ArticleProceedings of the National Academy of Sciences of the United States of America2013
Comparing a simple theoretical model for protein folding with all-atom molecular dynamics simulations.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 46 papers.
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Who cites it
46 citing papers in PubMed.
- Isomer-sourced structure iteration methods forComputational and structural biotechnology journal · 2024Article
- On the role of native contact cooperativity in protein folding.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- On the origin of cooperativity effects in the formation of self-assembled molecular networks at the liquid/solid interface.Chemical science · 2024Article
- Accurate prediction of protein folding mechanisms by simple structure-based statistical mechanical models.Nature communications · 2023Article
- Conformational Tuning Shapes the Balance between Functional Promiscuity and Specialization in ParalogousBiochemistry · 2023Article
- Einstein Model of a Graph to Characterize Protein Folded/Unfolded States.Molecules (Basel, Switzerland) · 2023Article
- Genetically encoded non-canonical amino acids reveal asynchronous dark reversion of chromophore, backbone, and side-chains in EL222.Protein science : a publication of the Protein Society · 2023Article
- Modular tipping points: How local network structure impacts critical transitions in networked spin systems.PloS one · 2023Article
- The Wako-Saitô-Muñoz-Eaton Model for Predicting Protein Folding and Dynamics.Molecules (Basel, Switzerland) · 2022Review
- Structural-Energetic Basis for Coupling between Equilibrium Fluctuations and Phosphorylation in a Protein Native Ensemble.ACS central science · 2022Article
- Critical transitions in degree mixed networks: A discovery of forbidden tipping regions in networked spin systems.PloS one · 2022Article
- The Protein Folding Problem: The Role of Theory.Journal of molecular biology · 2021Review
- Modern Kinetics and Mechanism of Protein Folding: A Retrospective.The journal of physical chemistry. B · 2021Article
- Weakening of interaction networks with aging in tip-link protein induces hearing loss.The Biochemical journal · 2021Article
- A hierarchy of coupling free energies underlie the thermodynamic and functional architecture of protein structures.Current research in structural biology · 2021Review
- Disordered proteins follow diverse transition paths as they fold and bind to a partner.Science (New York, N.Y.) · 2020Article
- Effects of Topology and Sequence in Protein Folding Linked via Conformational Fluctuations.Biophysical journal · 2020Article
- Competition of individual domain folding with inter-domain interaction in WW domain engineered repeat proteins.Physical chemistry chemical physics : PCCP · 2019Article
- Thermodynamics and folding landscapes of large proteins from a statistical mechanical model.Current research in structural biology · 2019Article
- Measuring the average shape of transition paths during the folding of a single biological molecule.Proceedings of the National Academy of Sciences of the United States of America · 2019Article
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3 authors.
Funding
Abstract
Advances in computing have enabled microsecond all-atom molecular dynamics trajectories of protein folding that can be used to compare with and test critical assumptions of theoretical models. We show that recent simulations by the Shaw group (10, 11, 14, 15) are consistent with a key assumption of an Ising-like theoretical model that native structure grows in only a few regions of the amino acid sequence as folding progresses. The distribution of mechanisms predicted by simulating the master equation of this native-centric model for the benchmark villin subdomain, with only two adjustable thermodynamic parameters and one temperature-dependent kinetic parameter, is remarkably similar to the distribution in the molecular dynamics trajectories.
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