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Related Concept Videos

Channel Rhodopsins01:11

Channel Rhodopsins

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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.
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At the molecular level, visual signals trigger transformations in photopigment molecules, resulting in changes in the photoreceptor cell's membrane potential. The photon's energy level is denoted by its wavelength, with each specific wavelength of visible light associated with a distinct color. The spectral range of visible light, classified as electromagnetic radiation, spans from 380 to 720 nm. Electromagnetic radiation wavelengths exceeding 720 nm fall under the infrared category,...
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Reaction centers are pigment-protein complexes that initiate energy conversion from photons to chemical entities. Therefore, photochemical reaction center is a more appropriate term that describes these complexes. The Nobel laureates Robert Emerson and William Arnold provided the first experimental evidence of photochemical reaction centers by demonstrating the participation of nearly 2,500 chlorophyll molecules for the release of just one molecule of oxygen. Despite thousands of photosynthetic...
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Plants and other photosynthetic organisms comprise pigments capable of absorption of direct sunlight. These pigments are present in the reaction center - the main site of photochemical reactions as well as in the antenna complex. Under average light conditions, the rate at which reaction center pigments absorb light is far below the electron transport chain's capacity. As a result, the reaction center alone cannot provide enough energy to drive photosynthesis. The photosynthetic efficiency can...
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The retina is a layer of nervous tissue at the back of the eye that transduces light into neural signals. This process, called phototransduction, is carried out by rod and cone photoreceptor cells in the back of the retina.
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The absorption of UV–visible light by conjugated systems causes the promotion of an electron from the ground state to the excited state. Consequently, photochemical electrocyclic reactions proceed via the excited-state HOMO rather than the ground-state HOMO. Since the ground- and excited-state HOMOs have different symmetries, the stereochemical outcome of electrocyclic reactions depends on the mode of activation; i.e., thermal or photochemical.
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Related Experiment Video

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Proton Transfer and Protein Conformation Dynamics in Photosensitive Proteins by Time-resolved Step-scan Fourier-transform Infrared Spectroscopy
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A multi-scale-multi-stable model for the rhodopsin photocycle.

Francesco Tavanti1, Valentina Tozzini2

  • 1NEST-Istituto Nanoscienze, CNR, Piazza San Silvestro 12, 56127 Pisa, Italy.

Molecules (Basel, Switzerland)
|September 20, 2014
PubMed
Summary

This study introduces a novel multi-scale simulation method combining united atoms (UA) and coarse-grained (CG) models to analyze the rhodopsin photocycle. The approach accurately captures meta-stable states and transitions, validated against experimental data for bacterial and mammalian rhodopsins.

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Area of Science:

  • Biophysics
  • Computational Biology
  • Molecular Dynamics

Background:

  • Rhodopsins are crucial membrane proteins involved in light sensing.
  • Understanding the rhodopsin photocycle is essential for various biological processes.
  • Previous simulation studies faced limitations in scale and accuracy.

Purpose of the Study:

  • To develop and validate a novel multi-scale simulation approach for the rhodopsin photocycle.
  • To accurately model the transitions between different functional states of rhodopsins.
  • To investigate the spontaneous emergence of meta-stable states in rhodopsin function.

Main Methods:

  • A hybrid quasi-atomistic (united atoms, UA) and coarse-grained (CG) simulation model was employed.
  • The model combines a detailed representation of retinal with a simplified protein structure (one-bead-per-amino acid).
  • Multi-stable parameterization enabled simulation of distinct states and transitions, analogous to QM/MM but at lower resolution.

Main Results:

  • The UA/CG model successfully simulated the entire photocycle of bacterial rhodopsin.
  • Simulations revealed the spontaneous appearance of meta-stable states.
  • Results for mammalian rhodopsins were also reported, showing quantitative agreement with experimental data.

Conclusions:

  • The developed multi-scale simulation strategy offers a powerful tool for studying rhodopsin dynamics.
  • The model accurately reproduces experimentally observed meta-stable states and photocycle transitions.
  • This approach facilitates a deeper understanding of light-driven molecular mechanisms in rhodopsins.