How do protons get through bacteriorhodopsin?

I’ve just received a copy of the special issue of ChemPhysChem (here) on water at molecular interfaces (Vol. 9, 2635-2879), containing presentations from the DFG Forschergruppe 436 meeting in Dortmund last July. I won’t list everything in it – there is too much that is all worth reading.

One of the contributions, from Klaus Gerwert and colleagues, looks at how vectorial proton transport is achieved in bacteriorhodopsin via a network of water molecules (p.2772). That is also the topic of a recent paper from Qiang Cui of the University of Wisconsin and colleagues (P. Phatak et al., PNAS 105, 19672; 2008 – paper here), who look specifically at the much-debated question of what the proton storage site in bR is. They argue, against the conclusions of Gerwert and coworkers (e.g. Nature 439, 109; 2006), that the proton is kept on a pair of glutamate residues (Glu 194/204), not on a nearby water cluster. I daresay the debate will continue.

Jeremy Smith and colleagues have looked at another aspect of the problem – the possible role of a bound water molecule on the cytoplasmic side of the retinal Schiff base chromophore in the initial transfer of a proton from this chromophore to Asp85, the first step in its motion to the extracellular side (A.-N. Bondar et al., J. Phys. Chem. B 112, 14729; 2008 – paper here). They report calculations which suggest that a water molecule bound to the ‘back’ of retinal in this way helps to direct proton transfer to Asp85 rather than towards Asp212 on the other side of the channel. A surprisingly subtle and indirect form of ‘water-tuning’.

Feng Gai and colleagues at the University of Pennsylvania have added to the unfolding (forgive me) story of how hydration influences amyloid aggregation (S. Mukherjee et al., J. Phys. Chem. B 10.1021/jp809817s – paper here). They have manipulated the degree of hydration of two amyloid-forming peptides by encapsulating them in reverse micelles, and find that aggregation is enhanced when hydration is lessened.

Ronen Zangi, Ruhong Zhou and Bruce Berne report simulations that support what seems to be a growing view that urea’s denaturing action results from direct interaction with hydrophobic surfaces and not any kind of ‘chaotropic’ effect on ‘water structure’ (R. Zangi et al., JACS 10.1021/ja807887g – paper here). They find that urea weakens hydrophobic interactions both in a hydrophobic model polymer and between hydrophobic (and graphene) plates, owing to its binding to the surface and acting as a kind of surfactant.