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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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Water pathways in the bacteriorhodopsin proton pump.

Ana-Nicoleta Bondar1, Stefan Fischer, Jeremy C Smith

  • 1Department of Physiology and Biophysics, Medical Science I, University of California at Irvine, Irvine, CA 92697-4560, USA. nicoleta.bondar@uci.edu

The Journal of Membrane Biology
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Summary

Internal water molecules are crucial for the bacteriorhodopsin proton pump. Computations reveal that while hydrogen bonds hinder water molecule w402 relocation, favorable interactions lower the energy cost, balancing the process.

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Area of Science:

  • Biophysics
  • Structural Biology
  • Computational Chemistry

Background:

  • The light-driven bacteriorhodopsin proton pump utilizes internal water molecules for its function.
  • The relocation of specific water molecules, like w402, across the retinal Schiff base is critical for the proton-pumping cycle.

Purpose of the Study:

  • To investigate the pathways and energetic factors governing the relocation of water molecule w402.
  • To understand the molecular mechanisms influencing water molecule movement during proton pumping.

Main Methods:

  • Classical mechanical computations.
  • Combined quantum mechanical/molecular mechanical (QM/MM) reaction path calculations.

Main Results:

  • Hydrogen bonding between w402 and Asp85/Asp212 significantly opposes water molecule repositioning.
  • Favorable hydrogen bonding with the Schiff base and Thr89, along with retinal polyene chain untwisting, reduces the energy barrier for w402 relocation.
  • A delicate balance exists between opposing and favorable energetic contributions to water relocation.

Conclusions:

  • The relocation of w402 is energetically feasible due to a balance of opposing and favorable interactions.
  • Accurate computational methods and detailed structural information are essential for understanding these complex processes.