Tuesday, April 17, 2012

RNA stuff

In case you (all one of you!) are wondering why I've been missing it's because of this:

So besides making awesome protein structures I've also been making a bunch of boring stuff like belt tensioners and other parts to improve my ultimaker and bring it to a functioning state. Well now that I've got it sort of figured out, I thought I'd print a bunch of protein structures WITH SUPPORT! Because support is the future, and cutting protein structures up takes time and effort.

The first thing I made was actually something I also made with Heffy but then decided to remake with support because I wasn't happy about the glueing together. And that is the T7 bacteriophage RNA polymerase! RNA polymerase makes RNA, and as such it is essential to transmitting messages from the nucleus to the cytoplasm, where proteins get made. In this case of course the T7 polymerase works in the cytoplasm transcribing virus DNA, and anyway it would be in a bacterium (hence bacteriophage) which doesn't have a nucleus. In any case this polymerase is really small and thus highly amenable to crystallization with DNA and RNA in tact, essentially caught in the act of transcription. Other, bigger eukaryotic (and prokaryotic! Bacteria care about their RNAs too) polymerases were not crystallized with complete double strands of DNA, so it was not as interesting to me to make those structures when they would not be "complete". Not to mention they are huge, and thus much harder to cut up.

The silver one was of course made with my ultimaker, printed with support and it came out very hairy because the ultimaker doesn't retract. It didn't quite finish too, as the ultimaker lost USB connection near the end of the print, so the top "nub" is not present. In any case the ultimaker print is a lot more contiguous (not obviously two halves glued together, thus easier to look at) but because of the hairy issue the surface quality is not the best. Heffy did much better on that count.

And since I liked how that DNA looked in the polymerase I thought I'd print out tRNA, because I think tRNA is super cool and though it's not a protein, it's pretty close and its surface structure is a lot more interesting than many proteins. tRNA is of course the physical embodiment of the genetic code, with an anticodon on one end and the corresponding amino acid at the other (anticodon at the bottom of this picture, amino acid at the top right). I hope to print out a ribosome at some point but at this scale the ribosome would probably be the size of my whole hand in that picture, relative to that tRNA. I'd definately want to sort out that hair issue before I make something of that size.

Oh here are the links to thingiverse as promised: polymerase tRNA