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Smoothing of the GB1 hairpin folding landscape by interfacial confinement.

ABSTRACT: We study the effects of confinement between planar walls on the folding thermodynamics of a ?-hairpin, using large-scale replica-exchange molecular-dynamics simulations with an all-atom model and explicit solvent. We find that the folding free-energy landscape of this peptide observed in bulk is significantly modified when the peptide is confined between the walls. Most notably, the propensity of the peptide to form a misfolded state observed in the bulk solution becomes negligible under confinement. The absence of the misfolded state under confinement can be explained by an increased tendency of hydrophobic aromatic side chains to stay near the walls, because the misfolded state is characterized by a nonnative arrangement of aromatic side chains. These results from a simple confinement model may provide clues about the role of chaperonin confinement in smoothing folding landscapes by avoiding trapped intermediates.

SUBMITTER: Bhattacharya A

PROVIDER: S-EPMC3414903 | biostudies-literature | 2012 Aug

REPOSITORIES: biostudies-literature

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Smoothing of the GB1 hairpin folding landscape by interfacial confinement.

Bhattacharya Apratim A Best Robert B RB Mittal Jeetain J

Biophysical journal 20120801 3

We study the effects of confinement between planar walls on the folding thermodynamics of a β-hairpin, using large-scale replica-exchange molecular-dynamics simulations with an all-atom model and explicit solvent. We find that the folding free-energy landscape of this peptide observed in bulk is significantly modified when the peptide is confined between the walls. Most notably, the propensity of the peptide to form a misfolded state observed in the bulk solution becomes negligible under confine ...[more]

PMID: 22947876

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