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Its interior was full of water, wires and apparatus, rather than the comfy dark upholstery and colorful controls Bond enjoyed.
In any case, it is apparent that no water wires connect the central proton-binding site and the periplasmic space in the L and O states, in any of the structures.
In the T state, by contrast, two narrow water wires form on the periplasmic face of the TM domain, again reaching into the proton-binding site, and approximately along the interface between the two repeats R1 and R2.
In the native membrane and at room temperature, the two repeats would be much more dynamic than what appears in the crystal lattice, and thus we envisage that both water wires co-exist, also in the wildtype protein, as we observe in the simulation.
Based on this analysis, the proton-binding site is open to the cytoplasm in the L and O states, via two possible channels (solid black lines), whereas in the T state it is open to the periplasm, also via two water wires (solid black lines).
Interestingly, E346 and D924 flank the entrance of each of these water wires; as mentioned earlier, both these side-chains are likely to be protonated in the L and T states and deprotonated in the O state, which suggests that E346 and D924 facilitate proton uptake by providing transient binding sites en route to D407/D408 (Fischer and Kandt, 2011).
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In contrast, if the protein were switched open to form a water wire, then diffusion-limited conductance would be expected.
On the cytoplasmic side, we also observed a narrow water wire, flanked by R971, which is thus unlikely to sustain proton transfer, as discussed below.
A third narrow wire in the T state seems to connect the proton-binding site to the cytoplasm (dashed black lines), but the positively charged R971, which traverses this water wire, likely blocks H+ leakage.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com