ArticleProceedings of the National Academy of Sciences of the United States of America2010
Protein folded states are kinetic hubs.
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. An erratum has been issued. Cited by 101 papers.
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101 citing papers in PubMed.
- Unveiling the Conformational Dynamics of the Histone Tails Using Markov State Modeling.Journal of chemical theory and computation · 2025Article
- Precision spatiotemporal analysis of large-scale compound-protein interactions through molecular dynamics simulation.PNAS nexus · 2025Article
- Exploring force-driven stochastic folding dynamics in mechano-responsive proteins and implications in phenotypic variation.Nature communications · 2025Article
- A Stochastic Landscape Approach for Protein Folding State Classification.Journal of chemical theory and computation · 2024Article
- Hierarchical consciousness: the Nested Observer Windows model.Neuroscience of consciousness · 2024Article
- Folding@home: Achievements from over 20 years of citizen science herald the exascale era.Biophysical journal · 2023Review
- Folding@home: achievements from over twenty years of citizen science herald the exascale era.ArXiv · 2023Article
- Molecular mechanisms of spontaneous curvature and softening in complex lipid bilayer mixtures.Biophysical journal · 2022Article
- The importance of the compact disordered state in the fuzzy interactions between intrinsically disordered proteins.Chemical science · 2022Article
- Unsupervised Learning Methods for Molecular Simulation Data.Chemical reviews · 2021Article
- Atomic resolution of short-range sliding dynamics of thymine DNA glycosylase along DNA minor-groove for lesion recognition.Nucleic acids research · 2021Article
- Heterogeneous folding and stretched kinetics.Proceedings of the National Academy of Sciences of the United States of America · 2020Article
- Global and Kinetic Profiles of Substrate Diffusion inACS omega · 2020Article
- Are RNA networks scale-free?Journal of mathematical biology · 2020Article
- EspcTM: Kinetic Transition Network Based on Trajectory Mapping in Effective Energy Rescaling Space.Frontiers in molecular biosciences · 2020Article
- Article
- Commonly used FRET fluorophores promote collapse of an otherwise disordered protein.Proceedings of the National Academy of Sciences of the United States of America · 2019Article
- Enspara: Modeling molecular ensembles with scalable data structures and parallel computing.The Journal of chemical physics · 2019Article
- Choice of Adaptive Sampling Strategy Impacts State Discovery, Transition Probabilities, and the Apparent Mechanism of Conformational Changes.Journal of chemical theory and computation · 2018Article
- Universal folding pathways of polyhedron nets.Proceedings of the National Academy of Sciences of the United States of America · 2018Article
41 more citing papers are in PubMed but not listed here.
Corrections and comments
- Erratum issued
Authors and funding
2 authors.
Funding
Abstract
Understanding molecular kinetics, and particularly protein folding, is a classic grand challenge in molecular biophysics. Network models, such as Markov state models (MSMs), are one potential solution to this problem. MSMs have recently yielded quantitative agreement with experimentally derived structures and folding rates for specific systems, leaving them positioned to potentially provide a deeper understanding of molecular kinetics that can lead to experimentally testable hypotheses. Here we use existing MSMs for the villin headpiece and NTL9, which were constructed from atomistic simulations, to accomplish this goal. In addition, we provide simpler, humanly comprehensible networks that capture the essence of molecular kinetics and reproduce qualitative phenomena like the apparent two-state folding often seen in experiments. Together, these models show that protein dynamics are dominated by stochastic jumps between numerous metastable states and that proteins have heterogeneous unfolded states (many unfolded basins that interconvert more rapidly with the native state than with one another) yet often still appear two-state. Most importantly, we find that protein native states are hubs that can be reached quickly from any other state. However, metastability and a web of nonnative states slow the average folding rate. Experimental tests for these findings and their implications for other fields, like protein design, are also discussed.
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