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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
Dynamics of proton transfer in bacteriorhodopsin
1Center for Molecular Modeling, Center for Information Technology, National Institutes of Health, Bethesda, Maryland 20892, USA. leeys@mail.nih.gov
Journal of the American Chemical Society
|February 20, 2004
Summary
Proton transfer in bacteriorhodopsin occurs via a water channel, even through hydrophobic regions. This rapid, concerted event facilitates proton movement from Asp96 to the Schiff base.
Area of Science:
- Biophysics
- Structural Biology
- Computational Chemistry
Background:
- Bacteriorhodopsin facilitates proton transport across membranes.
- Proton transfer is crucial for energy transduction.
- The mechanism of proton transfer through hydrophobic channels remains unclear.
Purpose of the Study:
- To investigate the mechanism of proton transfer through a partially hydrophobic channel in bacteriorhodopsin.
- To elucidate the role of water molecules in facilitating proton transfer.
- To understand the dynamics of proton transfer from Asp96 to the Schiff base.
Main Methods:
- A quantum mechanics/molecular mechanics (QM/MM) model was constructed using the bacteriorhodopsin E204Q mutant crystal structure.
- Ab initio dynamics simulations were performed using the CHARMM/GAMESS methodology.
- Key residues (Asp96, Asp85, Thr89) and the retinal chromophore were treated quantum mechanically.
Main Results:
- A water channel forms between Asp96 and the Schiff base in the M state.
- Proton transfer occurs as a fast (<1 ps), concerted event once a water chain is established.
- The proton transfer is independent of the protonation state of Asp85.
- The transfer is initiated by proton donation from Asp96 to the nearest water molecule.
Conclusions:
- Water molecules are essential for mediating proton transfer through hydrophobic regions of bacteriorhodopsin.
- A concerted, rapid proton transfer mechanism is facilitated by a structured water chain.
- This study provides insights into proton transfer dynamics in biological systems.
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