dorsal/arxiv
View SchemaRefolding upon force quench and pathways of mechanical and thermal unfolding of ubiquitin
| Authors | Mai Suan Li, Maksim Kouza, Chin-Kun Hu |
|---|---|
| Categories | |
| ArXiv ID | q-bio/0611080 |
| URL | https://arxiv.org/abs/q-bio/0611080 |
| DOI | 10.1529/biophysj.106.087684 |
| Journal | Biophysical Journal, 92, 547-561 (2007) |
Abstract
The refolding from stretched initial conformations of ubiquitin (PDB ID: 1ubq) under the quenched force is studied using the Go model and the Langevin dynamics. It is shown that the refolding decouples the collapse and folding kinetics. The force quench refolding times scale as tau_F ~ exp(f_q*x_F/k_B*T), where f_q is the quench force and x_F = 0.96 nm is the location of the average transition state along the reaction coordinate given by the end-to-end distance. This value is close to x_F = 0.8 nm obtained from the force-clamp experiments. The mechanical and thermal unfolding pathways are studied and compared with the experimental and all-atom simulation results in detail. The sequencing of thermal unfolding was found to be markedly different from the mechanical one. It is found that fixing the N-terminus of ubiquitin changes its mechanical unfolding pathways much more drastically compared to the case when the C-end is anchored. We obtained the distance between the native state and the transition state x_UF=0.24 nm which is in reasonable agreement with the experimental data.
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"abstract": "The refolding from stretched initial conformations of ubiquitin (PDB ID:\n1ubq) under the quenched force is studied using the Go model and the Langevin\ndynamics. It is shown that the refolding decouples the collapse and folding\nkinetics. The force quench refolding times scale as tau_F ~ exp(f_q*x_F/k_B*T),\nwhere f_q is the quench force and x_F = 0.96 nm is the location of the average\ntransition state along the reaction coordinate given by the end-to-end\ndistance. This value is close to x_F = 0.8 nm obtained from the force-clamp\nexperiments. The mechanical and thermal unfolding pathways are studied and\ncompared with the experimental and all-atom simulation results in detail. The\nsequencing of thermal unfolding was found to be markedly different from the\nmechanical one. It is found that fixing the N-terminus of ubiquitin changes its\nmechanical unfolding pathways much more drastically compared to the case when\nthe C-end is anchored. We obtained the distance between the native state and\nthe transition state x_UF=0.24 nm which is in reasonable agreement with the\nexperimental data.",
"arxiv_id": "q-bio/0611080",
"authors": [
"Mai Suan Li",
"Maksim Kouza",
"Chin-Kun Hu"
],
"categories": [
"q-bio.BM"
],
"doi": "10.1529/biophysj.106.087684",
"journal_ref": "Biophysical Journal, 92, 547-561 (2007)",
"title": "Refolding upon force quench and pathways of mechanical and thermal unfolding of ubiquitin",
"url": "https://arxiv.org/abs/q-bio/0611080"
},
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