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In Silico

Up Close and Personal

Something that’s come up in the last few posts around here is the way that we chemists think about the insides of enzymes. It’s a tricky subject, because when you picture things on that scale, the intuition you have for objects starts to betray you.
Consider water. We humans have a pretty good practical understanding of how water behaves in the bulk phase; we have the experience. But what about five water molecules sitting in the pocket of an enzyme? That’s not exactly a glass from the tap. These guys are interacting with the protein as much (or more) than they’re interacting with each other, and our intuition about water molecules is based on how they act when it’s surrounded by plenty of their own.
And if five water molecules are hard to handle, how about one? There’s no hope of seeing any bulk properties now, because there’s no bulk. We’re more used to having trouble in the other direction, predicting group behavior from individuals: you can’t tell much about a thousand-piece jigsaw puzzle from one piece that you found under the couch, and you wouldn’t be able to say much about the behavior of an ant colony from observing one ant in a jar. And neither of those are worth very much, compared to their group. But with molecules, the single-ant-in-a-jar situation is very important (that’s a single water molecule sitting in the active site of an enzyme), and knowledge of ant social behavior or water’s actions in a glass doesn’t help much.
Larger molecules than water are our business, of course, and those are tricky, too. We can study the shape and flexibility of our drug candidates in solution (by NMR, to pick the easiest method), and in the solid phase, surrounded by packed arrays of themselves (X-ray crystal structures). But the way that they look inside an enzyme’s active site doesn’t have to be related to either of those, although you might as well start there.
As single-molecule (and single-atom) techniques have become more possible, we’re starting to get an idea of how small clusters of them have to be before they stop acting like tiny pieces of what we’re used to, and starts acting like something else. But these experiments are usually done in isolation, in the gas phase or on some inert surface. The inside of a protein is another thing entirely; molecules there are the opposite of isolated. And studying them in those small spaces is no small task.

4 comments on “Up Close and Personal”

  1. Aspirin says:

    While the paper you cited is a very comprehensive study, there are some flaws in it, especially in the conclusions that ligands can bind proteins with strain energies as high as 15-20 kcal/mol. The measured binding affinity is what the protein expends in addition to the ligand strain penalty. So if you had a binding affinity of 5 kcal/mol and you thought the strain energy was 15 kcal/mol, then it basically means that the protein can deliver a total of 20 kcal/mol to bind the ligand. This is a huge number and highly improbable. It’s hard to think of strain energies being higher than 5-7 kcal/mol.
    You can also get high strain energies if you use ligands that have unrealistic conformations in electron densities because the crystallographer didn’t place them there well enough, sometimes because of insufficient ED and sometimes because of lack of attention to basic principles (like amides should not be cis). In these cases the bound conformation is unduly strained and high in energy.

  2. Wavefunction says:

    While NMR is a fantastic technique for determining conformations, one fundamental mistake that many make is in not recognizing that there are many conformations in solution for a flexible molecule and that the observed NMR data (coupling cosntants, distances from NOEs etc) is necessarily average data. They fit a single conformation to this average NMR data and claim that it is the dominant conformation in solution, a completely incorrect result. In fact the average conformation is non-existent, given that it’s by definition an evarege.

  3. kieth says:

    Derek, you have a good way of talking to other chemists without leaving the rest of us entirely blank. That was good. Comments are good too.

  4. Spooky says:

    Were i can found an warez site or an torrent to download the movie 🙂

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