ArticleBiophysical journal2007
The mechanical unfolding of ubiquitin through all-atom Monte Carlo simulation with a Go-type potential.
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 16 papers.
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Who cites it
16 citing papers in PubMed.
- ATP-independent unfolding of ubiquitin by Ufd1 initiates Cdc48/p97-mediated substrate processing.Nature structural & molecular biology · 2026Article
- Substrate processing by the Cdc48 ATPase complex is initiated by ubiquitin unfolding.Science (New York, N.Y.) · 2019Article
- The Role of Data in Model Building and Prediction: A Survey Through Examples.Entropy (Basel, Switzerland) · 2018Article
- Nanomechanics of β-rich proteins related to neuronal disorders studied by AFM, all-atom and coarse-grained MD methods.Journal of molecular modeling · 2014Article
- Folding simulations of the A and B domains of protein G.The journal of physical chemistry. B · 2012Article
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- The redundancy of NMR restraints can be used to accelerate the unfolding behavior of an SH3 domain during molecular dynamics simulations.BMC structural biology · 2011Article
- Water's role in the force-induced unfolding of ubiquitin.Proceedings of the National Academy of Sciences of the United States of America · 2010Article
- Molecular basis for the structural stability of an enclosed β-barrel loop.Journal of molecular biology · 2010Article
- Osmolyte-induced separation of the mechanical folding phases of ubiquitin.Proceedings of the National Academy of Sciences of the United States of America · 2009Article
- Insights from coarse-grained Gō models for protein folding and dynamics.International journal of molecular sciences · 2009Review
- Changing the mechanical unfolding pathway of FnIII10 by tuning the pulling strength.Biophysical journal · 2009Article
- The effects of macromolecular crowding on the mechanical stability of protein molecules.Protein science : a publication of the Protein Society · 2008Article
- Toward a molecular understanding of the anisotropic response of proteins to external forces: insights from elastic network models.Biophysical journal · 2008Article
- Universality and diversity of folding mechanics for three-helix bundle proteins.Proceedings of the National Academy of Sciences of the United States of America · 2008Article
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Authors and funding
2 authors.
Funding
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Abstract
The mechanical unfolding of proteins under a stretching force has an important role in living systems and is a logical extension of the more general protein folding problem. Recent advances in experimental methodology have allowed the stretching of single molecules, thus rendering this process ripe for computational study. We use all-atom Monte Carlo simulation with a Gō-type potential to study the mechanical unfolding pathway of ubiquitin. A detailed, robust, well-defined pathway is found, confirming existing results in this vein though using a different model. Additionally, we identify the protein's fundamental stabilizing secondary structure interactions in the presence of a stretching force and show that this fundamental stabilizing role does not persist in the absence of mechanical stress. The apparent success of simulation methods in studying ubiquitin's mechanical unfolding pathway indicates their potential usefulness for future study of the stretching of other proteins and the relationship between protein structure and the response to mechanical deformation.
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