Delineation of folding pathways of a β-sheet miniprotein

Wenwei Zheng, Bo Qi, Mary A. Rohrdanz, Amedeo Caflisch, Aaron R. Dinner, Cecilia Clementi

Research output: Contribution to journalArticle

31 Citations (Scopus)

Abstract

Several methods have been developed in the past few years for the analysis of molecular dynamics simulations of biological (macro)molecules whose complexity is difficult to capture by simple projections of the free-energy surface onto one or two geometric variables. The locally scaled diffusion map (LSDMap) method is a nonlinear dimensionality reduction technique for describing the dynamics of complex systems in terms of a few collective coordinates. Here, we compare LSDMap to two previously developed approaches for the characterization of the configurational landscape associated with the folding dynamics of a three-stranded antiparallel β-sheet peptide, termed Beta3s. The analysis is aided by an improved procedure for extracting pathways from the equilibrium transition network, which enables calculation of pathway-specific cut-based free energy profiles. We find that the results from LSDMap are consistent with analysis based on transition networks and allow a coherent interpretation of metastable states and folding pathways in terms of different time scales of transitions between minima on the free energy projections.

Original languageEnglish (US)
Pages (from-to)13065-13074
Number of pages10
JournalJournal of Physical Chemistry B
Volume115
Issue number44
DOIs
StatePublished - Nov 10 2011
Externally publishedYes

Fingerprint

delineation
folding
Free energy
free energy
projection
Molecular Dynamics Simulation
complex systems
metastable state
Peptides
peptides
Macros
Molecular dynamics
Large scale systems
molecular dynamics
Molecules
Computer simulation
profiles
molecules
simulation

ASJC Scopus subject areas

  • Physical and Theoretical Chemistry
  • Surfaces, Coatings and Films
  • Materials Chemistry

Cite this

Zheng, W., Qi, B., Rohrdanz, M. A., Caflisch, A., Dinner, A. R., & Clementi, C. (2011). Delineation of folding pathways of a β-sheet miniprotein. Journal of Physical Chemistry B, 115(44), 13065-13074. https://doi.org/10.1021/jp2076935

Delineation of folding pathways of a β-sheet miniprotein. / Zheng, Wenwei; Qi, Bo; Rohrdanz, Mary A.; Caflisch, Amedeo; Dinner, Aaron R.; Clementi, Cecilia.

In: Journal of Physical Chemistry B, Vol. 115, No. 44, 10.11.2011, p. 13065-13074.

Research output: Contribution to journalArticle

Zheng, W, Qi, B, Rohrdanz, MA, Caflisch, A, Dinner, AR & Clementi, C 2011, 'Delineation of folding pathways of a β-sheet miniprotein', Journal of Physical Chemistry B, vol. 115, no. 44, pp. 13065-13074. https://doi.org/10.1021/jp2076935
Zheng W, Qi B, Rohrdanz MA, Caflisch A, Dinner AR, Clementi C. Delineation of folding pathways of a β-sheet miniprotein. Journal of Physical Chemistry B. 2011 Nov 10;115(44):13065-13074. https://doi.org/10.1021/jp2076935
Zheng, Wenwei ; Qi, Bo ; Rohrdanz, Mary A. ; Caflisch, Amedeo ; Dinner, Aaron R. ; Clementi, Cecilia. / Delineation of folding pathways of a β-sheet miniprotein. In: Journal of Physical Chemistry B. 2011 ; Vol. 115, No. 44. pp. 13065-13074.
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