The Puzzling Paucity of Knotted Proteins
Leave a piece of string in your pocket, and the chances are it’ll be tangled and knotted when you take it out. And yet pick a string of amino acids, and the chances are this protein will not be knotted. Out of the 53,000 proteins in the Protein Data Bank (PDB), only 300 are knotted, and most of these are the same protein in different forms. In fact, it’s possible to reduce the total number of different knotted proteins to 17.

Why are knotted proteins so rare?
Today, Martin Lundgren at Uppsala University and his mate Antti Niemi make a tentative suggestion. They point out that biologically active proteins are compact objects, presumably because there is some kind of advantage in being small.
They then calculate the effect that a knot has on the size of a protein and find that knots tend to increase the size of short proteins with fewer than 400 central carbons in their structure. But for proteins with between 400 and 500 central carbon atoms, knots seem to make them more compact.
“The reason why knots are so rare in PDB data would then be partially explained by the fact that until now, the structure of only relatively short proteins have been reliably resolved,” they say.
So the implication is that knotted proteins aren’t rare at all–only undiscovered. That sounds like a challenge.
Ref: arxiv.org/abs/0906.4950: Knots and Swelling in Protein Folding
Deep Dive
Uncategorized
Capitalizing on machine learning with collaborative, structured enterprise tooling teams
Machine learning advances require an evolution of processes, tooling, and operations.
The Download: how to fight pandemics, and a top scientist turned-advisor
Plus: Humane's Ai Pin has been unveiled
The race to destroy PFAS, the forever chemicals
Scientists are showing these damaging compounds can be beat.
How scientists are being squeezed to take sides in the conflict between Israel and Palestine
Tensions over the war are flaring on social media—with real-life ramifications.
Stay connected
Get the latest updates from
MIT Technology Review
Discover special offers, top stories, upcoming events, and more.