Thursday, February 27, 2014

Lessons from crocheting alcohol dehydrogenase

  1. The difficulty of folding up tertiary structure does NOT scale linearly with amino acid length. One monomer of alcohol dehydrogenase is 374 amino acids long. That's only about 3x as long as lysozyme, but I nearly lost my mind. 
  2. Bobby pins are essential for the folding process. Use them to keep beta sheets flat as you fold, and also to space helices apart from one another. 
  3. Hang the structure as you fold it. Especially important early in the process.
  4. Chainbows are wonderful :)
I'm planning on writing up full instructions of this process, and maybe even making a tutorial video (my first!) Stay tuned.



Saturday, February 15, 2014

How to crochet DNA (with proper chirality)

From left to right: crocheting RIGHT handed; crocheting LEFT handed, and crocheting BACKWARDS RIGHT handed.

I've been interested in finding ways to represent biological molecules at something representing an accurate scale. To that end, I though it would be awesome to have a standard way of making a double helix of DNA. I tried a bunch of different stitch heights and increase ratios, and it turns out that something very simple works pretty well!

1. Make a chain of length = # desired base pairs/2
2. Chain 1
3. In 2nd chain from hook, make two single crochets in top loop. Repeat for each chain stitch.
4. At end, chain 1, slip in same stitch, chain 1.
4. Turn work
5. Beginning with the last-worked stitch in the base chain, make two single crochets in bottom loop of the base chain. Repeat for the remainder of the work.

This yields a helix with about 10-11 base pairs per turn - there's even a major and minor groove! One problem, though - if you do this RIGHT HANDED, you will end up with a left-handed helix. The double helix is in fact right-handed. (For more on helix chirality, check out figure 1.2 here) See the yellow helix in the picture above.

To solve the problem, I've been practicing crocheting LEFT HANDED. This was painfully clumsy at first, but also illuminating. I teach beginners to crochet from time to time, and this has given me fresh insight on how difficult and important tension is. With a bit of practice, I can get a more or less even helix (middle swatch in the photo above).

Though I'm improving, it's slow going. Once again Sandy suggested a clever solution to this problem: crocheting right handed, but BACKWARDS. In other words, inserting the hook through the loop of the chain back to front rather than front to back. Here's a tutorial for backwards crochet (note that this appears to be distinct from reverse crochet or crab stitch). One caveat, though - I've been seeing different stitch heights if I don't grab the yarn correctly to pull it through (ie, if I let it wrap around the hook). While barely noticeable on a stitch by stitch level, this has HUGE effects on the helix. Perhaps due to clumsiness or loose tension, the resulting helix (right, in the photo above) is still not as nice as the one I made working left handed, though I could tell I was working a bit faster. Was it worth it?

To answer this question, I timed myself. I can make 7 stitches a minute working left-handed, 8 working backwards right-handed, and 29 working right handed. It's probably time to take the advice in this helpful tweet:


Sunday, February 9, 2014

Crochet nucleosomes (and a size/scale wake-up call)

Even though I keep a printout of a beautiful reference guide from the Protein Data Bank above my bench, I guess I never really internalized the relative size DNA and proteins until I tried to crochet them side by side. I was originally hoping to represent each base and amino acid with an individual crochet stitch, but that would require scaling WAY down on the gauge for the protein. Laziness prevailed, and I represented the histones in these nucleosomes not as ribbon diagrams but with a crude surface view of the entire octamer.

Along the way, I also came across these beautiful renderings of ribosome tertiary structure that give a sense of the relative scale of protein secondary structure and nucleic acids.

Readers may note that this "DNA" has the wrong chirality. I know, I know. I've been kind of wanting to learn to crochet left-handed for a while now so I can more easily teach everyone...but this is definitely making it a higher priority.

Thursday, January 30, 2014

Protein structures -> crochet patterns

I've been working on a general method for making crochet patterns out of protein crystal structures. For example, here's a ribbon diagram of lysozyme. While the finished 3D structure would be overwhelming to tackle all at once, it's manageable to put together after making the secondary structure first.

Patterns for individual proteins as well as instructions for making your own "translations" are forthcoming.

Thanks to Sandy for teaching me the technique of working around a wire at the Fiber Arts Work Night at the Artisan's Asylum!

Saturday, January 18, 2014

Lacework diatoms: 11 free crochet patterns of microscopic life

Original samples
The biggest crochet project I've ever worked on was a book of 75 knit and crochet patterns representing marine life, published a little over a year ago now. Interestingly (and somewhat tragically), the patterns I was most excited about were the ones that had a lukewarm reception at the publishing company. I was hoping they might appear grouped together in a spread called "Under the Microscope," but instead they got cut from the manuscript altogether because they were predicted to draw little interest from the average reader. That's probably true, but I'd like to release them here in the hopes that someone (perhaps on the internet's long tail of bio-nerdiness) can have fun with them!
Rovag, Wikimedia Commons

Not only are diatoms awesome in and of themselves, but their complex shapes prompted me to learn some interesting lacework techniques in the quest to approximate them in yarn, which I wrote about here. Also, I had a great time constructing the radiolaria. I think you will too!

So, I put together one pdf containing all 11 of these patterns. They're basically in the format I supplied to the publishing company: the patterns are abbreviated, but there is a hand-drawn chart for each one. There's also a legend included on page 2 to help you decipher the text and charts.

PDF of Lacework Diatoms (EDIT: please first click on the link normally to go to Dropbox, then use their download link on that page. If you save-as the pdf at this address directly, you'll get a corrupted file.)

The whole thing is released under a CC BY-SA license. Enjoy!

Monday, May 6, 2013

More classes at Artisan's Asylum!

Thanks to all the wonderful people who joined me for my Intro to Crochet and Sculptural Crochet workshops at Artisan's Asylum in March! They were lots of fun to teach, and I wanted to share a couple of examples of what students have made after the class and shared with me through the magic of the interwebs: this lovely exploration of hyperbolic geometry by Meghan:
And also a beautiful doll made by Sarah:
This project was freeformed according to Sarah's own design!

I'm running these classes again soon: the Intro class on Saturday, May 25, and the Sculptural one on Saturday, June 1.

Saturday, April 6, 2013

Crocheted carboxysomes (and other geometric structures)


While preparing for a sculptural crochet workshop at Artisan's Asylum last month, I wanted to further expand an existing toolkit for making elemental forms. One thing that's missing is a scheme for making polygons.
It's simple, though: all that's needed to transform a circle is to repeat a high rate of increases directly over previous increases in the earlier rows. For example, to make points of a triangle, you can crochet 5 times in one stitch. When you come around to this area again, just crochet 5 times in the middle of that increase (the 3rd stitch).
Playing around with this got me excited about modeling biological compartments like the carboxysome, a carbon fixing structure in photosynthetic bacteria. Besides being ecologically important, they're amazing protein compartments in that are though to assemble with a very specific geometry: an icosahedron. Each face of shell protein forms an equilateral triangle, and a different protein forms the vertexes. Inside is packed RuBisCO, which fixes carbon. 
Prof. Todd O. Yeates, UCLA Dept. of Chem. and Biochem., Wikimedia Commons
Making the carboxysome simply involved accumulating 20 triangles, like the one above, and then sewing them together with a yarn needle by the front loop - this leaves a tiny groove of separation between the faces on the right side. Even with this effect, however, the crocheted version is very floppy, which is charming in its own way. I'd be interested to find a springy method for maintaining shape that doesn't rob the object of its softness like traditional stiffening...any tips?