Abstract
We have studied the folding mechanism of beta-hairpins in the proteins
1GB1, 3AIT and 1A2P by conducting unfolding simulations at moderately
high temperatures. The analysis of trajectories obtained from molecular
dynamics simulations in explicit aqueous solution suggests that the
positions of the hydrophobic core residues lead to subtle differences
in the details of folding dynamics. However, the folding of three
different hairpins can be explained by a unified mechanism that is a
blend of the hydrogen-bond-centric and the hydrophobic-centric models.
The initial stage of beta-hairpin folding involves various partially
folded intermediate structures which are stabilized by both the van der
Waals interactions of hydrophobic core residues and the electrostatic
interactions of non-native hydrogen bonds. The native structure is
obtained by forming native contacts in the final tune-up process.
Depending on the relative positions of the hydrophobic residues, the
actual mechanism of hairpin folding may or may not exhibit well-defined
intermediates.
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