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Related Concept Videos

Channel Rhodopsins01:11

Channel Rhodopsins

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,...
G-Protein Gated Ion Channels01:21

G-Protein Gated Ion Channels

GPCRs are primarily responsible for our sense of smell, taste, and vision.  The binding of a sensory stimulus activates GPCR to stimulate effector proteins, many of which are ion channels in the sensory organs. GPCRs modulate the opening and closing of the target ion channels either directly by binding them, or by releasing second messengers that activate these channels. As ions move across the membrane, the membrane potential is altered, which induces an appropriate response.
Sensory organs,...
Photoreceptors and Visual Pathways01:22

Photoreceptors and Visual Pathways

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, whereas...
The Photochemical Reaction Center01:29

The Photochemical Reaction Center

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...
Mechanically-gated Ion Channels01:12

Mechanically-gated Ion Channels

Mechanically-gated ion channels are proteins found in eukaryotic and prokaryotic cell membranes that open in response to mechanical stress. Tension, compression, swelling, and shear stress can alter the conformation of the protein, opening a transmembrane channel that allows the passage of ions for signal transmission. In eukaryotes, mechanically-gated channels are distributed in several regions like the neurons, lungs, skin, bladder, and heart, where they play critical roles in numerous...
Electron Transport Chain Components01:29

Electron Transport Chain Components

The electron transport chain (ETC) is a crucial metabolic pathway that facilitates energy conversion in prokaryotic and eukaryotic cells. In eukaryotes, the ETC comprises four membrane-associated protein complexes in the inner mitochondrial membrane. In prokaryotes, the ETC in the plasma membrane can vary in composition, with fewer or different complexes depending on the organism and environmental conditions. These complexes transfer electrons from electron donors, such as NADH and FADH2, to...

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Updated: Jun 27, 2026

Proton Transfer and Protein Conformation Dynamics in Photosensitive Proteins by Time-resolved Step-scan Fourier-transform Infrared Spectroscopy
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Proton Transfer and Protein Conformation Dynamics in Photosensitive Proteins by Time-resolved Step-scan Fourier-transform Infrared Spectroscopy

Published on: June 27, 2014

Potential proton-release channels in bacteriorhodopsin.

Alain Chaumont1, Marcel Baer, Gerald Mathias

  • 1Lehrstuhl für Theoretische Chemie, Ruhr-Universität Bochum, 44780 Bochum, Germany.

Chemphyschem : a European Journal of Chemical Physics and Physical Chemistry
|November 28, 2008
PubMed
Summary
This summary is machine-generated.

Bacteriorhodopsin uses proton transfer channels to release protons during its pumping cycle. Biomolecular simulations reveal two distinct channels, one gated by specific amino acids, facilitating efficient proton release via water networks.

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Area of Science:

  • Biophysics
  • Structural Biology
  • Membrane Protein Function

Background:

  • Bacteriorhodopsin is a light-driven proton pump essential for cellular energy generation.
  • Its function relies on a complex proton transfer cycle involving a retinal cofactor and multiple protonation sites.
  • Understanding the final proton release step is crucial for elucidating the overall pumping mechanism.

Purpose of the Study:

  • To investigate the molecular mechanisms of proton release from bacteriorhodopsin to the extracellular environment.
  • To identify and characterize potential proton release pathways.
  • To elucidate the role of water molecules and specific amino acid residues in facilitating proton transfer.

Main Methods:

  • Utilized biomolecular simulations to model proton transfer pathways in bacteriorhodopsin.
  • Analyzed the L photointermediate state to observe water dynamics and hydrogen-bonded networks.
  • Investigated the function of specific amino acid residues (Arg7, Glu9, Tyr79, Asn76/Pro77, Arg134/Lys129) in gating and facilitating proton release.

Main Results:

  • Proposed two distinct proton release channels connecting the release pocket to the extracellular medium.
  • Observed water molecules entering these channels and forming transient hydrogen-bonded networks, enabling Grotthuss mechanism-based proton transfer.
  • Identified a gating mechanism involving Arg7, Glu9, and Tyr79 in the first channel.
  • Characterized two release paths in the second channel, involving direct bulk exchange or diffusion towards Arg134/Lys129.

Conclusions:

  • The identified proton release channels are critical for the efficient functioning of bacteriorhodopsin.
  • Water molecules and specific amino acid residues play vital roles in mediating and regulating proton release.
  • These findings provide new insights into the terminal steps of the bacteriorhodopsin proton pumping cycle.