Pushing protons around

[This is the pre-edited version of my Crucible column for the February issue of Chemistry World.]

Life is pretty simple, when you come down to it. It’s a matter of shovelling stuff from one side of a wall to the other – the ‘stuff’ being hydrogen ions, and the wall a cell membrane. The biochemistry that follows from this is fearsome, but at root life is driven by piling up hydrogen ions and then letting them flow, like water released from a dam.

This imbalance of protons across a membrane creates a so-called protonmotive force. It is generated by proton pumps: proteins that can actively move protons ‘uphill, against a concentration gradient. They need energy to do that, and in the light-harvesting chloroplasts of plants that comes ultimately from sunlight, which sets an electron jumping between molecules. In our mitochondria the energy is generated by reactions that break down carbohydrates. In either case, the protonmotive force is used to power the enzyme ATP synthase, which rotates like a water wheel as it lets protons flow through, producing energy-rich ATP in the process.

So if that’s life in a nutshell, these proton pumps clearly need to be efficient and smooth-running pieces of molecular machinery. Even so, the ingenuity life displays in conducting and controlling the movement of protons is breathtaking.

That life exists in water is a boon from the outset – because one of the things water does that other liquids cannot is transport protons rapidly. The hydrogen ion travels faster than other small cations in water by hopping along hydrogen-bonded chains of water molecules: rather like a Newton’s cradle, a proton hits one end of the chain and almost at once (figuratively speaking) another proton pops off the other end. This hopping, called the Grotthuss mechanism after the nineteenth-century German scientist who proposed the basic idea, is exploited by biomolecules to shift protons. Some proteins, such as the light-powered bacterial proton pump bacteriorhodopsin and some cytochromes, are threaded by ‘water wires’, strings of water molecules that act as proton-conducting pathways.

A water wire also winds through the membrane protein aquaporin, which transports water across cell walls. But for aquaporin, letting protons through could be disastrous, as it would disrupt the delicate balance of pH and charge across the membrane. So it has to achieve the seemingly impossible feat of transporting water but not hydrogen ions. How it does so is still not fully clear, but one idea is that the water wire contains a defect: hydrogen-bonding to the amino-acid residues within the pore forces two waters in the chain to sit ‘back to back’, so that a proton can’t jump between them.

That would be an extraordinarily delicate feat of molecular manipulation. But it is possibly trumped by the latest revelation about why proton pumping works so well. Magnus Brändén of Stockholm University and his colleagues (Proc. Natl Acad. Sci. USA, doi:10.1073/pnas.0605909103) say that there are, in effect, little proton circuits written onto the surfaces of cell membranes that help guide protons from a transporter – a pump protein – to molecules that exploit the protonmotive force, such as ATP synthase. The image, then, is not that of a pump spouting out protons into the cytoplasm, where some gradually drift over to where they’re needed; instead, the protons pop out of the pump’s mouth and stick to the membrane before proceeding to hop across it. That way, fewer get lost.

In effect, then, the membrane lipids act as proton-collecting antennas – rather as accessory pigments serve as light-harvesting antennas to shunt light energy onto the photosynthetic reaction centre in photosynthesis.

This idea has been mooted for years, but Brändén and colleagues have pinned it down by looking at the protonation of a single fluorescein dye molecule embedded in the wall of liposomes (closed, cell-like assemblies of lipids). Protonation changes the dye’s fluorescence, and so fluctuations in its brightness can be related to the rate of proton exchange with the surroundings. The researchers show that this happens at a faster rate than would be expected if protons were just being exchanged with the water – so long as the lipid head groups can themselves be protonated. The lipids gather protons and pass them around.

It’s a reminder that molecular biology isn’t just about the cleverness of proteins and nucleic acids. Even the molecules often assumed to be just part of the background or the scaffolding, such as lipids and water, may have inventive roles to play.