Simulations of beta-hairpin folding confined to spherical pores using distributed computing.
We report the thermodynamics and kinetics of an off-lattice Go model beta-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, R(s), is nonmonotonic. The rates reach a maximum at R(s)/R(g,N)(b) approximately equal to 1.5, where R(g,N)(b) is the radius of gyration of the folded beta-hairpin in the bulk. The denatured state ensemble of the encapsulated beta-hairpin is highly structured even at substantially elevated temperatures. Remarkably, a profound effect of confinement is evident even when the beta-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.
Klimov
D K
DK
Institute for Physical Science and Technology, University of Maryland, College Park, MD 20742, USA. klimov@glue.umd.edu
Newfield
D
D
Thirumalai
D
D
D003198:Computer Simulation; D007700:Kinetics; D008958:Models, Molecular; D009419:Nerve Tissue Proteins / Q000737:chemistry* / Q000378:metabolism; D011487:Protein Conformation; D011489:Protein Denaturation; D017510:Protein Folding
C029152:G-substrate; D009419:Nerve Tissue Proteins