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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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Updated: Mar 30, 2026

Proton Transfer and Protein Conformation Dynamics in Photosensitive Proteins by Time-resolved Step-scan Fourier-transform Infrared Spectroscopy
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Proteorhodopsin Activation Is Modulated by Dynamic Changes in Internal Hydration.

Jun Feng1, Blake Mertz1

  • 1The C. Eugene Bennett Department of Chemistry, West Virginia University , 217 Clark Hall, Morgantown, West Virginia 26506, United States.

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Molecular dynamics simulations reveal that water molecules are crucial for proteorhodopsin

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Area of Science:

  • Biophysics
  • Structural Biology
  • Molecular Dynamics

Background:

  • Proteorhodopsin is a light-driven proton pump essential for cellular energy generation.
  • Its mechanism relies on intricate proton transfer pathways involving amino acids and water.
  • Understanding these pathways requires detailed structural and dynamic insights.

Purpose of the Study:

  • To elucidate the role of internal hydration in proteorhodopsin's proton-pumping mechanism.
  • To investigate the dynamic hydrogen-bonding networks involving water molecules.
  • To characterize water's contribution to proton transfer in photoactivated states.

Main Methods:

  • Microsecond timescale molecular dynamics simulations.
  • Analysis of dark and photoactivated states of blue proteorhodopsin.
  • Focus on protein internal hydration and water-mediated interactions.

Main Results:

  • Dynamic hydrogen-bonding networks involving water molecules facilitate proton transfer.
  • High hydration levels observed at key proton transfer sites (retinal pocket, uptake/release sites).
  • Increased water flux observed after retinal isomerization, connecting release and binding sites.

Conclusions:

  • Internal hydration is critical for proteorhodopsin's proton-pumping function.
  • Water molecules and channels mediate proton transfer across the protein.
  • Findings provide a foundation for understanding hydration's role in microbial retinal proteins.