ArticleThe journal of physical chemistry. B2009
Crowding effects on the mechanical stability and unfolding pathways of ubiquitin.
Article in The journal of physical chemistry. B, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed, 35 citations in OpenAlex.
- PEG-mCherry interactions beyond classical macromolecular crowding.Protein science : a publication of the Protein Society · 2025Article
- Crowder titrations enable the quantification of driving forces for macromolecular phase separation.Biophysical journal · 2024Article
- Reaching new levels of realism in modeling biological macromolecules in cellular environments.Journal of molecular graphics & modelling · 2013Review
- Antibody nanoparticle dispersions formed with mixtures of crowding molecules retain activity and in vivo bioavailability.Journal of pharmaceutical sciences · 2012Article
- A physics-based approach of coarse-graining the cytoplasm of Escherichia coli (CGCYTO).Biophysical journal · 2012Article
- Three-dimensional stochastic off-lattice model of binding chemistry in crowded environments.PloS one · 2012Article
- Power-law dependence of the melting temperature of ubiquitin on the volume fraction of macromolecular crowders.The Journal of chemical physics · 2011Article
- Unified regression model of binding equilibria in crowded environments.Scientific reports · 2011Article
- Article
- Effects of macromolecular crowding on protein conformational changes.PLoS computational biology · 2010Article
- Molecular crowding stabilizes folded RNA structure by the excluded volume effect.Journal of the American Chemical Society · 2010Article
- The folding transition-state ensemble of a four-helix bundle protein: helix propensity as a determinant and macromolecular crowding as a probe.Biophysical journal · 2010Article
- Models of macromolecular crowding effects and the need for quantitative comparisons with experiment.Current opinion in structural biology · 2010Review
- Generalized fundamental measure theory for atomistic modeling of macromolecular crowding.Physical review. E, Statistical, nonlinear, and soft matter physics · 2010Article
- Insights from coarse-grained Gō models for protein folding and dynamics.International journal of molecular sciences · 2009Review
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
Abstract
The interiors of cells are crowded, thus making it important to assess the effects of macromolecules on the folding of proteins. Using the self-organized polymer (SOP) model, which is a coarse-grained representation of polypeptide chains, we probe the mechanical stability of ubiquitin (Ub) monomers and trimers ((Ub)(3)) in the presence of monodisperse spherical crowding agents. Crowding increases the volume fraction (Phi(c))-dependent average force (f(u)(Phi(c))), relative to the value at Phi(c) = 0, needed to unfold Ub and the polyprotein. For a given Phi(c), the values of f(u)(Phi(c)) increase as the diameter (sigma(c)) of the crowding particles decreases. The average unfolding force f(u)(Phi(c)) depends on the ratio D/R(g), where D approximately sigma(c)(pi/6Phi(c))(1/3), with R(g) being the radius of gyration of Ub (or (Ub)(3)) in the unfolded state. Examination of the unfolding pathways shows that, relative to Phi(c) = 0, crowding promotes reassociation of ruptured secondary structural elements. Both the nature of the unfolding pathways and f(u)(Phi(c)) for (Ub)(3) are altered in the presence of crowding particles, with the effect being most dramatic for the subunit that unfolds last. We predict, based on SOP simulations and theoretical arguments, that f(u)(Phi(c)) approximately Phi(c)(1/3nu), where nu is the Flory exponent that describes the unfolded (random coil) state of the protein.
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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.