ArticleJournal of molecular biology2012
The folding transition state of protein L is extensive with nonnative interactions (and not small and polarized).
Article in Journal of molecular biology, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed.
- Rapid estimation of protein folding pathways from sequence alone using AlphaFold2.Nature communications · 2025Article
- AlphaFold2bioRxiv : the preprint server for biology · 2024Article
- Engineered Metal-Binding Sites to Probe Protein Folding Transition States: Psi Analysis.Methods in molecular biology (Clifton, N.J.) · 2022Article
- Slow Folding of a Helical Protein: Large Barriers, Strong Internal Friction, or a Shallow, Bumpy Landscape?The journal of physical chemistry. B · 2020Article
- Perplexing cooperative folding and stability of a low-sequence complexity, polyproline 2 protein lacking a hydrophobic core.Proceedings of the National Academy of Sciences of the United States of America · 2017Article
- Structure-Based Prediction of Protein-Folding Transition Paths.Biophysical journal · 2016Article
- Cooperative folding near the downhill limit determined with amino acid resolution by hydrogen exchange.Proceedings of the National Academy of Sciences of the United States of America · 2016Article
- Even with nonnative interactions, the updated folding transition states of the homologs Proteins G & L are extensive and similar.Proceedings of the National Academy of Sciences of the United States of America · 2015Article
- Loss of conformational entropy in protein folding calculated using realistic ensembles and its implications for NMR-based calculations.Proceedings of the National Academy of Sciences of the United States of America · 2014Article
- Direct observation of parallel folding pathways revealed using a symmetric repeat protein system.Biophysical journal · 2014Article
- A comparison of the folding kinetics of a small, artificially selected DNA aptamer with those of equivalently simple naturally occurring proteins.Protein science : a publication of the Protein Society · 2014Article
- Revealing what gets buried first in protein folding.Proceedings of the National Academy of Sciences of the United States of America · 2013Article
- Probing the protein-folding mechanism using denaturant and temperature effects on rate constants.Proceedings of the National Academy of Sciences of the United States of America · 2013Article
- Simplified protein models: predicting folding pathways and structure using amino acid sequences.Physical review letters · 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
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7 authors.
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Abstract
Progress in understanding protein folding relies heavily upon an interplay between experiment and theory. In particular, readily interpretable experimental data that can be meaningfully compared to simulations are required. According to standard mutational ϕ analysis, the transition state for Protein L contains only a single hairpin. However, we demonstrate here using ψ analysis with engineered metal ion binding sites that the transition state is extensive, containing the entire four-stranded β sheet. Underreporting of the structural content of the transition state by ϕ analysis also occurs for acyl phosphatase [Pandit, A. D., Jha, A., Freed, K. F. & Sosnick, T. R., (2006). Small proteins fold through transition states with native-like topologies. J. Mol. Biol.361, 755-770], ubiquitin [Sosnick, T. R., Dothager, R. S. & Krantz, B. A., (2004). Differences in the folding transition state of ubiquitin indicated by ϕ and ψ analyses. Proc. Natl Acad. Sci. USA 101, 17377-17382] and BdpA [Baxa, M., Freed, K. F. & Sosnick, T. R., (2008). Quantifying the structural requirements of the folding transition state of protein A and other systems. J. Mol. Biol.381, 1362-1381]. The carboxy-terminal hairpin in the transition state of Protein L is found to be nonnative, a significant result that agrees with our Protein Data Bank-based backbone sampling and all-atom simulations. The nonnative character partially explains the failure of accepted experimental and native-centric computational approaches to adequately describe the transition state. Hence, caution is required even when an apparent agreement exists between experiment and theory, thus highlighting the importance of having alternative methods for characterizing transition states.
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