transport Mechanisms — Linking Liver Receptors to Vision Health Through RBPR2 and RBP4 Interactions

Published on: October 4, 2024

1.6K
A Rhodopsin Transport Assay by High-Content Imaging Analysis
12:11

A Rhodopsin Transport Assay by High-Content Imaging Analysis

Published on: January 16, 2019

7.0K
Strategic Screening and Characterization of the Visual GPCR-mini-G Protein Signaling Complex for Successful Crystallization
09:19

Strategic Screening and Characterization of the Visual GPCR-mini-G Protein Signaling Complex for Successful Crystallization

Published on: March 16, 2020

7.7K

Area of Science:

  • Biochemistry
  • Structural Biology
  • Vision Science

Background:

  • Rhodopsin, a G-protein coupled receptor, is crucial for vertebrate vision.
  • Numerous rhodopsin structures in different conformational states are available, enabling large-scale interaction analysis.
  • Understanding retinal binding dynamics is key to elucidating rhodopsin activation.

Purpose of the Study:

  • To quantitatively analyze retinal binding affinities across diverse rhodopsin conformational states.
  • To compare the binding of 11-cis-retinal and all-trans-retinal to various rhodopsin structures.
  • To investigate how protein binding partners and mutations affect retinal-rhodopsin interactions.

Main Methods:

  • Database creation of 66 bovine rhodopsin structures from the Protein Data Bank.
  • Classification of structures into dark-state, opsin, meta-rhodopsin II, and photo-intermediate states.
  • Computational analysis using DiffDock and GNINA for minimized affinity calculations.

Main Results:

  • Meta-rhodopsin II structures preferentially bind all-trans-retinal; dark-state structures bind 11-cis-retinal.
  • Photo-intermediate states (lumi- and batho-rhodopsin) show enhanced binding affinity for both retinal isomers due to pocket flexibility.
  • Retinal binding affinity decreases in opsin and active states bound to proteins.

Conclusions:

  • Rhodopsin's binding pocket flexibility significantly influences retinal affinity across different conformational states.
  • The study provides quantitative data on retinal-rhodopsin interactions, advancing our understanding of the visual cycle.
  • Novel insights into the rhodopsin activation mechanism are offered through large-scale structural and computational analysis.