Physics, Software

Will It Bend?


That is the question. A look at using bleeding-edge simulation techniques to understand the inhibition behaviour of Myosin-VII. I gave this presentation as part of my undergraduate final project in early 2016. It’s aimed at people who are familiar with basic physics concepts, but not biology or biophysics. You can find more technical information about the project here.

Some updates to give since this presentation was originally written:

  • I’m currently working on an improved model for structures such as alpha-helices and coiled-coils! So I guess that answers that question.
  • My experimental collaborator for this project has since found that Myosin-VII may bind light chains other than calmodulin.
  • I feel like I should issue the following clarification: at the start of the presentation I show an MD simulation of Myosin-VII and say that it’s really too large to simulate using MD. This isn’t really true (as you can probably tell), it’s more that MD simulations don’t make sense for the timescale that Myosin-VII folds on. You can see later on the end-to-end distance graph that Myosin-VII’s biggest normal mode is on the many-microseconds timescale, meaning that it’s way, way too slow for MD. The video I show of MD is a bit cherrypicked, although it shows the molecule starting to fold in half, it doesn’t normally do that.

Last updated January 11, 2022.

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