ArticleJournal of molecular biology2008
Denatured-state energy landscapes of a protein structural database reveal the energetic determinants of a framework model for folding.
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 17 papers.
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Who cites it
17 citing papers in PubMed, 28 citations in OpenAlex.
- Ensemble molecular mimicry correlates with antibody cross-reactivity in proteome-wide studies.Frontiers in immunology · 2026Article
- Statistical Thermodynamics of the Protein Ensemble: Mediating Function and Evolution.Annual review of biophysics · 2025Review
- Impact of local unfolding fluctuations on the evolution of regional sequence preferences in proteins.Protein science : a publication of the Protein Society · 2025Article
- Intrinsically disordered regions that drive phase separation form a robustly distinct protein class.The Journal of biological chemistry · 2023Article
- A Thermodynamic Atlas of Proteomes Reveals Energetic Innovation across the Tree of Life.Molecular biology and evolution · 2022Article
- Structural and Energetic Characterization of the Denatured State from the Perspectives of Peptides, the Coil Library, and Intrinsically Disordered Proteins.Molecules (Basel, Switzerland) · 2021Review
- Hidden dynamic signatures drive substrate selectivity in the disordered phosphoproteome.Proceedings of the National Academy of Sciences of the United States of America · 2020Article
- The role of negative selection in protein evolution revealed through the energetics of the native state ensemble.Proteins · 2016Article
- Temperature and urea have opposing impacts on polyproline II conformational bias.Biochemistry · 2013Article
- Residual structure in unfolded proteins.Current opinion in structural biology · 2012Review
- Ensemble-based methods for describing protein dynamics.Current opinion in pharmacology · 2010Review
- Denatured states of low-complexity polypeptide sequences differ dramatically from those of foldable sequences.Proceedings of the National Academy of Sciences of the United States of America · 2010Article
- Thermodynamics of loop formation in the denatured state of rhodopseudomonas palustris cytochrome c': scaling exponents and the reconciliation problem.Journal of molecular biology · 2009Article
- Peptide conformer acidity analysis of protein flexibility monitored by hydrogen exchange.Biochemistry · 2009Article
- An energetic representation of protein architecture that is independent of primary and secondary structure.Biophysical journal · 2009Article
- Energetic profiling of protein folds.Methods in enzymology · 2009Article
- Characterization of the unfolded state of repeat proteins.HFSP journal · 2008Article
Corrections and comments
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Authors and funding
5 authors at 1 institution in 1 country.
Funding
Abstract
Position-specific denatured-state thermodynamics were determined for a database of human proteins by use of an ensemble-based model of protein structure. The results of modeling denatured protein in this manner reveal important sequence-dependent thermodynamic properties in the denatured ensembles as well as fundamental differences between the denatured and native ensembles in overall thermodynamic character. The generality and robustness of these results were validated by performing fold-recognition experiments, whereby sequences were matched with their respective folds based on amino acid propensities for the different energetic environments in the protein, as determined through cluster analysis. Correlation analysis between structure and energetic information revealed that sequence segments destined for beta-sheet in the final native fold are energetically more predisposed to a broader repertoire of states than are sequence segments destined for alpha-helix. These results suggest that within the subensemble of mostly unstructured states, the energy landscapes are dominated by states in which parts of helices adopt structure, whereas structure formation for sequences destined for beta-strand is far less probable. These results support a framework model of folding, which suggests that, in general, the denatured state has evolutionarily evolved to avoid low-energy conformations in sequences that ultimately adopt beta-strand. Instead, the denatured state evolved so that sequence segments that ultimately adopt alpha-helix and coil will have a high intrinsic structure formation capability, thus serving as potential nucleation sites.
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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.