To me this protein image looks wet and gooey. Initially I found that disconcerting, because I'm used to the dry solid appearance of the more standard visualizations. But now I think that 'wet and gooey' is actually a realistic description of the surface properties of any protein.
I would imagine soluble proteins as being "wet and gooey", especially since the would be surrounded by the waters from the solvation spheres, but I imagine transmembrane proteins as having a "dry" section in the middle, where the protein interacts with the membrane.
ReplyDeleteHi, anon, you seem quite expert on the subject. Lately I'm pondering how many water molecules might be (functionally)associated with a (voltage gated)potassium channel. Anything in the order of 3200 would mean that on average one of those water molecules is actually HDO, which might have some influence on the accuracy of the channel. What is your guess?
DeleteAre proteins wet? Yes and no. The surface representations that you show do not have any water included in them so they are not wet, by definition. Under physiological conditions, most proteins are hydrated, however. Are proteins gooey? Proteins have mechanical properties close to plexiglass, so that's not very gooey.
ReplyDeleteI think the previous commenters are missing the point. I don't think Rosie's point was that proteins are "wet" in the sense of "associated with water molecules" nor "gooey" in the sense of being deformable and sticky on a macroscopic level.
ReplyDeleteI think instead she's referring to the implicit mental model we have of how proteins behave on a molecular level (not a macroscopic one). The typical protein molecule picture uses a surface texture/composition which puts one in mind of hard, smooth, shiny surfaces - as if protein molecules were made up of a number of billiard balls all epoxied together. The issue, of course, is that proteins don't behave (on a molecular level) like they're composed of hard spheres cemented together.
Despite any *intellectual* protestations that "well, of course they're not hard spheres, they're quantum mechanical ...", I doubt that most scientists really grasp that on an *intuitive* level - or whatever level they use to heuristically predict how proteins behave without resorting to the Schrodinger equation. The visualizations guide our conceptualizations.
For what it's worth, I believe I recognize where Rosie is coming from because I had a similar epiphany. Not with gooey proteins, but with fuzzy ones (specifically HHMI's videos like this one). If you were to explicitly have asked me, I of course knew that the sidechains on the replicase were constantly moving, but I don't think I really intuited it until I saw that video.
Thank you, yes! That's exactly what I was thinking. (Love the billiard ball analogy!)
DeleteI had a moment like that in grad school when looking at someone's MD simulations. Of course, I knew that biomolecules are subject to Brownian motion and everything is twitching around at random and occasionally, there's also a dramatic conformational change. That didn't stop my mind from boggling when I watched that molecule squirming in that guy's video, though.
DeleteWet and gooey are emergent properties. They probably only happen with large ensembles of molecules.
ReplyDelete" I don't think Rosie's point was that proteins are "wet" in the sense of "associated with water molecules" nor "gooey" in the sense of being deformable and sticky on a macroscopic level."
ReplyDeleteThen she shouldn't have used those words! Precision in language is critical in science.