I'm tired, and want a nap. I'm not going to let myself nap, though. Partially because I'll be working in my advisor's office from 2-4 (assuming he hasn't scheduled himself elsewhere), and partially because I want to make myself get some work done. it's 1:30... I can make myself stay awake for another 3.5 hours. Maybe this'll also encourage me to go to bed earlier. (Which would be smart, since I'm getting together with B tomorrow morning... late morning, but still morning.)
Even though I was up late again last night, I caught an earlier bus than yesterday (still not as early as I'd like, but I'm working on that). I'm going to make myself catch a reasonable bus all next week. And go to bed on time.
Well, that was a five minute break... back to paper reading. I'm reading an interesting one that looks at the effects of point mutations in proteins, and how the resulting structure changes very little. Looks like combinatorial rigidity can say something here too. :)
Speaking of which, I should check to see the effects of backbone vs sidechain hydrogen bonds on structure. I wonder if I can say anything interesting there. Alpha helices are rigid, but are beta sheets? What makes a protien choose to fold the way it does? Both helices and sheets have the same backbones (obviously), but I think they tend to have different sidechains. Curious. Proteins are very curious beasts.
(Oops... now this has been a ten minute break. Talk to you later.)
1 comment:
Thanks!
Actually, I'm coming at the problem from a computer science point of view, and so some of this stuff is still a mystery to me. What's RER?
When you get down to details, there's still a lot the scientists don't really understand. Given a random amino acid sequence, they won't be able to predict exactly how it folds. People have ideas, but no one has completely figured out how to determine structure merely from amino acids.
I'm modelling proteins as bar and joint frameworks, and then studying their structural properties. I'm ignoring small motions like vibrations of atoms, and minor bending of bond angles, etc. In my model with fixed bond lengths and angles, alpha helices are rigid. One protein I'm working with, PXR, has a beta sheet that's rigid if all hydrogen bonds are included, but I haven't checked how much of a difference the sidechain bonds make.
Thanks for the comment! (And good luck with dinner! ;) )
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