ArticleProceedings of the National Academy of Sciences of the United States of America2004
Differences in the folding transition state of ubiquitin indicated by phi and psi analyses.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2004. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 44 papers.
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44 citing papers in PubMed.
- DreamFold: A World Model to efficiently generate protein folding pathways in the latent space.Protein science : a publication of the Protein Society · 2026Article
- Rapid estimation of protein folding pathways from sequence alone using AlphaFold2.Nature communications · 2025Article
- Structure of a transient protein-folding intermediate by pressure-jump NMR spectroscopy.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Effects of binding partners on thermal reversion rates of photoswitchable molecules.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- AlphaFold2bioRxiv : the preprint server for biology · 2024Article
- Proline Peptide Bond Isomerization in Ubiquitin Under Folding and Denaturing Conditions by Pressure-Jump NMR.Journal of molecular biology · 2024Article
- Residue-based correlation between equilibrium and rate constants is an experimental formulation of the consistency principle for smooth structural changes of proteins.Biophysics and physicobiology · 2023Article
- DMSO-Quenched H/D-Exchange 2D NMR Spectroscopy and Its Applications in Protein Science.Molecules (Basel, Switzerland) · 2022Review
- Effects of ionic strength on the folding and stability of SAMP1, a ubiquitin-like halophilic protein.Biophysical journal · 2022Article
- Engineered Metal-Binding Sites to Probe Protein Folding Transition States: Psi Analysis.Methods in molecular biology (Clifton, N.J.) · 2022Article
- Residual Structure of Unfolded Ubiquitin as Revealed by Hydrogen/Deuterium-Exchange 2D NMR.Biophysical journal · 2020Article
- Interrupted Pressure-Jump NMR Experiments Reveal Resonances of On-Pathway Protein Folding Intermediate.The journal of physical chemistry. B · 2018Article
- 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
- 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
- The loop hypothesis: contribution of early formed specific non-local interactions to the determination of protein folding pathways.Biophysical reviews · 2013Review
- A "slow" protein folds quickly in the end.Proceedings of the National Academy of Sciences of the United States of America · 2013Article
- Atomic-level description of ubiquitin folding.Proceedings of the National Academy of Sciences of the United States of America · 2013Article
- The folding transition state of protein L is extensive with nonnative interactions (and not small and polarized).Journal of molecular biology · 2012Article
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Abstract
We compare the folding transition state (TS) of ubiquitin previously identified by using psi analysis to that determined by using analysis. Both methods attempt to identify interactions and their relative populations at the rate-limiting step for folding. The TS ensemble derived from psi analysis has an extensive native-like chain topology, with a four-stranded beta-sheet network and a portion of the major helix. According to analysis, however, the TS is much smaller and more polarized, with only a local helix/hairpin motif. We find that structured regions can have values far from unity, the canonical value for such sites, because of structural relaxation of the TS. Consequently, these sites may be incorrectly interpreted as contributing little to the structure of the TS. These results stress the need for caution when interpreting and drawing conclusions from analysis alone and highlight the need for more specific tools for examining the structure and energetics of the TS ensemble.
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