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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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Solvent accessible surface area of the protein in all simulations.Blue: water, orange: urea50%, magenta: urea75%, green: urea100%, black: urea150%. The lines show traces smoothed by a running average over 500 ps. The histogram in the right panel shows the frequency of the respective SAS.
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pcbi-1000221-g003: Solvent accessible surface area of the protein in all simulations.Blue: water, orange: urea50%, magenta: urea75%, green: urea100%, black: urea150%. The lines show traces smoothed by a running average over 500 ps. The histogram in the right panel shows the frequency of the respective SAS.

Mentions: Having shown that upscaling or downscaling urea partial charges has the desired effect on the interaction strengths between urea and the different amino acids, we can now turn our attention to the influence on protein stability. Accordingly, we monitored the SAS for the different urea partial charge scalings (Figure 3). As can be seen, for hypopolar urea, the protein unfolds in all nine simulations (urea75% and urea50%, magenta and orange lines, respectively). In contrast, for hyperpolar urea150%, the SAS remains close to the native value and the protein remains stable in all simulations (black lines). In fact, the SAS is even smaller for hyperpolar urea than for regular urea, which suggests that hyperpolar urea compacts the folded state. Furthermore, this result suggests that urea150% would actually be a weaker denaturant than urea100%.


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

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

Solvent accessible surface area of the protein in all simulations.Blue: water, orange: urea50%, magenta: urea75%, green: urea100%, black: urea150%. The lines show traces smoothed by a running average over 500 ps. The histogram in the right panel shows the frequency of the respective SAS.
© Copyright Policy
Related In: Results  -  Collection

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

pcbi-1000221-g003: Solvent accessible surface area of the protein in all simulations.Blue: water, orange: urea50%, magenta: urea75%, green: urea100%, black: urea150%. The lines show traces smoothed by a running average over 500 ps. The histogram in the right panel shows the frequency of the respective SAS.
Mentions: Having shown that upscaling or downscaling urea partial charges has the desired effect on the interaction strengths between urea and the different amino acids, we can now turn our attention to the influence on protein stability. Accordingly, we monitored the SAS for the different urea partial charge scalings (Figure 3). As can be seen, for hypopolar urea, the protein unfolds in all nine simulations (urea75% and urea50%, magenta and orange lines, respectively). In contrast, for hyperpolar urea150%, the SAS remains close to the native value and the protein remains stable in all simulations (black lines). In fact, the SAS is even smaller for hyperpolar urea than for regular urea, which suggests that hyperpolar urea compacts the folded state. Furthermore, this result suggests that urea150% would actually be a weaker denaturant than urea100%.

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