Pathways and kinetic barriers in mechanical unfolding and refolding of RNA and proteins

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dc.creatorHyeon, Changbong
dc.creatorDima, Ruxandra I
dc.creatorThirumalai, D.
dc.date2006-11-16
dc.date.accessioned2026-07-07T07:33:59Z
dc.date.available2026-07-07T07:33:59Z
dc.descriptionUsing 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.
dc.description33 pages 7 figures
dc.identifierhttps://arxiv.org/abs/q-bio/0611050
dc.identifierhttp://arxiv.org/abs/q-bio/0611050
dc.identifierStructure (2006) vol 14. 1633-1645
dc.identifier.urihttp://salesiana.dossiersoluciones.com/handle/123456789/119654
dc.subjectBiomolecules
dc.subjectSoft Condensed Matter
dc.titlePathways and kinetic barriers in mechanical unfolding and refolding of RNA and proteins
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