3 ms·
Some context: the author, David Baker, is a preeminent figure in the world of protein structure prediction. His lab has consistently had the best protein struct
by entee 10y ago
Some context: the author, David Baker, is a preeminent figure in the world of protein structure prediction. His lab has consistently had the best protein structure prediction software out there (Rosetta). They recently released a paper detailing the structures of a large number of unknown proteins using their technique as an aid [1].
Some of the ideas in this article are quite cool, but I think it's important to add a caveat: we don't often know what structure will yield what result. In other words, if I want to do X, I don't know what protein structure will get me X, which makes it hard to engineer such a protein.
Nevertheless, when you have some understanding of the problem, you can in fact engineer proteins. Baker gives several examples in the article. In many of those cases, the best approach is to start with a variety of engineered proteins, then use in-vitro simulated evolution to pick the winners and get pretty substantial improvements over the original design.
Protein engineering is quite a cool area, and hopefully over time we'll get better at understanding the other parts of biochemistry so that we can more effectively design useful proteins.
[1] http://science.sciencemag.org/content/355/6322/294 http://science.sciencemag.org/content/355/6322/294
- jfarlow 10y agoThere are a lot of approaches, and they do not all require a brute force simulation. Nature herself seems to have a library of functional domains from which she can mix and match to produce a larger mechanical device - in addition to the atomic resolution mutations, and tertiary structural features. There are a lot of very useful ways people do design proteins right now that do not involve structural prediction. Further, very much unlike the digital sciences, a gigantic library of parts, functions, routines and 'example code' already exist. If you want a piece of nano-technology that does X, just go look for an organism that lives in a condition where X is useful - and in there genome it will be. We have a huge pile of hyper-advanced alien source code that we can dig through. We don't have to reinvent it all on our own.
- adrianN 10y agoI'm convinced that synthetic proteins are the most viable way to Drexler type nanotech. Biology demonstrates that it works, we "just" have to understand how.
- jfarlow 10y agoAt the sub 10nm scale you need stiff linkages to have predictable and consistent structures. Covalent 'organic' bonds give you stiff linkages at that scale while metals are goopy and electronically inconsistent. Proteins are organic nanotechnology where the 3D feature sizes of the (wet) tools is measured in fractions of angstroms. The best Intel can do is ~ two orders of magnitude larger resolution, 2D, dry.