Water pathways in the Bacteriorhodopsin proton pump.

A.N. Bondar, S. Fischer, J.C. Smith.

J. of Membrane Biology, vol. 239, p.73-84 (2011) .


The bacteriorhodopsin proton pump uses light to translocate one proton per photon across the plasma membrane. After photon absorption and electronic relaxation, the retinal chromophore is in a twisted cis conformation. Here we investigate whether, before the first proton transfer step (L to M state) occurs, the critical water molecule w402 can translocate from the extracellular to the cytoplasmic side of the cis-retinal Schiff base.
This is investigated by computing minimum energy paths with the Conjugate Peak Refinement (CPR) method, using a Quantum Mechanical/Molecular Mechanical (QM/MM) description of the protein.  Two pathways were investigated: one passing on the Thr89-side of retinal, the other passing on the Asp212-side of retinal.
The results show that using a purely classical description underestimates the barrier of translocation by ~5kcal/mol.  The QM/MM energy barrier to water translocation is between 13.4 (Asp212 side) and 15.2 kcal/mol (Thr89 side). This corresponds to a time-scale of  1 to 10 miliseconds, slower than the microsecond timescale of the K-to-L or L-to-M steps.

Active site of Bacteriorhodopsin before the retinal photo-isomerization (i.e., in trans):

active site
Movie1: Translocation of water w402 on the Thr89-side of retinal.  First the hydrogen bond between water w402 and Asp212 breaks, followed by the opening of a lumen between the protein and the retinal (S). In the LM intermediate, water w402 makes a bridge between the positive Shiff-base and the negative Asp85. Finally water w402 adopts a bridging position between Thr89 and the cis-Schiff base in the product (P). The rate-limiting barrier is 15.2kcal/mol.
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Energy profile along the movie.

Energy profile on the Thr89 side
Movie2: Translocation of water w402 on the Asp212-side of retinal.
Same as movie 1, but in the LM-intermediate w402 is strongly H-bonding to Asp212.  The lumen is formed on the Asp212 side of cis-retinal (S). The rate-limiting barrier is 13.4 kcal/mol.
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Energy profile along the movie.

Energy profile on Asp212 side

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