Simulations of β-hairpin folding confined to spherical pores using distributed computing

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Abstract
We report the thermodynamics and kinetics of an off-lattice Go model β-hairpin from Ig-binding protein confined to an inert spherical pore. Confinement enhances the stability of the hairpin due to the decrease in the entropy of the unfolded state. Compared with their values in the bulk, the rates of hairpin formation increase in the spherical pore. Surprisingly, the dependence of the rates on the pore radius, Rs, is nonmonotonic. The rates reach a maximum at Rs/R ≃ 1.5, where R is the radius of gyration of the folded β-hairpin in the bulk. The denatured state ensemble of the encapsulated β-hairpin is highly structured even at substantially elevated temperatures. Remarkably, a profound effect of confinement is evident even when the β-hairpin occupies less than a 10th of the sphere volume. Our calculations show that the emergence of substantial structure in the denatured state of proteins in inert pores is a consequence of confinement. In contrast, the structure of the bulk denatured state ensemble depends dramatically on the extent of denaturation.