ArticleProceedings of the National Academy of Sciences of the United States of America2015
Even with nonnative interactions, the updated folding transition states of the homologs Proteins G & L are extensive and similar.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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Who cites it
11 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
- A Glimpse into the Structural Properties of the Intermediate and Transition State in the Folding of Bromodomain 2 Domain 2 by Φ Value Analysis.International journal of molecular sciences · 2021Article
- Validation of DBFOLD: An efficient algorithm for computing folding pathways of complex proteins.PLoS computational biology · 2020Article
- Water as a Good Solvent for Unfolded Proteins: Folding and Collapse are Fundamentally Different.Journal of molecular biology · 2020Review
- Evolution of All-Atom Protein Force Fields to Improve Local and Global Properties.The journal of physical chemistry letters · 2019Article
- Kinetic and thermodynamic studies reveal chemokine homologues CC11 and CC24 with an almost identical tertiary structure have different folding pathways.BMC biophysics · 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
- Microscopic interpretation of folding ϕ-values using the transition path ensemble.Proceedings of the National Academy of Sciences of the United States of America · 2016Article
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8 authors.
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Abstract
Experimental and computational folding studies of Proteins L & G and NuG2 typically find that sequence differences determine which of the two hairpins is formed in the transition state ensemble (TSE). However, our recent work on Protein L finds that its TSE contains both hairpins, compelling a reassessment of the influence of sequence on the folding behavior of the other two homologs. We characterize the TSEs for Protein G and NuG2b, a triple mutant of NuG2, using ψ analysis, a method for identifying contacts in the TSE. All three homologs are found to share a common and near-native TSE topology with interactions between all four strands. However, the helical content varies in the TSE, being largely absent in Proteins G & L but partially present in NuG2b. The variability likely arises from competing propensities for the formation of nonnative β turns in the naturally occurring proteins, as observed in our TerItFix folding algorithm. All-atom folding simulations of NuG2b recapitulate the observed TSEs with four strands for 5 of 27 transition paths [Lindorff-Larsen K, Piana S, Dror RO, Shaw DE (2011) Science 334(6055):517-520]. Our data support the view that homologous proteins have similar folding mechanisms, even when nonnative interactions are present in the transition state. These findings emphasize the ongoing challenge of accurately characterizing and predicting TSEs, even for relatively simple proteins.
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