Free energy surfaces from single-distance information.
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.
Department of Biochemistry, University of Zürich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland.
Philipp
P
Schuetz
René
R
Wuttke
Benjamin
B
Schuler
Amedeo
A
Caflisch
D031541:Fluorescence Resonance Energy Transfer / Q000379:methods; D007700:Kinetics; D056004:Molecular Dynamics Simulation; D010455:Peptides / Q000737:chemistry*; D011487:Protein Conformation; D011489:Protein Denaturation; D017510:Protein Folding; D013816:Thermodynamics
D010455:Peptides