ArticleJournal of molecular biology2008
Subdomain competition, cooperativity, and topological frustration in the folding of CheY.
Article in Journal of molecular biology, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 30 papers.
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Who cites it
30 citing papers in PubMed, 55 citations in OpenAlex.
- Structures of permuted halves of a modern ribose-binding protein.Acta crystallographica. Section D, Structural biology · 2023Article
- Confinement and Crowding Effects on Folding of a Multidomain Y-Family DNA Polymerase.Journal of chemical theory and computation · 2020Article
- Cotranslational folding allows misfolding-prone proteins to circumvent deep kinetic traps.Proceedings of the National Academy of Sciences of the United States of America · 2020Article
- Structure of the archaeal chemotaxis protein CheY in a domain-swapped dimeric conformation.Acta crystallographica. Section F, Structural biology communications · 2019Article
- Frustration and folding of a TIM barrel protein.Proceedings of the National Academy of Sciences of the United States of America · 2019Article
- The Role of Data in Model Building and Prediction: A Survey Through Examples.Entropy (Basel, Switzerland) · 2018Article
- Folding a viral peptide in different membrane environments: pathway and sampling analyses.Journal of biological physics · 2018Article
- Optimal allosteric stabilization sites using contact stabilization analysis.Journal of computational chemistry · 2017Article
- Atomistic structural ensemble refinement reveals non-native structure stabilizes a sub-millisecond folding intermediate of CheY.Scientific reports · 2017Article
- Evidence for the principle of minimal frustration in the evolution of protein folding landscapes.Proceedings of the National Academy of Sciences of the United States of America · 2017Article
- Sequence-, structure-, and dynamics-based comparisons of structurally homologous CheY-like proteins.Proceedings of the National Academy of Sciences of the United States of America · 2017Article
- Evolution of a protein folding nucleus.Protein science : a publication of the Protein Society · 2016Article
- Conformational frustration in calmodulin-target recognition.Journal of molecular recognition : JMR · 2015Article
- Geometrical Frustration in Interleukin-33 Decouples the Dynamics of the Functional Element from the Folding Transition State Ensemble.PloS one · 2015Article
- Modulation of frustration in folding by sequence permutation.Proceedings of the National Academy of Sciences of the United States of America · 2014Article
- Sequence analysis on the information of folding initiation segments in ferredoxin-like fold proteins.BMC structural biology · 2014Article
- Binding and folding of the small bacterial chaperone HdeA.The journal of physical chemistry. B · 2013Article
- Improvements in Markov State Model Construction Reveal Many Non-Native Interactions in the Folding of NTL9.Journal of chemical theory and computation · 2013Article
- De novo prediction of protein folding pathways and structure using the principle of sequential stabilization.Proceedings of the National Academy of Sciences of the United States of America · 2012Article
- The dominant folding route minimizes backbone distortion in SH3.PLoS computational biology · 2012Article
Corrections and comments
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
Abstract
The folding of multidomain proteins often proceeds in a hierarchical fashion with individual domains folding independent of one another. A large single-domain protein, however, can consist of multiple modules whose folding may be autonomous or interdependent in ways that are unclear. We used coarse-grained simulations to explore the folding landscape of the two-subdomain bacterial response regulator CheY. Thermodynamic and kinetic characterization shows the landscape to be highly analogous to the four-state landscape reported for another two-subdomain protein, T4 lysozyme. An on-pathway intermediate structured in the more stable nucleating subdomain was observed, as were transient states frustrated in off-pathway contacts prematurely structured in the weaker subdomain. Local unfolding, or backtracking, was observed in the frustrated state before the native conformation could be reached. Nonproductive frustration was attributable to competition for van der Waals contacts between the two subdomains. In an accompanying article, stopped-flow kinetic measurements support an off-pathway burst-phase intermediate, seemingly consistent with our prediction of early frustration in the folding landscape of CheY. Comparison of the folding mechanisms for CheY, T4 lysozyme, and interleukin-1 beta leads us to postulate that subdomain competition is a general feature of large single-domain proteins with multiple folding modules.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.