Volume 76, Number 1, October 2006
|Page(s)||156 - 162|
|Section||Interdisciplinary physics and related areas of science and technology|
|Published online||13 September 2006|
Predictive folding of a β-hairpin protein in an all-atom free-energy model
Forschungszentrum Karlsruhe, Institut für Nanotechnologie PO Box 2640, 76021 Karlsruhe, Germany
Accepted: 17 August 2006
Using an all-atom free-energy model we reproducibly and predictively fold a monomeric stable tryptophane-zipper (pdb-code 1LE1) from unfolded starting conformations to experimental accuracy. We construct the folding free-energy landscape under physiological conditions with a fraction of the cost of methods that simulate the folding pathway. We identify a metastable helical ensemble of conformations in the folding funnel and discuss its impact on the folding scenario. A comparison of the energetic contributions of the competing ensembles rationalizes the stabilization of the native ensemble and illustrates opportunities for peptide design.
PACS: 87.15.Cc – Folding and sequence analysis / 02.70.Ns – Molecular dynamics and particle methods / 02.60.Pn – Numerical optimization
© EDP Sciences, 2006
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