dorsal/arxiv
View SchemaPathways and kinetic barriers in mechanical unfolding and refolding of RNA and proteins
| Authors | Changbong Hyeon, Ruxandra I Dima, D. Thirumalai |
|---|---|
| Categories | |
| ArXiv ID | q-bio/0611050 |
| URL | https://arxiv.org/abs/q-bio/0611050 |
| Journal | Structure (2006) vol 14. 1633-1645 |
Abstract
Using self-organized polymer models, we predict mechanical unfolding and refolding pathways of ribo-zymes, and the green fluorescent protein. In agreement with experiments, there are between six and eight unfolding transitions in the Tetrahymena ribozyme. Depending on the loading rate, the number of rips in the force-ramp unfolding of the Azoarcus ribozymes is between two and four. Force-quench refolding of the P4-P6 subdomain of the Tetrahymena ribozyme occurs through a compact intermediate. Subsequent formation of tertiary contacts between helices P5b-P6a and P5a/P5c-P4 leads to the native state. The force-quench refolding pathways agree with ensemble experiments. In the dominant unfolding route, the N-terminal a helix of GFP unravels first, followed by disruption of the N terminus b strand. There is a third intermediate that involves disruption of three other strands. In accord with experiments, the force-quench refolding pathway of GFP is hierarchic, with the rate-limiting step being the closure of the barrel.
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"abstract": "Using self-organized polymer models, we predict mechanical unfolding and\nrefolding pathways of ribo-zymes, and the green fluorescent protein. In\nagreement with experiments, there are between six and eight unfolding\ntransitions in the Tetrahymena ribozyme. Depending on the loading rate, the\nnumber of rips in the force-ramp unfolding of the Azoarcus ribozymes is between\ntwo and four. Force-quench refolding of the P4-P6 subdomain of the Tetrahymena\nribozyme occurs through a compact intermediate. Subsequent formation of\ntertiary contacts between helices P5b-P6a and P5a/P5c-P4 leads to the native\nstate. The force-quench refolding pathways agree with ensemble experiments. In\nthe dominant unfolding route, the N-terminal a helix of GFP unravels first,\nfollowed by disruption of the N terminus b strand. There is a third\nintermediate that involves disruption of three other strands. In accord with\nexperiments, the force-quench refolding pathway of GFP is hierarchic, with the\nrate-limiting step being the closure of the barrel.",
"arxiv_id": "q-bio/0611050",
"authors": [
"Changbong Hyeon",
"Ruxandra I Dima",
"D. Thirumalai"
],
"categories": [
"q-bio.BM",
"cond-mat.soft"
],
"journal_ref": "Structure (2006) vol 14. 1633-1645",
"title": "Pathways and kinetic barriers in mechanical unfolding and refolding of RNA and proteins",
"url": "https://arxiv.org/abs/q-bio/0611050"
},
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