December 9, 2011

Tags: silk, protein structure, music, Giesa, Spivak, Buehler

Silk was one of the first fibrous proteins to be investigated in the early 20th century. Spider silk's exceptional properties have long inspired researchers from fields ranging from mechanical engineering to biotech. Now three MIT researchers from the Departments of Mathematics and Civil and Environmental Engineering have used a new concept called ontology logs, from the category theory branch of mathematics, to examine the relationship between spider silk's structure and function.

The really different aspect of this research? They conducted their examination by comparing spider silk and classical music. And they present their findings as a demonstration of a new way of gaining insight into various structures built on smaller and smaller substructures. Read more at MITnews.

The original paper, by Tristan Giesa, David I. Spivak, and Markus J. Buehler, is published in BioNanoScience.

Tough Genetic Stuff

October 18, 2010

Tags: genetics, protein structure, silk, Latrodectus, Zhao, Ayoub, Hayashi

Genetics papers can be pretty impenetrable to us non-geneticists. But geneticists don't write the way they do just so they'll be perceived as eggheads.

It took me, an English major with not much science background beyond high school courses, many months to learn how to decipher the genetics papers that inform Spider Silk. Of course, I was lucky enough to have Cay Craig guide me through these papers and steer me back on track when I veered astray. During this process, I came to realize that genes and genetic research is even more complicated than most of us non-biologists realize. For many of us, it's a mystery why news reports about exciting discoveries in genetics don't lead rapidly to successful medical or other practical applications.

I now get that it's no mystery, or conspiracy. This longer-than-usual post is an attempt to walk through an intriguing paper by a genetics team that writes unusually clearly. Even so, the paper is shot through with terms such as "paralog," "diploid," "retroposition," and "fluorescence in situ hybridization." These terms immediately convey images and lines of logic to other geneticists but gaping black holes to the rest of us. I'm going to avoid such terms as much as possible as I walk through the paper. But I think you'll still see how many interlocking and complex concepts and techniques evolutionary geneticists have to wrestle with, and why even dazzling genetics papers usually lead to more papers rather than to immediate, dramatic applications. (more…)

Silk: From Liquid to Solid

June 14, 2010

Tags: silk, protein structure

A group of scientists in Norway and Sweden reported in the journal Nature last month that they've figured out something new about how spider silk self-assembles. Spider silk, which is a protein, starts out as liquid dope in spiders' silk glands. A protein molecule is a chain of amino acid molecules. As the amino acids up and down the chain interlock with each other in characteristic patterns, the liquid dope transforms into fibers.

The timing of this self-assembly is crucial. If it happened too soon, a spider would be left with balls of silk fiber clogging up its silk glands--useless. Why do the same molecules form a liquid in the glands but form fibers as they emerge from the spinnerets?

Like all proteins, silk protein molecules have two ends and a middle. One end is known as the C-terminus. The middle of silk protein molecules is made up of repeating sequences of amino acids that interlock to form the fiber. And the other end is known as the N-terminus. Silk scientists have known for a while that the C-terminus plays an important role in ensuring correct fiber self-assembly. The new report indicates that the N-terminus determines the timing of self-assembly.

As silk molecules move through the ducts leading from silk glands to spinnerets, they encounter gradually decreasing pH levels--that is, their surroundings become more acidic. The molecular structure of the N-terminus makes it sensitive to such a change, and it in turns influences how the middle, repeating segment of the silk molecule twists back and forth on itself. The researchers found that the N-terminus actually inhibits fiber formation in basic or neutral environments and hastens it at the levels of acidity found out in the spinnerets. So spider silk fibers self-assemble right on time.

One more example of how spider silk proteins may help us understand all sorts of other proteins.


"...a compelling introduction to evolution in action through the lens of spiders and their silks."

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