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Polar or apolar--the role of polarity for urea-induced protein denaturation.

Stumpe MC, Grubmüller H - PLoS Comput. Biol. (2008)

Bottom Line: Indeed, protein unfolding was observed in all simulations with decreased urea polarity.These results strongly suggest that apolar urea-protein interactions, and not polar interactions, are the dominant driving force for denaturation.After the transition state, unfolding pathways show large structural heterogeneity.

View Article: PubMed Central - PubMed

Affiliation: Department of Theoretical and Computational Biophysics, Max-Planck-Institute for Biophysical Chemistry, Göttingen, Germany.

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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Interaction coefficient CUW for all amino acids types in the CI2 protein, as well as the backbone average (“bb”).The four panels show CUW for the different urea partial charge scalings (A: 50%, B: 75%, C: 100%, D: 150%). The color characterizes the amino acids. Red: charged, yellow: polar, gray: aliphatic, blue: aromatic, green: apolar. For better comparability, all CUW are sorted according to CUW in urea50%.
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pcbi-1000221-g002: Interaction coefficient CUW for all amino acids types in the CI2 protein, as well as the backbone average (“bb”).The four panels show CUW for the different urea partial charge scalings (A: 50%, B: 75%, C: 100%, D: 150%). The color characterizes the amino acids. Red: charged, yellow: polar, gray: aliphatic, blue: aromatic, green: apolar. For better comparability, all CUW are sorted according to CUW in urea50%.

Mentions: To check whether this trend holds not only for tripeptides [46], but also for the whole protein, we quantified these interactions using the contact coefficient CUW. Figure 2C shows the CUW values for each amino acid type in the CI2, averaged over time and over the three simulations in aqueous urea solution (). Indeed, the obtained contact coefficients are largely similar to those calculated for the individual amino acids in tripeptides [46]. In particular, apolar and aromatic amino acids, as well as the backbone, have pronounced contact preferences for urea, whereas charged amino acids have preferences for water contact. This finding confirms that polarity/apolarity is clearly a determining factor for the specific interactions of urea with the CI2 protein residues, and provides further motivation for our approach to investigate protein stability in solutions of urea with modified polarity.


Polar or apolar--the role of polarity for urea-induced protein denaturation.

Stumpe MC, Grubmüller H - PLoS Comput. Biol. (2008)

Interaction coefficient CUW for all amino acids types in the CI2 protein, as well as the backbone average (“bb”).The four panels show CUW for the different urea partial charge scalings (A: 50%, B: 75%, C: 100%, D: 150%). The color characterizes the amino acids. Red: charged, yellow: polar, gray: aliphatic, blue: aromatic, green: apolar. For better comparability, all CUW are sorted according to CUW in urea50%.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2570617&req=5

pcbi-1000221-g002: Interaction coefficient CUW for all amino acids types in the CI2 protein, as well as the backbone average (“bb”).The four panels show CUW for the different urea partial charge scalings (A: 50%, B: 75%, C: 100%, D: 150%). The color characterizes the amino acids. Red: charged, yellow: polar, gray: aliphatic, blue: aromatic, green: apolar. For better comparability, all CUW are sorted according to CUW in urea50%.
Mentions: To check whether this trend holds not only for tripeptides [46], but also for the whole protein, we quantified these interactions using the contact coefficient CUW. Figure 2C shows the CUW values for each amino acid type in the CI2, averaged over time and over the three simulations in aqueous urea solution (). Indeed, the obtained contact coefficients are largely similar to those calculated for the individual amino acids in tripeptides [46]. In particular, apolar and aromatic amino acids, as well as the backbone, have pronounced contact preferences for urea, whereas charged amino acids have preferences for water contact. This finding confirms that polarity/apolarity is clearly a determining factor for the specific interactions of urea with the CI2 protein residues, and provides further motivation for our approach to investigate protein stability in solutions of urea with modified polarity.

Bottom Line: Indeed, protein unfolding was observed in all simulations with decreased urea polarity.These results strongly suggest that apolar urea-protein interactions, and not polar interactions, are the dominant driving force for denaturation.After the transition state, unfolding pathways show large structural heterogeneity.

View Article: PubMed Central - PubMed

Affiliation: Department of Theoretical and Computational Biophysics, Max-Planck-Institute for Biophysical Chemistry, Göttingen, Germany.

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.

Show MeSH