ArticleProtein science : a publication of the Protein Society2004
The effects of nonnative interactions on protein folding rates: theory and simulation.
Article in Protein science : a publication of the Protein Society, 2004. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 71 papers.
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71 citing papers in PubMed.
- The physical and evolutionary energy landscapes of devolved protein sequences corresponding to pseudogenes.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Coevolution-derived native and non-native contacts determine the emergence of a novel fold in a universally conserved family of transcription factors.Protein science : a publication of the Protein Society · 2022Article
- Nanomechanics combined with HDX reveals allosteric drug binding sites of CFTR NBD1.Computational and structural biotechnology journal · 2022Article
- Coarse-Grained Simulations of Protein Folding: Bridging Theory and Experiments.Methods in molecular biology (Clifton, N.J.) · 2022Article
- Investigating the Conformational Ensembles of Intrinsically Disordered Proteins with a Simple Physics-Based Model.The journal of physical chemistry. B · 2020Article
- Mechanistic Insights into Protein Stability and Self-aggregation in GLUT1 Genetic Variants Causing GLUT1-Deficiency Syndrome.The Journal of membrane biology · 2020Review
- Unfolded states under folding conditions accommodate sequence-specific conformational preferences with random coil-like dimensions.Proceedings of the National Academy of Sciences of the United States of America · 2019Article
- Position-, disorder-, and salt-dependent diffusion in binding-coupled-folding of intrinsically disordered proteins.Physical chemistry chemical physics : PCCP · 2019Article
- The Role of Data in Model Building and Prediction: A Survey Through Examples.Entropy (Basel, Switzerland) · 2018Article
- Size and topology modulate the effects of frustration in protein folding.Proceedings of the National Academy of Sciences of the United States of America · 2018Article
- Elucidation of the structural stability and dynamics of heterogeneous intermediate ensembles in unfolding pathway of the N-terminal domain of TDP-43.RSC advances · 2018Article
- Nonnative Energetic Frustrations in Protein Folding at Residual Level: A Simulation Study of Homologous Immunoglobulin-likeInternational journal of molecular sciences · 2018Article
- Frustration, function and folding.Current opinion in structural biology · 2018Review
- Evidence for the principle of minimal frustration in the evolution of protein folding landscapes.Proceedings of the National Academy of Sciences of the United States of America · 2017Article
- Localized structural frustration for evaluating the impact of sequence variants.Nucleic acids research · 2016Article
- 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
- Markov State Models and tICA Reveal a Nonnative Folding Nucleus in Simulations of NuG2.Biophysical journal · 2016Article
- SMOG 2: A Versatile Software Package for Generating Structure-Based Models.PLoS computational biology · 2016Article
- Constructing sequence-dependent protein models using coevolutionary information.Protein science : a publication of the Protein Society · 2016Article
11 more citing papers are in PubMed but not listed here.
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2 authors.
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Abstract
Proteins are minimally frustrated polymers. However, for realistic protein models, nonnative interactions must be taken into account. In this paper, we analyze the effect of nonnative interactions on the folding rate and on the folding free energy barrier. We present an analytic theory to account for the modification on the free energy landscape upon introduction of nonnative contacts, added as a perturbation to the strong native interactions driving folding. Our theory predicts a rate-enhancement regime at fixed temperature, under the introduction of weak, nonnative interactions. We have thoroughly tested this theoretical prediction with simulations of a coarse-grained protein model, by using an off-lattice C(alpha)model of the src-SH3 domain. The strong agreement between results from simulations and theory confirm the nontrivial result that a relatively small amount of nonnative interaction energy can actually assist the folding to the native structure.
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