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J Phys Chem B. 2011 Jul 14;115(27):8806-12. doi: 10.1021/jp2008623. Epub 2011 Jun 22.

Exploring the folding free energy landscape of a β-hairpin miniprotein, chignolin, using multiscale free energy landscape calculation method.

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Department of Physics, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Tokyo, 113-0033, Japan.


The folding process for a β-hairpin miniprotein, chignolin, was investigated by free energy landscape (FEL) calculations using the recently proposed multiscale free energy landscape calculation method (MSFEL). First, coarse-grained molecular dynamics simulations searched a broad conformational space, then multiple independent, all-atom molecular dynamics simulations with explicit solvent determined the detailed local FEL using massively distributed computing. The combination of the two models enabled efficient calculation of the free energy landscapes. The MSFEL analysis showed that chignolin has an intermediate state as well as a misfolded state. The folding process is initiated by the formation of a β-hairpin turn, followed by the formation of contacts in the hydrophobic core between Tyr2 and Trp9. Furthermore, mutation of Tyr2 shifts the population to the misfolded conformation. The results indicate that the hydrophobic core plays an important role in stabilizing the native state of chignolin.

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