ArticleProceedings of the National Academy of Sciences of the United States of America2005
Statistical coil model of the unfolded state: resolving the reconciliation problem.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2005. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 131 papers.
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131 citing papers in PubMed, 299 citations in OpenAlex.
- Nearest-Neighbor Effects in Short Unfolded Peptides: An Assessment of Molecular Dynamics Force Fields.Journal of chemical information and modeling · 2026Article
- In Search of Shape in the Unshaped: Constructing Ensembles of Intrinsically Disordered Proteins.Biophysics reviews · 2026Article
- Nearest neighbour interactions between amino acid residues in short peptides and coil libraries.RSC advances · 2026Article
- Classification of intramolecular side-chain hydrogen bonds in coil fragments of globular proteins.Protein science : a publication of the Protein Society · 2025Article
- AutoRNC: An automated modeling program for building atomic models of ribosome-nascent chain complexes.Structure (London, England : 1993) · 2024Article
- Using NMR diffusion data to validate MD models of disordered proteins: Test case of N-terminal tail of histone H4.Biophysical journal · 2024Article
- Generation of unfolded outer membrane protein ensembles defined by hydrodynamic properties.European biophysics journal : EBJ · 2023Article
- Exploring Nearest Neighbor Interactions and Their Influence on the Gibbs Energy Landscape of Unfolded Proteins and Peptides.International journal of molecular sciences · 2022Review
- Randomizing of Oligopeptide Conformations by Nearest Neighbor Interactions between Amino Acid Residues.Biomolecules · 2022Article
- Accurate prediction of protein torsion angles using evolutionary signatures and recurrent neural network.Scientific reports · 2021Article
- Tandem domain structure determination based on a systematic enumeration of conformations.Scientific reports · 2021Article
- CheSPI: chemical shift secondary structure population inference.Journal of biomolecular NMR · 2021Article
- Effects of pH on an IDP conformational ensemble explored by molecular dynamics simulation.Biophysical chemistry · 2021Article
- Comprehensive Structural and Thermodynamic Analysis of Prefibrillar WT α-Synuclein and Its G51D, E46K, and A53T Mutants by a Combination of Small-Angle X-ray Scattering and Variational Bayesian Weighting.Journal of chemical information and modeling · 2020Article
- Impact of Heat on Coil Hydrodynamic Size Yields the Energetics of Denatured State Conformational Bias.The journal of physical chemistry. B · 2019Article
- On the Interpretation of Force-Induced Unfolding Studies of Membrane Proteins Using Fast Simulations.Biophysical journal · 2019Article
- Commonly used FRET fluorophores promote collapse of an otherwise disordered protein.Proceedings of the National Academy of Sciences of the United States of America · 2019Article
- Investigating the Formation of Structural Elements in Proteins Using Local Sequence-Dependent Information and a Heuristic Search Algorithm.Molecules (Basel, Switzerland) · 2019Article
- The Evolution of Tau Phosphorylation and Interactions.Frontiers in aging neuroscience · 2019Article
- What DrivesBiophysical journal · 2018Article
71 more citing papers are in PubMed but not listed here.
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Authors and funding
4 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
An unfolded state ensemble is generated by using a self-avoiding statistical coil model that is based on backbone conformational frequencies in a coil library, a subset of the Protein Data Bank. The model reproduces two apparently contradicting behaviors observed in the chemically denatured state for a variety of proteins, random coil scaling of the radius of gyration and the presence of significant amounts of local backbone structure (NMR residual dipolar couplings). The most stretched members of our unfolded ensemble dominate the residual dipolar coupling signal, whereas the uniformity of the sign of the couplings follows from the preponderance of polyproline II and beta conformers in the coil library. Agreement with the NMR data substantially improves when the backbone conformational preferences include correlations arising from the chemical and conformational identity of neighboring residues. Although the unfolded ensembles match the experimental observables, they do not display evidence of native-like topology. By providing an accurate representation of the unfolded state, our statistical coil model can be used to improve thermodynamic and kinetic modeling of protein folding.
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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.