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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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CI2 in native conformation.(A) Cα-RMSD. (B) SAS for the two simulations in water (blue) and the 3 simulations in aqueous urea with regular charges (green). The solid bold lines show traces smoothed by a running average over 500 ps; dim lines show raw data.
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pcbi-1000221-g001: CI2 in native conformation.(A) Cα-RMSD. (B) SAS for the two simulations in water (blue) and the 3 simulations in aqueous urea with regular charges (green). The solid bold lines show traces smoothed by a running average over 500 ps; dim lines show raw data.

Mentions: As a reference, we first analyzed the dynamics and stability of the folded CI2 protein as well as its protein-solvent interactions both in water and in 8 M aqueous urea solution. Figure 1 shows the Cα root-mean-square-deviation (RMSD, panel A) and the solvent accessible hydrophobic surface area (SAS, panel B) for the simulations in water (W1,2, blue) and in 8 M urea solution (, green). As can be seen, the Cα-RMSD of the protein in both solvents shows similar fluctuations with an average value of 0.3 nm, and no significant differences between both solvents are seen. In particular, no unfolding is observed, which is expected from the measured millisecond time scale for CI2 denaturation [47].


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

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

CI2 in native conformation.(A) Cα-RMSD. (B) SAS for the two simulations in water (blue) and the 3 simulations in aqueous urea with regular charges (green). The solid bold lines show traces smoothed by a running average over 500 ps; dim lines show raw data.
© Copyright Policy
Related In: Results  -  Collection

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

pcbi-1000221-g001: CI2 in native conformation.(A) Cα-RMSD. (B) SAS for the two simulations in water (blue) and the 3 simulations in aqueous urea with regular charges (green). The solid bold lines show traces smoothed by a running average over 500 ps; dim lines show raw data.
Mentions: As a reference, we first analyzed the dynamics and stability of the folded CI2 protein as well as its protein-solvent interactions both in water and in 8 M aqueous urea solution. Figure 1 shows the Cα root-mean-square-deviation (RMSD, panel A) and the solvent accessible hydrophobic surface area (SAS, panel B) for the simulations in water (W1,2, blue) and in 8 M urea solution (, green). As can be seen, the Cα-RMSD of the protein in both solvents shows similar fluctuations with an average value of 0.3 nm, and no significant differences between both solvents are seen. In particular, no unfolding is observed, which is expected from the measured millisecond time scale for CI2 denaturation [47].

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