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| Quote (dvunkannon @ June 15 2010,14:49) | A query to y'all sciency types:
I was reading Nick Lane's "The 10 Great Inventions of Evolution" last week. At one point he is describing the historical path to understanding how RNA led to protein formation, and the realization that amino acids didn't just attach to random spots on the mRNA chain, instead the ribsome mediated the growth of the protein as it walked the length of the messenger RNA.
I was suddenly struck by the question of whether any protein folding algorithm actually works the same the way the ribosome does.
My general impression of ab initio protein folding algorithms is that they start with the whole linear string of peptides floating freely in a solvent, and then let the whole string twist and collapse under the influence of local force fields. They don't, to my knowledge, build up the protein one AA at a time from one end which is tethered to a large object (ribosome + mRNA). Not surprisingly, they often don't fold into the native conformation.
Reinforcing my general impression, a google search on 'incremental protein folding algorithm' didn't generate any decent hits.
So I ask you - do you know of any such algorithm? Is this an idea that has been tried and discarded? It would seem to me to be much faster in some ways. Any suggestions on where/who could provide better insights? |
The search you're looking for is "algorithm cotranslational protein folding"
Since co-translational folding is a known (but fought over) mechanism, that makes solution folding of a whole denatured protein and the folding of a nascent peptide during translation different, this is important.
http://www.jbc.org/content/275/22/16597.full
And people are starting to work on it:
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1523309/
"Molecular Simulations of Cotranslational Protein Folding: Fragment Stabilities, Folding Cooperativity, and Trapping in the Ribosome"
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