ArticlePLoS computational biology2008
Polar or apolar--the role of polarity for urea-induced protein denaturation.
Article in PLoS computational biology, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed.
- Urea-aromatic interactions in biology.Biophysical reviews · 2020Review
- Exploring the differences and similarities between urea and thermally driven denaturation of bovine serum albumin: intermolecular forces and solvation preferences.Journal of molecular modeling · 2018Article
- Time-dependent X-ray diffraction studies on urea/hen egg white lysozyme complexes reveal structural changes that indicate onset of denaturation.Scientific reports · 2016Article
- Article
- Quantitative assessments of the distinct contributions of polypeptide backbone amides versus side chain groups to chain expansion via chemical denaturation.Journal of the American Chemical Society · 2015Article
- The structural basis of urea-induced protein unfolding in β-catenin.Acta crystallographica. Section D, Biological crystallography · 2014Article
- Toward an atomistic description of the urea-denatured state of proteins.Proceedings of the National Academy of Sciences of the United States of America · 2013Article
- Exploring early stages of the chemical unfolding of proteins at the proteome scale.PLoS computational biology · 2013Article
- Quantitative characterization of local protein solvation to predict solvent effects on protein structure.Biophysical journal · 2012Article
- Interconnection of salt-induced hydrophobic compaction and secondary structure formation depends on solution conditions: revisiting early events of protein folding at single molecule resolution.The Journal of biological chemistry · 2012Article
- The CLN025 decapeptide retains a β-hairpin conformation in urea and guanidinium chloride.The journal of physical chemistry. B · 2011Article
- Comment on "urea-mediated protein denaturation: a consensus view".The journal of physical chemistry. B · 2011Article
- Calculation of local water densities in biological systems: a comparison of molecular dynamics simulations and the 3D-RISM-KH molecular theory of solvation.The journal of physical chemistry. B · 2011Article
- Mechanisms of amphipathic helical peptide denaturation by guanidinium chloride and urea: a molecular dynamics simulation study.Journal of computer-aided molecular design · 2010Article
- Interconvertibility of lipid- and translocon-bound forms of the bacterial Tat precursor pre-SufI.Molecular microbiology · 2009Article
- Urea impedes the hydrophobic collapse of partially unfolded proteins.Biophysical journal · 2009Article
Corrections and comments
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Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Urea-induced protein denaturation is widely used to study protein folding and stability; however, the molecular mechanism and driving forces of this process are not yet fully understood. In particular, it is unclear whether either hydrophobic or polar interactions between urea molecules and residues at the protein surface drive denaturation. To address this question, here, many molecular dynamics simulations totalling ca. 7 micros of the CI2 protein in aqueous solution served to perform a computational thought experiment, in which we varied the polarity of urea. For apolar driving forces, hypopolar urea should show increased denaturation power; for polar driving forces, hyperpolar urea should be the stronger denaturant. Indeed, protein unfolding was observed in all simulations with decreased urea polarity. Hyperpolar urea, in contrast, turned out to stabilize the native state. Moreover, the differential interaction preferences between urea and the 20 amino acids turned out to be enhanced for hypopolar urea and suppressed (or even inverted) for hyperpolar urea. These results strongly suggest that apolar urea-protein interactions, and not polar interactions, are the dominant driving force for denaturation. Further, the observed interactions provide a detailed picture of the underlying molecular driving forces. Our simulations finally allowed characterization of CI2 unfolding pathways. Unfolding proceeds sequentially with alternating loss of secondary or tertiary structure. After the transition state, unfolding pathways show large structural heterogeneity.
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