If you asked me which superhero’s powers I would like to have this week, I would choose Ant-Man. I’d never considered choosing Ant-Man before. He seemed a bit dorky and clueless from the Marvel Cinematic Universe. (He might be more interesting in the comic books but I haven’t read them.) Why Ant-Man? I continue to spend lots of time prepping for Biochemistry class. Most recently I’ve been working on a lecture that encompasses protein folding and denaturation.
It’s challenging to study protein folding experimentally. Levinthal’s paradox argues that it cannot be random sampling of conformational space and must be guided in some way. We do know that proteins already begin the folding process even as the polypeptide is being synthesized on the ribosome, and that molecular chaperones play a role to ensure the protein folds correctly so that it can perform its functions. But capturing the dynamics and the details is very difficult. If only we could, like Ant-Man, shrink ourselves to the size of molecules, we could directly examine each step of the process as it happens in living cells. Without Ant-Man powers we have to resort to killing the cell as we tease it apart to figuring out what’s going on inside.
A complementary approach is to use computational methods. In preparation for that lecture, I’ve been perusing the primary literature for examples to use in class. Using state-of-the-art molecular dynamics simulations, we can now see small proteins approaching the millisecond timescale. These don’t include the chaperones or the ribosome but rather rely solely on the thermodynamics and kinetics of the peptide in water. By that I mean a model of the peptide in a model water box. As a computational chemist with some knowledge of this field (although it’s not my specific area of expertise), I can say that the models are well-parameterized and do a decent job. We scientists have learned a lot from such model simulations and they keep getting better.
When I watch a molecular dynamics simulation, it’s a bit like being molecular-sized Ant-Man. Even more so if I immerse myself in a virtual reality setup. I can track what individual atoms are doing, I can see larger-scale globular movements, and I can observe how the protein folds and unfolds dynamically. Maybe I already have Ant-Man-like powers; and with faster computer processors, faster algorithms, and more accurate models, my powers would increase. But I would need to guzzle much more energy than Ant-Man would require, and I likely wouldn’t have the same visceral feeling that Ant-Man would have if he went into a cell and observed molecules up close and personal. In computer simulations, atoms look like bright colored balls of different sizes, and it might feel like I’m in a playground. In the actual cell, it might be much more sinister and scary.
I don’t even know what atoms would actually look like. What is an electron cloud? All our imaginations of atoms and molecules are models. We’ve never seen an atom with the naked eye, although we have seen images from a scanning tunneling microscope translated on to a screen. In my quantum chemistry class, I try to help my students “see” electron clouds (orbitals) through mathematical equations. It’s a tall order. If we could be Ant-Man and the Wasp making our way through quantum world, maybe we’ll be truly enlightened. So far I have been unimpressed by MCU’s rendition of the quantum world. But I haven’t seen the third installment yet, Quantummania. The DVD recently came to my local library so I will be watching it soon, and if I find anything noteworthy it might be a future blog post.
P.S. I did use Ant-Man in earlier blog posts about resizing chemistry!
No comments:
Post a Comment