ArticleBiophysical journal2011
Backbone and side-chain contributions in protein denaturation by urea.
Article in Biophysical journal, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 34 papers.
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Who cites it
34 citing papers in PubMed.
- A Computational Perspective to Intermolecular Interactions and the Role of the Solvent on Regulating Protein Properties.Chemical reviews · 2025Review
- Interplay of protein fluctuation and associated water dynamics in osmolyte-induced stabilization.Biophysical journal · 2025Article
- OSaMPle workflow for salivary metaproteomics analysis reveals dysbiosis in inflammatory bowel disease patients.NPJ biofilms and microbiomes · 2025Article
- Solvent accessible surface area-assessed molecular basis of osmolyte-induced protein stability.RSC advances · 2024Article
- Molecular mechanism of the common and opposing cosolvent effects of fluorinated alcohol and urea on a coiled coil protein.Protein science : a publication of the Protein Society · 2023Article
- Review
- Tuning Protein Hydrogel Mechanics through Modulation of Nanoscale Unfolding and Entanglement in Postgelation Relaxation.ACS nano · 2022Article
- Atomic view of cosolute-induced protein denaturation probed by NMR solvent paramagnetic relaxation enhancement.Proceedings of the National Academy of Sciences of the United States of America · 2021Article
- Urea-aromatic interactions in biology.Biophysical reviews · 2020Review
- Thermally versus Chemically Denatured Protein States.Biochemistry · 2019Article
- Contrasting Effects of Guanidinium Chloride and Urea on the Activity and Unfolding of Lysozyme.ACS omega · 2018Article
- Peptide Solubility Limits: Backbone and Side-Chain Interactions.The journal of physical chemistry. B · 2018Article
- Simulated pressure denaturation thermodynamics of ubiquitin.Biophysical chemistry · 2017Article
- Experimental Atom-by-Atom Dissection of Amide-Amide and Amide-Hydrocarbon Interactions in HJournal of the American Chemical Society · 2017Article
- The Proline/Glycine-Rich Region of the Biofilm Adhesion Protein Aap Forms an Extended Stalk that Resists Compaction.Journal of molecular biology · 2017Article
- Probing the Action of Chemical Denaturant on an Intrinsically Disordered Protein by Simulation and Experiment.Journal of the American Chemical Society · 2016Article
- Time-dependent X-ray diffraction studies on urea/hen egg white lysozyme complexes reveal structural changes that indicate onset of denaturation.Scientific reports · 2016Article
- Solvation Thermodynamics of Oligoglycine with Respect to Chain Length and Flexibility.Biophysical journal · 2016Article
- Article
- Single-Molecule Chemo-Mechanical Spectroscopy Provides Structural Identity of Folding Intermediates.Biophysical journal · 2016Article
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2 authors.
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Abstract
Urea is a commonly used protein denaturant, and it is of great interest to determine its interaction with various protein groups to elucidate the molecular basis of its effect on protein stability. Using the Trp-cage miniprotein as a model system, we report what we believe to be the first computation of changes in the preferential interaction coefficient of the protein upon urea denaturation from molecular-dynamics simulations and examine the contributions from the backbone and the side-chain groups. The preferential interaction is obtained from reversible folding/unfolding replica exchange molecular-dynamics simulations of Trp-cage in presence of urea, over a wide range of urea concentration. The increase in preferential interaction upon unfolding is dominated by the side-chain contribution, rather than the backbone. Similar trends are observed in simulations using two different force fields, Amber94 and Amber99sb, for the protein. The magnitudes of the side-chain and backbone contributions differ in the two force fields, despite containing identical protein-solvent interaction terms. The differences arise from the unfolded ensembles sampled, with Amber99sb favoring conformations with larger surface area and lower helical content. These results emphasize the importance of the side-chain interactions with urea in protein denaturation, and highlight the dependence of the computed driving forces on the unfolded ensemble sampled.
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