One-dimensional barrier-preserving free-energy projections of a beta-sheet miniprotein: New insights into the folding process

TitleOne-dimensional barrier-preserving free-energy projections of a beta-sheet miniprotein: New insights into the folding process
Publication TypeJournal Article
Year of Publication2008
AuthorsKrivov S.V, Muff S., Caflisch A., Karplus M.
JournalThe Journal of Physical Chemistry B
Volume112
Issue29
Pagination8701-8714
Date Published2008 Jul 24
Type of ArticleResearch Article
ISSN1520-6106
KeywordsAlgorithms, Computer Simulation, Kinetics, Protein Denaturation, Protein Folding, Protein Structure, Secondary, Proteins, Thermodynamics
Abstract

The conformational space of a 20-residue three-stranded antiparallel β-sheet peptide (double hairpin) was sampled by equilibrium folding/unfolding molecular dynamics simulations for a total of 20 μs. The resulting one-dimensional free-energy profiles (FEPs) provide a detailed description of the free-energy basins and barriers for the folding reaction. The similarity of the FEPs obtained using the probability of folding before unfolding (pfold) or the mean first passage time supports the robustness of the procedure. The folded state and the most populated free-energy basins in the denatured state are described by the one-dimensional FEPs, which avoid the overlap of states present in the usual one- or two-dimensional projections. Within the denatured state, a basin with fluctuating helical conformations and a heterogeneous entropic state are populated near the melting temperature at about 11% and 33%, respectively. Folding pathways from the helical basin or enthalpic traps (with only one of the two hairpins formed) reach the native state through the entropic state, which is on-pathway and is separated by a low barrier from the folded state. A simplified equilibrium kinetic network based on the FEPs shows the complexity of the folding reaction and indicates, as augmented by additional analyses, that the basins in the denatured state are connected primarily by the native state. The overall folding kinetics shows single-exponential behavior because barriers between the non-native basins and the folded state have similar heights.

DOI10.1021/jp711864r
pubindex

0099

Alternate JournalJ. Phys. Chem. B
PubMed ID18590307
PubMed Central IDPMC2736680
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