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One of the less obvious amazing things about biological science is that the reductionist approach, generally, works. You can take a protein–an enzyme, say–put it in a dilute solution with some salts and buffer, and find out how it works or what it does with a reasonable degree of certainty that it will do the same things in a cell in the body. That’s amazing because the cellular environment is more than a little dissimilar. It’s not just the surrounding salt and the pH that we take a guess at when doing biochemistry, but we also forget about all the other things that our enzyme would be in close contact with if it were still in a cell. The reducing potential of cytoplasm is not only much stronger than attainable in biochemical buffers but varies between sub-cellular compartments. And critically, thirty percent of a cell’s volume is taken up with macromolecules, equivalent to a protein concentration of about 200 mg ml^-1.

So there has been a lot of work looking at how molecular crowding affects the behaviour of proteins and DNA. Crowding agents tend to ‘stabilize’ proteins, and you can approximate molecular crowding using synthetic materials or biological molecules. Some people use polystyrene beads; I once looked at the effect of polyethylene glycol on polymerization of a particlar protein. When I was in Sydney a colleague asked if I had a supply of GFP he could use for neutron diffraction experiments in crowded solutions (a request that led to one of my coolest cloning experiments).

GFP cloning experiment

Synthetic–or at least, biologically irrelevant–materials have been used for crowding experiments because they’re easier to define, and can stabilize proteins while (presumably) not interacting meaningfully with the molecule you’re studying. This should allow one to distinguish crowding effects from biological ones. But sometimes it’s important to model biological crowding effects, and this is where it gets tricky. My friend in Sydney ran into trouble when he started using GFP for his experiments, for example, because strange things started to happen. It now turns out, according to a paper evaluated by Joan Shea, that biological crowding can, contrary to our expectations, destabilize proteins.

While the excluded volume effects of the biological crowding agents do tend to stabilize other proteins, non-specific interactions, such as electrostatic interactions between the different proteins, score a bizarre kind of protein own-goal. The authors say this results in ‘tunable stability’, no doubt opening the way to ever more interesting theoretical analysis and cellular experiments. Biology continues to surprise us all.