ArticlePhysical review letters2013
Simplified protein models: predicting folding pathways and structure using amino acid sequences.
Article in Physical review letters, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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Who cites it
11 citing papers in PubMed.
- Recent Advances in Protein Folding Pathway Prediction through Computational Methods.Current medicinal chemistry · 2024Review
- Water as a Good Solvent for Unfolded Proteins: Folding and Collapse are Fundamentally Different.Journal of molecular biology · 2020Review
- Modeling of Disordered Protein Structures Using Monte Carlo Simulations and Knowledge-Based Statistical Force Fields.International journal of molecular sciences · 2019Review
- Trajectory-based training enables protein simulations with accurate folding and Boltzmann ensembles in cpu-hours.PLoS computational biology · 2018Article
- The case for defined protein folding pathways.Proceedings of the National Academy of Sciences of the United States of America · 2017Article
- Cooperative folding near the downhill limit determined with amino acid resolution by hydrogen exchange.Proceedings of the National Academy of Sciences of the United States of America · 2016Article
- Even with nonnative interactions, the updated folding transition states of the homologs Proteins G & L are extensive and similar.Proceedings of the National Academy of Sciences of the United States of America · 2015Article
- 3dRNAscore: a distance and torsion angle dependent evaluation function of 3D RNA structures.Nucleic acids research · 2015Article
- The nature of protein folding pathways.Proceedings of the National Academy of Sciences of the United States of America · 2014Review
- Folding of a large protein at high structural resolution.Proceedings of the National Academy of Sciences of the United States of America · 2013Article
- Revealing what gets buried first in protein folding.Proceedings of the National Academy of Sciences of the United States of America · 2013Article
Corrections and comments
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Authors and funding
3 authors.
Funding
Abstract
We demonstrate the ability of simultaneously determining a protein's folding pathway and structure using a properly formulated model without prior knowledge of the native structure. Our model employs a natural coordinate system for describing proteins and a search strategy inspired by the observation that real proteins fold in a sequential fashion by incrementally stabilizing nativelike substructures or "foldons." Comparable folding pathways and structures are obtained for the twelve proteins recently studied using atomistic molecular dynamics simulations [K. Lindorff-Larsen, S. Piana, R. O. Dror, D. E. Shaw, Science 334, 517 (2011)], with our calculations running several orders of magnitude faster. We find that nativelike propensities in the unfolded state do not necessarily determine the order of structure formation, a departure from a major conclusion of the molecular dynamics study. Instead, our results support a more expansive view wherein intrinsic local structural propensities may be enhanced or overridden in the folding process by environmental context. The success of our search strategy validates it as an expedient mechanism for folding both in silico and in vivo.
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