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© Research
Publication : Journal of the American Chemical Society

The unfolded ensemble and folding mechanism of the C-terminal GB1 beta-hairpin

Scientific Fields
Diseases
Organisms
Applications
Technique

Published in Journal of the American Chemical Society - 24 Sep 2008

Bonomi M, Branduardi D, Gervasio FL, Parrinello M

Link to Pubmed [PMID] – 18811160

J. Am. Chem. Soc. 2008 Oct;130(42):13938-44

In this work, we shed new light on a much-studied case of beta-hairpin folding by means of advanced molecular dynamics simulations. A fully atomistic description of the protein and the solvent molecule is used, together with metadynamics, to accelerate the sampling and estimate free-energy landscapes. This is achieved using the path collective variables approach, which provides an adaptive description of the mechanism under study. We discover that the folding mechanism is a multiscale process where the turn region conformation leads to two different energy pathways that are connected by elongated structures. The former displays a stable 2:4 native-like structure in which an optimal hydrophobic packing and hydrogen bond pattern leads to 8 kcal/mol of stabilization. The latter shows a less-structured 3:5 beta-sheet, where hydrogen bonds and hydrophobic packing provide only 2.5 kcal/mol of stability. This perspective is fully consistent with experimental evidence that shows this to be a prototypical two-state folder, while it redefines the nature of the unfolded state.

https://www.ncbi.nlm.nih.gov/pubmed/18811160