Hi Peterson students and friends! I've arrived at the University of Cambridge and started working on my new research project, which involves doing computer simulations of protein folding. I'm doing this work with Dr. Robert Best, a fellow in the Cambridge Department of Chemistry. I'd love to tell you all about it and answer any questions you might have.
This will hopefully be the first of a series of posts on my blog about what proteins are, how they fold into complicated 3D structures, and why that is important for life. I apologize in advance if some of what I'm saying is unclear. It will hopefully become clearer as I go on...
But first, here's an animation of one of my first simulations. The coiled tube represents an amino acid chain (a.k.a. polypeptide). You can see three major coiled parts of the chain that pack against each other. These are called alpha helices--more on those later. The structural motif that they form is called a three-helix bundle. The animation shows what happens to the simulated protein if you add to the simulation a strong pulling force between the two ends of the polypeptide chain. The protein quickly comes apart or unfolds. (People have actually done this sort of experiment in real life...but more on that later!)
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