ArticleJournal of the American Chemical Society2013
Native states of fast-folding proteins are kinetic traps.
Article in Journal of the American Chemical Society, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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Who cites it
23 citing papers in PubMed.
- The Role of the Electronic Structure during Protein Folding through Electron Density-Based Quantum Chemical Descriptors.ACS omega · 2026Article
- Effect of Main and Side Chains on the Folding Mechanism of the Trp-Cage Miniprotein.ACS omega · 2023Article
- Enhanced-Sampling Simulations for the Estimation of Ligand Binding Kinetics: Current Status and Perspective.Frontiers in molecular biosciences · 2022Review
- Unsupervised Learning Methods for Molecular Simulation Data.Chemical reviews · 2021Article
- REVO: Resampling of ensembles by variation optimization.The Journal of chemical physics · 2019Article
- Mapping the Ligand Binding Landscape.Biophysical journal · 2018Article
- Multiple Ligand Unbinding Pathways and Ligand-Induced Destabilization Revealed by WExplore.Biophysical journal · 2017Article
- Capturing a Dynamic Chaperone-Substrate Interaction Using NMR-Informed Molecular Modeling.Journal of the American Chemical Society · 2016Article
- Approximating frustration scores in complex networks via perturbed Laplacian spectra.Physical review. E, Statistical, nonlinear, and soft matter physics · 2015Article
- Free energy landscape of activation in a signalling protein at atomic resolution.Nature communications · 2015Article
- Structural disorder of folded proteins: isotope-edited 2D IR spectroscopy and Markov state modeling.Biophysical journal · 2015Article
- Hierarchical Conformational Analysis of Native Lysozyme Based on Sub-Millisecond Molecular Dynamics Simulations.PloS one · 2015Article
- Benchmarking all-atom simulations using hydrogen exchange.Proceedings of the National Academy of Sciences of the United States of America · 2014Article
- Efficient in silico exploration of RNA interhelical conformations using Euler angles and WExplore.Nucleic acids research · 2014Article
- Quantifying the Sources of Kinetic Frustration in Folding Simulations of Small Proteins.Journal of chemical theory and computation · 2014Article
- WExplore: hierarchical exploration of high-dimensional spaces using the weighted ensemble algorithm.The journal of physical chemistry. B · 2014Article
- A molecular interpretation of 2D IR protein folding experiments with Markov state models.Biophysical journal · 2014Article
- Visualization of protein folding funnels in lattice models.PloS one · 2014Article
- High-Resolution Free-Energy Landscape Analysis of α-Helical Protein Folding: HP35 and Its Double Mutant.Journal of chemical theory and computation · 2013Article
- Effects of Zn2+ binding on the structural and dynamic properties of amyloid β peptide associated with Alzheimer's disease: Asp1 or Glu11?ACS chemical neuroscience · 2013Article
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2 authors.
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Abstract
It has been suggested that the native state of a protein acts as a kinetic hub that can facilitate transitions between nonnative states. Using recently developed tools to quantify mediation probabilities ("hub scores"), we quantify hub-like behavior in atomic resolution trajectories for the first time. We use a data set of trajectory ensembles for 12 fast-folding proteins previously published by D. E. Shaw Research (Lindorff-Larsen, K.; et al. How Fast-Folding Proteins Fold. Science2011, 334, 517) with an aggregate simulation time of over 8.2 ms. We visualize the free-energy landscape of each molecule using configuration space networks, and show that dynamic quantities can be qualitatively understood from visual inspection of the networks. Modularity optimization is used to provide a parameter-free means of tessellating the network into a group of communities. Using hub scores, we find that the percentage of trajectories that are mediated by the native state is 31% when averaged over all molecules, and reaches a maximum of 52% for the homeodomain and chignolin. Furthermore, for these mediated transitions, we use Markov models to determine whether the native state acts as a facilitator for the transition, or as a trap (i.e., an off-pathway detour). Although instances of facilitation are found in 4 of the 12 molecules, we conclude that the native state acts primarily as a trap, which is consistent with the idea of a funnel-like landscape.
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