Friday, December 13, 2013

70S Ribosome

Here is my finished image of the 70S Ribosome:

I created this piece with Maya, molecular Maya, After Effects and Illustrator. This was an exercise in learning more about molecular Maya and nParticles, and to create an informative molecular visualization using real data. The 70S ribosome exists in prokaryotes (i.e. bacteria and archaebacteria) and also in mitochondria. The two subunits clamp around a piece of mRNA and proceed to translate the genetic information into a growing polypeptide chain, reading from 5′ to 3′. Interestingly, the ribosomal RNA, or rRNA provides the catalytic function of the ribosome, rather than the protein components. The exploded view in the image includes a slightly longer polypeptide chain, since this “second” ribosome has translated more of the mRNA. This polypetide is beginning to fold, although this is artist’s representation, and I believe that folding (such as formation of alpha helices) actually begins in the exit tunnel within the 50S subunit.

I've copied the text for this post from our research group's site:


Thursday, December 12, 2013

Some particle experiments

I've been doing some experiments in Maya at work to get a better understanding of nParticles and molecular Maya. The first series involves creating chaotic molecular motion with random collisions. The particles here are not to scale (the water is huge and not plentiful enough) but it serves the desired technical purpose.

I've also been creating an explanatory still image of a bacterial ribosome. A screenshot of the piece in progress is below. You can see that these are large complex structures, and it's been really fun examining the structural data to determine where and how the molecules fit together. Most of that information is embedded in the pdb data, but I had to look elsewhere to see how the growing nascent polypeptide navigates through the exit tunnel. The final piece will show this better I hope. I also didn't have mRNA data, so I generated a RNA-like structure with nParticles converted to geometry.

If you enlarge the image, you can probably see that I'm working with almost 6 million polygons (not by counting; the number is in the upper left). But the viewport (thanks to the Quadro K4000) is still butter smooth, tumbling and zooming.