Key role of water: Primary proton transfer via water-B in bacteriorhodopsin.

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

J. Phys. Chem. B 112, p. 14729-14741 (2008)


The primary proton-transfer step in bacteriorhodopsin is from the protonated Schiff base (PSB) of retinal to Asp85. One question concerning the mechanism of this proton transfer step is how the presence of a water molecule located on the cytoplasmic side of retinal (called here water B) and making a hydrogen-bond to the PSB would influence the primary proton transfer.
This is addressed by performing quantum mechanical/molecular mechanical (QM/MM) reaction path calculations with the  Conjugate Peak Refinement  (CPR) method. These show that the proton transfer is energetically feasible in the presence of water B:  a low-energy conformation exists in which the positively charged PSB and the negatively-charged Asp85 are bridged by water B. From this conformer, concerted proton transfer occurs via water B with a rate-limiting energy barrier of ~10 kcal/mol.
Molecular dynamics simulations demonstrate that, when water B is absent, the intrinsic flexibility of the retinal chain enables the transient formation of a hydrogen bond between the retinal Schiff base and Asp85, thus making direct proton transfer possible. This confirms previous reaction path calculations, which had also shown that such a transfer is energetically allowed. An alternative route in absence of water molecule B is via a proton wire through Asp212, on the other side of the retinal.

Location of water B :

Waters around retinal
Below are shown the energy profiles of two proton transfers via water B.

Insets give the geometries in the reactant,
product, the rate-limiting transition states, and the local minima discussed in the paper.

The transferring protons are depicted as small spheres. The reaction coordinate L gives the sum along the entire path of the
changes in all atomic coordinates calculated as a root-mean-squared difference: At L=0, the Schiff base is protonated and Asp85 is negatively
charged; at L=1, Asp85 is protonated and the Schiff base is neutral. The energies are for QM/MM-optimized geometries.

1a:  Proton transfer via water B.   Download the movie  (1.3 Mb)
Energy profile of path 1a
First, water B moves to a location where it bridges between the Schiff base and Asp85. Then, concerted proton transfer via water B occurs, crossing a rate-limiting barrier of 9.7 kcal/mol, which is consistent with the 10 microseconds experimental timescale of the primary proton transfer step (L to M). Finally, water B remains hydrogen-bonded to the deprotonated Schiff base.

Path 2a:  Proton transfer via water B and Thr89.  Download the movie  (1.5 Mb)
Energy profile of path 2a

In the starting state, a hydrogen-bonded network already extends from the Schiff base to Asp85 via water molecule B and Thr89. Therefore, the proton transfer requires only minute structural rearrangements, crossing a rate-limiting barrier of 13.8 kcal/mol.

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