{"id":862,"date":"2006-11-30T10:44:42","date_gmt":"2006-11-30T10:44:42","guid":{"rendered":"http:\/\/scienceblogs.com\/principles\/2006\/11\/30\/you-got-general-relativity-on\/"},"modified":"2006-11-30T10:44:42","modified_gmt":"2006-11-30T10:44:42","slug":"you-got-general-relativity-on","status":"publish","type":"post","link":"http:\/\/chadorzel.com\/principles\/2006\/11\/30\/you-got-general-relativity-on\/","title":{"rendered":"You Got General Relativity on My Protein Folding!"},"content":{"rendered":"

There’s a brief squib in the AIP Physics News Updates today about new work on protein folding<\/a>. “Protein folding” is a simple-sounding term for a really difficult problem: protein molecules are made up of chains of amino acids, which can be bent into a huge number of different possible configurations. In nature, though, these proteins are normally found in only one configuration. Correctly predicting the folded configuration of a given protein is an extremely difficult computational problem.<\/p>\n

The paper highlighted by the AIP takes a new approach to the problem, employing some calculational tricks lifted from General Relativity:<\/p>\n

\n

Lapo Casetti (casetti@fi.infn.it) and Lorenzo Mazzoni have attempted to make the “energy landscape” method even more geometrical by characterizing the folding forces at work as being a form of curvature in the bowl-like well in which the protein is operating. This is analogous to what Albert Einstein did in characterizing gravity as the curvature of spacetime in which planets and stars move about. Mazzoni and Casetti seek to determine what it is about the curvature of the energy landscape that encourages proteins to fold and other polymers not to fold.<\/p>\n<\/blockquote>\n

If ever there was a calculational technique to make me run shrieking in horror, this would have to be it…<\/p>\n

<\/p>\n

My only real exposure to GR was a thoroughly bewildering crash course in tensor calculus as part of a “Cosmology for Idiots” class my junior year in college. Fifteen years later, I still have to suppress a shudder when I hear the words “Cristoffel Symbol.”<\/p>\n

And protein folding was the topic of the single most annoying talk I’ve ever sat through, back in graduate school. It was part of a mandatory seminar series, and the speaker spent the better part of forty-five minutes talking in soul-crushing detail about the approximations they made, and the computational techniques they used, before ending with five minutes of material that can be summarized as “We find this one configuration, and when we check it against X-Ray crystallography, the actual configuration is something else. We’re not even close, and have no idea why. Thanks for listening, I’ll take questions now.”<\/p>\n

That was ten years ago, and I’d still like to bash that guy in the head with a chair for wasting an hour of my life.<\/p>\n

So the thought of applying general relativity to protein folding…. Well, let’s just say that it makes me glad to be an experimentalist.<\/p>\n

Of course, the next question is how long it will take before some calculational technique from string theory gets applied to these calculations, and we’re treated to lots of preprints with titles like “AdS\/CFT and β-amyloid”? Because, you know, that would just make my day…<\/p>\n","protected":false},"excerpt":{"rendered":"

There’s a brief squib in the AIP Physics News Updates today about new work on protein folding. “Protein folding” is a simple-sounding term for a really difficult problem: protein molecules are made up of chains of amino acids, which can be bent into a huge number of different possible configurations. In nature, though, these proteins… Continue reading You Got General Relativity on My Protein Folding!<\/span><\/a><\/p>\n","protected":false},"author":2,"featured_media":0,"comment_status":"open","ping_status":"1","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[7],"tags":[],"class_list":["post-862","post","type-post","status-publish","format-standard","hentry","category-physics","entry"],"_links":{"self":[{"href":"http:\/\/chadorzel.com\/principles\/wp-json\/wp\/v2\/posts\/862","targetHints":{"allow":["GET"]}}],"collection":[{"href":"http:\/\/chadorzel.com\/principles\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"http:\/\/chadorzel.com\/principles\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"http:\/\/chadorzel.com\/principles\/wp-json\/wp\/v2\/users\/2"}],"replies":[{"embeddable":true,"href":"http:\/\/chadorzel.com\/principles\/wp-json\/wp\/v2\/comments?post=862"}],"version-history":[{"count":0,"href":"http:\/\/chadorzel.com\/principles\/wp-json\/wp\/v2\/posts\/862\/revisions"}],"wp:attachment":[{"href":"http:\/\/chadorzel.com\/principles\/wp-json\/wp\/v2\/media?parent=862"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"http:\/\/chadorzel.com\/principles\/wp-json\/wp\/v2\/categories?post=862"},{"taxonomy":"post_tag","embeddable":true,"href":"http:\/\/chadorzel.com\/principles\/wp-json\/wp\/v2\/tags?post=862"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}