4 ms·
Chemists tie a trefoil knot using only 54 atoms
- dekhn 3y agoIn grad school I got interested in knots while doing structural biology and asked my advisor (extremely well known chemist) if it would be possible to make proteins that fold into knots and he pointed out (correctly) that entropy makes it very unlikely this would happen, as the process of folding into a knot typically decreases the degrees of freedom a protein can adopt. It was a reasonable point and I ignored the problem for some time. It turned out later that a small number of proteins are found in a knotted conformation experimentally, https://en.wikipedia.org/wiki/Knotted_protein https://en.wikipedia.org/wiki/Knotted_protein and alphafold even helped design a knotted protein. I can imagine there are also enzymatic modifications you can make to proteins that would generate knots without paying the entropic cost of threading the needle, so to speak.
- COGlory 3y agoIs there any evidence that the entropic restraints on a knotted protein are greater than the entropic restraints from the hydrophobic effect?
- flyer_go 3y agoWhat would be the benefit of this?
- iouwhldkfjgklj 3y agoIt's interesting. That's the benefit.
- photonthug 3y agoA category theory textbook opens the "motivation and use cases" section with the following poem: There's a tiresome young man in Bayshore. / When his fiance cried 'I adore / the beautiful sea' / he replied 'I agree, / it's pretty, but what is it for?'
- dekhn 3y agoProtein design is a multi-billion dollar field. A single observation- thermostable proteases- was incorporated into modern laundry detergents, making Genentech and Corning billions of dollars in IP.
- frangolino 3y ago[dead]
- gilleain 3y agoThermal stability, as far as I know. So hyperthermophiles, presumably. edit: hmmm. from this interesting review - https://www.sciencedirect.com/science/article/pii/S0959440X23001835 https://www.sciencedirect.com/science/article/pii/S0959440X2... (open article) - it looks like some knots might increase mechanical stability and resitance to proteolysis
- dekhn 3y agoOh, cool- they turned a not-truly-a-knot (open ends) protein into a truly knotted one (connected ends) and then unfolded it using urea and it stayed knotted. That's what you'd expect but it's also pretty cool.
- empath-nirvana 3y ago> if it would be possible to make proteins that fold into knots and he pointed out (correctly) that entropy makes it very unlikely this would happen This is exactly the opposite argument I'd make from entropy: https://www.npr.org/sections/bryantpark/2008/01/knot_theory_why_everything_tan.html https://www.npr.org/sections/bryantpark/2008/01/knot_theory_... There's many ways that a string can be knotted and only one way it can not be knotted.
- dekhn 3y agoNote I am talking about entropy of "folding" as a verb- the process by which a fold is adopted. Not the entropy of the final state (which is confusing called a "fold" by some practioners, although that habit is decreasing). the argument is that the folding process would require the protein to go through an intermediate: forming a loop and then getting one end to go through the loop requires a very specific set of conformations, and reducing the number of conformations has an "entropic cost". Note also that the final post-folding form of a knotted protein isn't really a continuum of many different conformations, but probably one "locked" one which means there really is only a small set of conformations the protein can adopt once locked into the folded, knotted state. In protein folding, there is not "only one way it can not be knotted"; you have to include all the degrees of freedom in the backbone available in the unfolded state (I am ignoring hydrophobicity and other important sources of entropy which help proteins fold rapidly to the "correct" final state). We already know this pretty well from more basic polymer physics, but, entropy being subtle, I'm sure there are many different forces at play.
- function_seven 3y agoI think with proteins the ways it can be "not knotted" are basically infinite. Topologically-speaking, yeah, it's just a deformed ring. But the deformations (folds) are the huge thing that makes a protein do its job. So there are tons of folding configurations, and entering a knotted state restricts a lot of the freedom-to-fold a protein would have
- topaz0 3y agoTopology gets its utility from collapsing lots of degrees of freedom into a small number of equivalence classes. That's great for reasoning about topological properties, where those degrees of freedom are not relevant, but it doesn't mean those degrees of freedom just go away.
- dang 3y ago[stub for offtopicness]
- ourmandave 3y agoDamn, that's a really small wedding.
- UncleOxidant 3y agoI thought it might be something like the Emperor's New Wedding where the wedding ring was invisible and everyone is pretending to see it.
- crtified 3y ago(coming to theatres soon!) He thought he had clothes. He didn't. Now, his secret is exposed. And he is KNOT amused. The Emperor's Tiny Ring
- bee_rider 3y agoIMO they should have to reproduce it intentionally to get the “record.”
- Kerb_ 3y ago
- gibolt 3y agoIf several of these could be looped together, could you get a structure stronger (or at least more resilient to tension) than carbon nanotubes?