ArticleBiophysical journal2007
Refolding upon force quench and pathways of mechanical and thermal unfolding of ubiquitin.
Article in Biophysical journal, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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Who cites it
12 citing papers in PubMed.
- Is Posttranslational Folding More Efficient Than Refolding from a Denatured State: A Computational Study.The journal of physical chemistry. B · 2023Article
- The Role of Data in Model Building and Prediction: A Survey Through Examples.Entropy (Basel, Switzerland) · 2018Article
- The role of binding site on the mechanical unfolding mechanism of ubiquitin.Scientific reports · 2015Article
- Article
- Minimum energy compact structures in force-quench polyubiquitin folding are domain swapped.Proceedings of the National Academy of Sciences of the United States of America · 2011Article
- Molecular basis for the structural stability of an enclosed β-barrel loop.Journal of molecular biology · 2010Article
- Thermostability of the N-terminal RNA-binding domain of the SARS-CoV nucleocapsid protein: experiments and numerical simulations.Biophysical journal · 2009Article
- Insights from coarse-grained Gō models for protein folding and dynamics.International journal of molecular sciences · 2009Review
- Crowding effects on the mechanical stability and unfolding pathways of ubiquitin.The journal of physical chemistry. B · 2009Article
- Changing the mechanical unfolding pathway of FnIII10 by tuning the pulling strength.Biophysical journal · 2009Article
- Secondary structure, mechanical stability, and location of transition state of proteins.Biophysical journal · 2007Article
- Force-clamp spectroscopy of single-protein monomers reveals the individual unfolding and folding pathways of I27 and ubiquitin.Biophysical journal · 2007Article
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The refolding from stretched initial conformations of ubiquitin (PDB ID: 1ubq) under the quenched force is studied using the C(alpha)-Gō 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) approximately exp(f(q)Deltax(F)/k(B)T), where f(q) is the quench force and Deltax(F) approximately 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 Deltax(F) approximately 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 Deltax(UF) approximately 0.24 nm, which is in reasonable agreement with the experimental data.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.