ArticleProceedings of the National Academy of Sciences of the United States of America2008
Assessing the solvent-dependent surface area of unfolded proteins using an ensemble model.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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19 citing papers in PubMed, 42 citations in OpenAlex.
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- Accessibility of Carboxypeptidase A-bound Zinc to Chelation Correlates with an Intermediate State in the Protein's Unfolding Pathway.Biochemistry · 2025Article
- In silico discovery of a novel potential allosteric PI3Kα inhibitor incorporating 2-oxopropyl urea targeting head and neck squamous cell carcinoma.BMC chemistry · 2025Article
- Structural architecture of the acidic region of the B domain of coagulation factor V.Journal of thrombosis and haemostasis : JTH · 2024Article
- Sequence- and Temperature-Dependent Properties of Unfolded and Disordered Proteins from Atomistic Simulations.The journal of physical chemistry. B · 2015Article
- A comprehensive database of verified experimental data on protein folding kinetics.Protein science : a publication of the Protein Society · 2014Article
- On methods for determining solvent accessible surface area for proteins in their unfolded state.BMC research notes · 2014Article
- The Role of Aromatic-Aromatic Interactions in Strand-Strand Stabilization of β-Sheets.Journal of molecular biology · 2013Article
- Conformational properties of polyglutamine sequences in guanidine hydrochloride solutions.Biophysical journal · 2012Article
- Scaling properties of glycine-rich sequences in guanidine hydrochloride solutions.Biophysical journal · 2012Article
- Residual structure in unfolded proteins.Current opinion in structural biology · 2012Review
- Guanidine-HCl dependent structural unfolding of M-crystallin: fluctuating native state like topologies and intermolecular association.PloS one · 2012Article
- Fractal dimension of an intrinsically disordered protein: small-angle X-ray scattering and computational study of the bacteriophage λ N protein.Protein science : a publication of the Protein Society · 2011Article
- Osmolyte effects on protein stability and solubility: a balancing act between backbone and side-chains.Biophysical chemistry · 2011Article
- Counting peptide-water hydrogen bonds in unfolded proteins.Protein science : a publication of the Protein Society · 2011Article
- In silico characterization of thermostable lipases.Extremophiles : life under extreme conditions · 2011Article
- Article
- ProtSA: a web application for calculating sequence specific protein solvent accessibilities in the unfolded ensemble.BMC bioinformatics · 2009Article
- Structures, basins, and energies: a deconstruction of the Protein Coil Library.Protein science : a publication of the Protein Society · 2008Article
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2 authors at 1 institution in 1 country.
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No grant is acknowledged in the PubMed record.
Abstract
We present a physically rigorous method to calculate solvent-dependent accessible surface areas (ASAs) of amino acid residues in unfolded proteins. ASA values will be larger in a good solvent, where solute-solvent interactions dominate and promote chain extension. Conversely, they will be smaller in a poor solvent, where solute-solute interactions dominate and promote chain collapse. In the method described here, these solvent-dependent effects are modeled by Boltzmann-weighting a simulated ensemble for solvent quality-good or poor. Solvent quality is parameterized as intramolecular hydrogen bond strength, using a "hydrogen bond dial" that can be varied from "off" to "high" (i.e., from 0 to -6 kcal/mol per hydrogen bond). When plotted as a function of hydrogen bond strength, the Boltzmann-weighted distribution of conformers describes a sigmoidal curve, with a transition midpoint near 1.5 kcal/mol per hydrogen bond. ASA tables for the 20 residues are provided under good solvent conditions and at this transition midpoint. For the backbone, these midpoint ASA values are found to be in good agreement with the earlier estimate of unfolded state ASA given by the mean of Creamer's upper and lower bounds [Creamer TP, et al. (1997) Biochemistry 36:2832-2835], a gratifying result in that cosolvents of experimental interest, such as urea (good solvent) and trimethylamine N-oxide (poor solvent), are known to affect the backbone predominantly. Unanticipated results from our simulations predict that a significant population of three-residue, hydrogen-bonded turns (inverse gamma-turns) will be detectable in blocked polyalanyl heptamers in poor solvent-an experimentally verifiable conjecture.
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