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• W2122220546 endingPage "169" @default.
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• W2122220546 abstract "We have used distributed computing techniques and a supercluster of thousands of computer processors to study folding of the C-terminal β-hairpin from protein G in atomistic detail using the GB/SA implicit solvent model at 300 K. We have simulated a total of nearly 38 μs of folding time and obtained eight complete and independent folding trajectories. Starting from an extended state, we observe relaxation to an unfolded state characterized by non-specific, temporary hydrogen bonding. This is followed by the appearance of interactions between hydrophobic residues that stabilize a bent intermediate. Final formation of the complete hydrophobic core occurs cooperatively at the same time that the final hydrogen bonding pattern appears. The folded hairpin structures we observe all contain a closely packed hydrophobic core and proper β-sheet backbone dihedral angles, but they differ in backbone hydrogen bonding pattern. We show that this is consistent with the existing experimental data on the hairpin alone in solution. Our analysis also reveals short-lived semi-helical intermediates which define a thermodynamic trap. Our results are consistent with a three-state mechanism with a single rate-limiting step in which a varying final hydrogen bond pattern is apparent, and semi-helical off-pathway intermediates may appear early in the folding process. We include details of the ensemble dynamics methodology and a discussion of our achievements using this new computational device for studying dynamics at the atomic level." @default.
• W2122220546 created "2016-06-24" @default.
• W2122220546 creator A5032418986 @default.
• W2122220546 creator A5032864967 @default.
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• W2122220546 date "2001-10-01" @default.
• W2122220546 modified "2023-10-14" @default.
• W2122220546 title "β-hairpin folding simulations in atomistic detail using an implicit solvent model 1 1Edited by F. Cohen" @default.
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• W2122220546 doi "https://doi.org/10.1006/jmbi.2001.5033" @default.
• W2122220546 hasPubMedId "https://pubmed.ncbi.nlm.nih.gov/11601853" @default.
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