ArticleProtein science : a publication of the Protein Society2010
Non-native interactions play an effective role in protein folding dynamics.
Article in Protein science : a publication of the Protein Society, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed.
- Heterogeneous folding landscapes and predetermined breaking points within a protein family.Protein science : a publication of the Protein Society · 2024Article
- IDPConformerGenerator: A Flexible Software Suite for Sampling the Conformational Space of Disordered Protein States.The journal of physical chemistry. A · 2022Article
- Effect of Protein Structure on Evolution of Cotranslational Folding.Biophysical journal · 2020Article
- Effects of Topology and Sequence in Protein Folding Linked via Conformational Fluctuations.Biophysical journal · 2020Article
- 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
- Nonnative Energetic Frustrations in Protein Folding at Residual Level: A Simulation Study of Homologous Immunoglobulin-likeInternational journal of molecular sciences · 2018Article
- Conformations of a Metastable SH3 Domain Characterized by smFRET and an Excluded-Volume Polymer Model.Biophysical journal · 2016Article
- Fold and flexibility: what can proteins' mechanical properties tell us about their folding nucleus?Journal of the Royal Society, Interface · 2015Article
- Native contact density and nonnative hydrophobic effects in the folding of bacterial immunity proteins.PLoS computational biology · 2015Article
- Knotted proteins: A tangled tale of Structural Biology.Computational and structural biotechnology journal · 2015Review
- Quantifying the Sources of Kinetic Frustration in Folding Simulations of Small Proteins.Journal of chemical theory and computation · 2014Article
- Energetic frustrations in protein folding at residue resolution: a homologous simulation study of Im9 proteins.PloS one · 2014Article
- Native contacts determine protein folding mechanisms in atomistic simulations.Proceedings of the National Academy of Sciences of the United States of America · 2013Article
- Effects of knots on protein folding properties.PloS one · 2013Article
- De novo prediction of protein folding pathways and structure using the principle of sequential stabilization.Proceedings of the National Academy of Sciences of the United States of America · 2012Article
- Di-Cysteine S,S-Tetrazine: A Potential Ultra-fast Photochemical Trigger to Explore the Early Events of Peptide/Protein Folding.Journal of photochemistry and photobiology. A, Chemistry · 2012Article
- How difficult is it to fold a knotted protein? In silico insights from surface-tethered folding experiments.PloS one · 2012Article
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4 authors.
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Abstract
Systematic Monte Carlo simulations of simple lattice models show that the final stage of protein folding is an ordered process where native contacts get locked (i.e., the residues come into contact and remain in contact for the duration of the folding process) in a well-defined order. The detailed study of the folding dynamics of protein-like sequences designed as to exhibit different contact energy distributions, as well as different degrees of sequence optimization (i.e., participation of non-native interactions in the folding process), reveals significant differences in the corresponding locking scenarios--the collection of native contacts and their average locking times, which are largely ascribable to the dynamics of non-native contacts. Furthermore, strong evidence for a positive role played by non-native contacts at an early folding stage was also found. Interestingly, for topologically simple target structures, a positive interplay between native and non-native contacts is observed also toward the end of the folding process, suggesting that non-native contacts may indeed affect the overall folding process. For target models exhibiting clear two-state kinetics, the relation between the nucleation mechanism of folding and the locking scenario is investigated. Our results suggest that the stabilization of the folding transition state can be achieved through the establishment of a very small network of native contacts that are the first to lock during the folding process.
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