How do enzymes work? People have been trying to answer that, in detail, for decades. There's no point in trying to do it without running down all those details, either, because we already know the broad picture: enzymes work by bringing reactive groups together under extremely favorable conditions so that reaction rates speed up tremendously. Great! But how do they bring those things together, how does their reactivity change, and what kinds of favorable conditions are we talking about here?
And some of this we know, too. You can see, in many enzyme active sites, that the protein is stabilizing the transition state of the reaction, lowering its energy so it's easier to jump over the hump to product. It wouldn't surprise me to see the energies of some starting materials being raised to effect that same barrier-lowering, although I don't know of any examples of that off the top of my head. But even this level of detail raises still more questions: what interactions are these that lower and raise these energies? How much of a price is paid, thermodynamically, to do these things, and how does that break out into entropic and enthalpic terms?
Some of those answers are known, to some degree, in some systems. But still more questions remain. One of the big ones has been the degree to which protein motion contributes to enzyme action. Now, we can see some big conformational changes taking place with some proteins, but what about the normal background motions? Intellectually, it makes sense that enzymes would have learned, over the millennia, to take advantage of this, since it's for sure that their structures are always vibrating. But proving that is another thing entirely.
Modern spectroscopy may have done the trick. This new paper from groups at Manchester and Oxford reports painstaking studies on B-12 dependent ethanolamine ammonia lyase. Not an enzyme I'd ever heard of, that one, but "enzymes I've never heard of" is a rather roomy category. It's an interesting one, though, partly because it goes through a free radical mechanism, and partly because it manages to speed things up by about a trillion-fold over the plain solution rate.
Just how it does that has been a mystery. There's no sign of any major enzyme conformational change as the substrate binds, for one thing. But using stopped-flow techniques with IR spectroscopy, as well as ultrafast time-resolved IR, there seem to be structural changes going on at the time scale of the actual reaction. It's hard to see this stuff, but it appears to be there - so what is it? Isotopic labeling experiments seem to say that these IR peaks represent a change in the protein, not the B12 cofactor. (There are plenty of cofactor changes going on, too, and teasing these new peaks out of all that signal was no small feat).
So this could be evidence for protein motion being important right at the enzymatic reaction itself. But I should point out that not everyone's buying that. Nature Chemistry had two back-to-back articles earlier this year, the first advocating this idea, and the second shooting it down. The case against this proposal - which would modify transition-state theory as it's usually understood - is that there can be a number of conformations with different reactivities, some of which take advantage of quantum-mechanical tunneling effects, but all of which perform "traditional" transition-state chemistry, each in their own way. Invoking fast motions (on the femtosecond time scale) to explain things is, in this view, a layer of complexity too far.
I realize that all this can sound pretty esoteric - it does even to full-time chemists, and if you're not a chemist, you probably stopped reading quite a while ago. But we really do need to figure out exactly how enzymes do their jobs, because we'd like to be able to do the same thing. Enzymatic reactions are, in most cases, so vastly superior to our own ways of doing chemistry that learning to make them to order would revolutionize things in several fields at once. We know this chemistry can be done - we see it happen, and the fact that we're alive and walking around depends on it - but we can't do it ourselves. Yet.