ArticleProceedings of the National Academy of Sciences of the United States of America2007
Anatomy of energetic changes accompanying urea-induced protein denaturation.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 112 papers.
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112 citing papers in PubMed, 276 citations in OpenAlex.
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- Prediction and Validation of a Protein's Free Energy Surface Using Hydrogen Exchange and (Importantly) Its Denaturant Dependence.Journal of chemical theory and computation · 2022Article
- Frustrated peptide chains at the fibril tip control the kinetics of growth of amyloid-β fibrils.Proceedings of the National Academy of Sciences of the United States of America · 2021Article
- 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
- Force Field Parameterization for the Description of the Interactions between Hydroxypropyl-β-Cyclodextrin and Proteins.The journal of physical chemistry. B · 2021Article
- Revealing the Hidden Sensitivity of Intrinsically Disordered Proteins to their Chemical Environment.The journal of physical chemistry letters · 2020Article
- Experimentally determined strengths of favorable and unfavorable interactions of amide atoms involved in protein self-assembly in water.Proceedings of the National Academy of Sciences of the United States of America · 2020Article
52 more citing papers are in PubMed but not listed here.
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
Abstract
Because of its protein-denaturing ability, urea has played a pivotal role in the experimental and conceptual understanding of protein folding and unfolding. The measure of urea's ability to force a protein to unfold is given by the m value, an experimental quantity giving the free energy change for unfolding per molar urea. With the aid of Tanford's transfer model [Tanford C (1964) J Am Chem Soc 86:2050-2059], we use newly obtained group transfer free energies (GTFEs) of protein side-chain and backbone units from water to 1 M urea to account for the m value of urea, and the method reveals the anatomy of protein denaturation in terms of residue-level free energy contributions of groups newly exposed on denaturation. The GTFEs were obtained by accounting for solubility and activity coefficient ratios accompanying the transfer of glycine from water to 1 M urea. Contrary to the opinions of some researchers, the GTFEs show that urea does not denature proteins through favorable interactions with nonpolar side chains; what drives urea-induced protein unfolding is the large favorable interaction of urea with the peptide backbone. Although the m value is said to be proportional to surface area newly exposed on denaturation, only approximately 25% of the area favorably contributes to unfolding (because of newly exposed backbone units), with approximately 75% modestly opposing urea-induced denaturation (originating from side-chain exposure). Use of the transfer model and newly determined GTFEs achieves the long-sought goal of predicting urea-dependent cooperative protein unfolding energetics at the level of individual amino acid residues.
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