ArticleProceedings of the National Academy of Sciences of the United States of America2013
Experiments and simulations show how long-range contacts can form in expanded unfolded proteins with negligible secondary structure.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 43 papers.
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43 citing papers in PubMed, 85 citations in OpenAlex.
- Signatures of protein fold switching in the unfolded state.Biophysical journal · 2026Article
- Distinguishing near- versus off-critical phase behaviors of intrinsically disordered proteins.Reports on progress in physics. Physical Society (Great Britain) · 2026Article
- Hydrogen-exchange behavior of the L20A mutant of the protein A B domain in guanidinium chloride: evidence for persistent native-like contacts.Scientific reports · 2026Article
- Article
- Molecular insights into the interaction between a disordered protein and a folded RNA.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Molecular insights into the interaction between a disordered protein and a folded RNA.bioRxiv : the preprint server for biology · 2024Article
- SOURSOP: A Python Package for the Analysis of Simulations of Intrinsically Disordered Proteins.Journal of chemical theory and computation · 2023Article
- The biophysics of disordered proteins from the point of view of single-molecule fluorescence spectroscopy.Essays in biochemistry · 2022Article
- Exploring Nearest Neighbor Interactions and Their Influence on the Gibbs Energy Landscape of Unfolded Proteins and Peptides.International journal of molecular sciences · 2022Review
- Residual Structure in the Denatured State of the Fast-Folding UBA(1) Domain from the Human DNA Excision Repair Protein HHR23A.Biochemistry · 2022Article
- Denatured State Conformational Biases in Three-Helix Bundles Containing Divergent Sequences Localize near Turns and Helix Capping Residues.Biochemistry · 2021Article
- Controlling Structure and Dimensions of a Disordered Protein via Mutations.Biochemistry · 2020Article
- Dissecting the Energetics of Intrinsically Disordered Proteins via a Hybrid Experimental and Computational Approach.The journal of physical chemistry. B · 2019Article
- Unfolded states under folding conditions accommodate sequence-specific conformational preferences with random coil-like dimensions.Proceedings of the National Academy of Sciences of the United States of America · 2019Article
- Tau local structure shields an amyloid-forming motif and controls aggregation propensity.Nature communications · 2019Article
- Engineering Order and Cooperativity in a Disordered Protein.Biochemistry · 2019Article
- Improvements to the ABSINTH Force Field for Proteins Based on Experimentally Derived Amino Acid Specific Backbone Conformational Statistics.Journal of chemical theory and computation · 2019Article
- Experimentally Derived and Computationally Optimized Backbone Conformational Statistics for Blocked Amino Acids.Journal of chemical theory and computation · 2019Article
- Local and non-local topological information in the denatured state ensemble of a β-barrel protein.Protein science : a publication of the Protein Society · 2018Article
- Exploring the Denatured State Ensemble by Single-Molecule Chemo-Mechanical Unfolding: The Effect of Force, Temperature, and Urea.Journal of molecular biology · 2018Article
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Authors and funding
5 authors at 2 institutions in 1 country.
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No grant is acknowledged in the PubMed record.
Abstract
The sizes of unfolded proteins under highly denaturing conditions scale as N(0.59) with chain length. This suggests that denaturing conditions mimic good solvents, whereby the preference for favorable chain-solvent interactions causes intrachain interactions to be repulsive, on average. Beyond this generic inference, the broader implications of N(0.59) scaling for quantitative descriptions of denatured state ensembles (DSEs) remain unresolved. Of particular interest is the degree to which N(0.59) scaling can simultaneously accommodate intrachain attractions and detectable long-range contacts. Here we present data showing that the DSE of the N-terminal domain of the L9 (NTL9) ribosomal protein in 8.3 M urea lacks detectable secondary structure and forms expanded conformations in accord with the expected N(0.59) scaling behavior. Paramagnetic relaxation enhancements, however, indicate the presence of detectable long-range contacts in the denatured-state ensemble of NTL9. To explain these observations we used atomistic thermal unfolding simulations to identify ensembles whose properties are consistent with all of the experimental observations, thus serving as useful proxies for the DSE of NTL9 in 8.3 M urea. Analysis of these ensembles shows that residual attractions are present under mimics of good solvent conditions, and for NTL9 they result from low-likelihood, medium/long-range contacts between hydrophobic residues. Our analysis provides a quantitative framework for the simultaneous observation of N(0.59) scaling and low-likelihood long-range contacts for the DSE of NTL9. We propose that such low-likelihood intramolecular hydrophobic clusters might be a generic feature of DSEs that play a gatekeeping role to protect against aggregation during protein folding.
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