ArticleProceedings of the National Academy of Sciences of the United States of America2010
Competition between native topology and nonnative interactions in simple and complex folding kinetics of natural and designed proteins.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 40 papers.
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Who cites it
40 citing papers in PubMed.
- Article
- On the role of native contact cooperativity in protein folding.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- A Method for Assessing the Robustness of Protein Structures by Randomizing Packing Interactions.Frontiers in molecular biosciences · 2022Article
- Fuzziness and Frustration in the Energy Landscape of Protein Folding, Function, and Assembly.Accounts of chemical research · 2021Review
- A hierarchy of coupling free energies underlie the thermodynamic and functional architecture of protein structures.Current research in structural biology · 2021Review
- Single molecule force spectroscopy reveals the context dependent folding pathway of the C-terminal fragment of Top7.Chemical science · 2020Article
- Modeling of Disordered Protein Structures Using Monte Carlo Simulations and Knowledge-Based Statistical Force Fields.International journal of molecular sciences · 2019Review
- Disordered linkers in multidomain allosteric proteins: Entropic effect to favor the open state or enhanced local concentration to favor the closed state?Protein science : a publication of the Protein Society · 2018Article
- Nonnative Energetic Frustrations in Protein Folding at Residual Level: A Simulation Study of Homologous Immunoglobulin-likeInternational journal of molecular sciences · 2018Article
- Molecular recognition and packing frustration in a helical protein.PLoS computational biology · 2017Article
- As Simple As Possible, but Not Simpler: Exploring the Fidelity of Coarse-Grained Protein Models for Simulated Force Spectroscopy.PLoS computational biology · 2016Article
- Quantifying Nonnative Interactions in the Protein-Folding Free-Energy Landscape.Biophysical journal · 2016Article
- Theoretical Insights into the Biophysics of Protein Bi-stability and Evolutionary Switches.PLoS computational biology · 2016Article
- The Folding of de Novo Designed Protein DS119 via Molecular Dynamics Simulations.International journal of molecular sciences · 2016Article
- Dimensions, energetics, and denaturant effects of the protein unstructured state.Protein science : a publication of the Protein Society · 2016Article
- Constructing sequence-dependent protein models using coevolutionary information.Protein science : a publication of the Protein Society · 2016Article
- Domains of Pyrococcus furiosus L-asparaginase fold sequentially and assemble through strong intersubunit associative forces.Extremophiles : life under extreme conditions · 2015Article
- Native contact density and nonnative hydrophobic effects in the folding of bacterial immunity proteins.PLoS computational biology · 2015Article
- Biophysics of protein evolution and evolutionary protein biophysics.Journal of the Royal Society, Interface · 2014Article
- Frustration in biomolecules.Quarterly reviews of biophysics · 2014Review
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2 authors.
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Abstract
We compared folding properties of designed protein Top7 and natural protein S6 by using coarse-grained chain models with a mainly native-centric construct that accounted also for nonnative hydrophobic interactions and desolvation barriers. Top7 and S6 have similar secondary structure elements and are approximately equal in length and hydrophobic composition. Yet their experimental folding kinetics were drastically different. Consistent with experiment, our simulated folding chevron arm for Top7 exhibited a severe rollover, whereas that for S6 was essentially linear, and Top7 model kinetic relaxation was multiphasic under strongly folding conditions. The peculiar behavior of Top7 was associated with several classes of kinetic traps in our model. Significantly, the amino acid residues participating in nonnative interactions in trapped conformations in our Top7 model overlapped with those deduced experimentally. These affirmations suggest that the simple ingredients of native topology plus sequence-dependent nonnative interactions are sufficient to account for some key features of protein folding kinetics. Notably, when nonnative interactions were absent in the model, Top7 chevron rollover was not correctly predicted. In contrast, nonnative interactions had little effect on the quasi linearity of the model folding chevron arm for S6. This intriguing distinction indicates that folding cooperativity is governed by a subtle interplay between the sequence-dependent driving forces for native topology and the locations of favorable nonnative interactions entailed by the same sequence. Constructed with a capability to mimic this interplay, our simple modeling approach should be useful in general for assessing a designed sequence's potential to fold cooperatively.
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