Limits...
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.

Show MeSH
Per-residue Cα-RMSD in the initial unfolding phases.Blue corresponds to low, red to high RMSD. The numbers on the left denote the start and end times of the respective displayed trajectory segment in ns. Top row: root-mean-square-fluctuations per residue in the native state. In the one-letter sequence code below, red marks the α-helix and blue β-strands.
© Copyright Policy
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC2570617&req=5

pcbi-1000221-g005: Per-residue Cα-RMSD in the initial unfolding phases.Blue corresponds to low, red to high RMSD. The numbers on the left denote the start and end times of the respective displayed trajectory segment in ns. Top row: root-mean-square-fluctuations per residue in the native state. In the one-letter sequence code below, red marks the α-helix and blue β-strands.

Mentions: Next, we investigated whether regions of the CI2 exist where unfolding is particularly likely to start. To this end, the RMSD per residue was calculated for the initial phase of unfolding (defined by a significant increase in the SAS from the native value) for each of the simulations U75% and U50% (Figure 5). For comparison, the top row shows the root-mean-square-fluctuations per residue in the native state (simulation W300K). Many initial unfolding steps are seen to occur in regions that exhibit large fluctuations already in the native state in water at 300 K. Examples are the C-terminal end of the α-helix (res. Q22) and the adjacent turn-region (res. D23–E26, simulations ), as well as the coil- and turn-regions between β-strands 2 and 3 (simulations ). In contrast, regions that show only small fluctuation in the native state, e.g. res. 5–18 in simulations , tend to unfold later. In summary, no unique unfolding “hot-spot” is found, but rather several regions where unfolding likely begins.


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

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

Per-residue Cα-RMSD in the initial unfolding phases.Blue corresponds to low, red to high RMSD. The numbers on the left denote the start and end times of the respective displayed trajectory segment in ns. Top row: root-mean-square-fluctuations per residue in the native state. In the one-letter sequence code below, red marks the α-helix and blue β-strands.
© Copyright Policy
Related In: Results  -  Collection

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

pcbi-1000221-g005: Per-residue Cα-RMSD in the initial unfolding phases.Blue corresponds to low, red to high RMSD. The numbers on the left denote the start and end times of the respective displayed trajectory segment in ns. Top row: root-mean-square-fluctuations per residue in the native state. In the one-letter sequence code below, red marks the α-helix and blue β-strands.
Mentions: Next, we investigated whether regions of the CI2 exist where unfolding is particularly likely to start. To this end, the RMSD per residue was calculated for the initial phase of unfolding (defined by a significant increase in the SAS from the native value) for each of the simulations U75% and U50% (Figure 5). For comparison, the top row shows the root-mean-square-fluctuations per residue in the native state (simulation W300K). Many initial unfolding steps are seen to occur in regions that exhibit large fluctuations already in the native state in water at 300 K. Examples are the C-terminal end of the α-helix (res. Q22) and the adjacent turn-region (res. D23–E26, simulations ), as well as the coil- and turn-regions between β-strands 2 and 3 (simulations ). In contrast, regions that show only small fluctuation in the native state, e.g. res. 5–18 in simulations , tend to unfold later. In summary, no unique unfolding “hot-spot” is found, but rather several regions where unfolding likely begins.

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