ArticlePloS one2012
Discrete kinetic models from funneled energy landscape simulations.
Article in PloS one, 2012. 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 14 papers.
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Who cites it
14 citing papers in PubMed.
- Reassessing the exon-foldon correspondence using frustration analysis.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Evolution and folding of repeat proteins.Proceedings of the National Academy of Sciences of the United States of America · 2022Article
- Comparing the Aggregation Free Energy Landscapes of Amyloid Beta(1-42) and Amyloid Beta(1-40).Journal of the American Chemical Society · 2017Article
- Network representation of conformational transitions between hidden intermediates of Rd-apocytochrome b562.The Journal of chemical physics · 2015Article
- Capturing coevolutionary signals inrepeat proteins.BMC bioinformatics · 2015Article
- Improved cryoEM-Guided Iterative Molecular Dynamics--Rosetta Protein Structure Refinement Protocol for High Precision Protein Structure Prediction.Journal of chemical theory and computation · 2015Article
- Kinetics of protein-ligand unbinding: Predicting pathways, rates, and rate-limiting steps.Proceedings of the National Academy of Sciences of the United States of America · 2015Article
- Folding pathway of a multidomain protein depends on its topology of domain connectivity.Proceedings of the National Academy of Sciences of the United States of America · 2014Article
- Frustration in biomolecules.Quarterly reviews of biophysics · 2014Review
- Learning To Fold Proteins Using Energy Landscape Theory.Israel journal of chemistry · 2014Article
- Detecting repetitions and periodicities in proteins by tiling the structural space.The journal of physical chemistry. B · 2013Article
- Funneling and frustration in the energy landscapes of some designed and simplified proteins.The Journal of chemical physics · 2013Article
- Stepwise protein folding at near amino acid resolution by hydrogen exchange and mass spectrometry.Proceedings of the National Academy of Sciences of the United States of America · 2013Article
- A disorder-induced domino-like destabilization mechanism governs the folding and functional dynamics of the repeat protein IκBα.PLoS computational biology · 2013Article
Corrections and comments
- Erratum issued
Authors and funding
6 authors.
Funding
Abstract
A general method for facilitating the interpretation of computer simulations of protein folding with minimally frustrated energy landscapes is detailed and applied to a designed ankyrin repeat protein (4ANK). In the method, groups of residues are assigned to foldons and these foldons are used to map the conformational space of the protein onto a set of discrete macrobasins. The free energies of the individual macrobasins are then calculated, informing practical kinetic analysis. Two simple assumptions about the universality of the rate for downhill transitions between macrobasins and the natural local connectivity between macrobasins lead to a scheme for predicting overall folding and unfolding rates, generating chevron plots under varying thermodynamic conditions, and inferring dominant kinetic folding pathways. To illustrate the approach, free energies of macrobasins were calculated from biased simulations of a non-additive structure-based model using two structurally motivated foldon definitions at the full and half ankyrin repeat resolutions. The calculated chevrons have features consistent with those measured in stopped flow chemical denaturation experiments. The dominant inferred folding pathway has an "inside-out", nucleation-propagation like character.
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