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Free energy surfaces from single-distance information


Schuetz, P; Wuttke, R; Schuler, B; Caflisch, A (2010). Free energy surfaces from single-distance information. Journal of Physical Chemistry. B, 114(46):15227-15235.

Abstract

We propose a network-based method for determining basins and barriers of complex free energy surfaces (e.g., the protein folding landscape) from the time series of a single intramolecular distance. First, a network of transitions is constructed by clustering the points of the time series according to the short-time distribution of the signal. The transition network, which reflects the short-time kinetics, is then used for the iterative determination of individual basins by the minimum-cut-based free energy profile, a barrier-preserving one-dimensional projection of the free energy surface. The method is tested using the time series of a single C(β)-C(β) distance extracted from equilibrium molecular dynamics (MD) simulations of a structured peptide (20 residue three-stranded antiparallel β-sheet). Although the information of only one distance is employed to describe a system with 645 degrees of freedom, both the native state and the unfolding barrier of about 10 kJ/mol are determined with remarkable accuracy. Moreover, non-native conformers are identified by comparing long-time distributions of the same distance. To examine the applicability to single-molecule Förster resonance energy transfer (FRET) experiments, a time series of donor and acceptor photons is generated using the MD trajectory. The native state of the β-sheet peptide is determined accurately from the emulated FRET signal. Applied to real single-molecule FRET measurements on a monomeric variant of λ-repressor, the network-based method correctly identifies the folded and unfolded populations, which are clearly separated in the minimum-cut-based free energy profile.

Abstract

We propose a network-based method for determining basins and barriers of complex free energy surfaces (e.g., the protein folding landscape) from the time series of a single intramolecular distance. First, a network of transitions is constructed by clustering the points of the time series according to the short-time distribution of the signal. The transition network, which reflects the short-time kinetics, is then used for the iterative determination of individual basins by the minimum-cut-based free energy profile, a barrier-preserving one-dimensional projection of the free energy surface. The method is tested using the time series of a single C(β)-C(β) distance extracted from equilibrium molecular dynamics (MD) simulations of a structured peptide (20 residue three-stranded antiparallel β-sheet). Although the information of only one distance is employed to describe a system with 645 degrees of freedom, both the native state and the unfolding barrier of about 10 kJ/mol are determined with remarkable accuracy. Moreover, non-native conformers are identified by comparing long-time distributions of the same distance. To examine the applicability to single-molecule Förster resonance energy transfer (FRET) experiments, a time series of donor and acceptor photons is generated using the MD trajectory. The native state of the β-sheet peptide is determined accurately from the emulated FRET signal. Applied to real single-molecule FRET measurements on a monomeric variant of λ-repressor, the network-based method correctly identifies the folded and unfolded populations, which are clearly separated in the minimum-cut-based free energy profile.

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Additional indexing

Item Type:Journal Article, refereed, original work
Communities & Collections:04 Faculty of Medicine > Department of Biochemistry
07 Faculty of Science > Department of Biochemistry
Dewey Decimal Classification:570 Life sciences; biology
Language:English
Date:2010
Deposited On:26 Jan 2011 17:16
Last Modified:05 Apr 2016 14:28
Publisher:American Chemical Society
ISSN:1520-5207
Publisher DOI:https://doi.org/10.1021/jp1053698
PubMed ID:20964427

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