title: Sequential data assimilation for single-molecule FRET photon-counting data.
abstract: Data assimilation is a statistical method designed to improve the quality of numerical simulations in combination with real observations. Here, we develop a sequential data assimilation method that incorporates one-dimensional time-series data of smFRET (single-molecule Förster resonance energy transfer) photon-counting into conformational ensembles of biomolecules derived from "replicated" molecular dynamics (MD) simulations. A particle filter using a large number of "replicated" MD simulations with a likelihood function for smFRET photon-counting data is employed to screen the conformational ensembles that match the experimental data. We examine the performance of the method using emulated smFRET data and coarse-grained (CG) MD simulations of a dye-labeled polyproline-20. The method estimates the dynamics of the end-to-end distance from smFRET data as well as revealing that of latent conformational variables. The particle filter is also able to correct model parameter dependence in CG MD simulations. We discuss the applicability of the method to real experimental data for conformational dynamics of biomolecules.
authors.affiliation: Advanced Institute for Computational Science, RIKEN, 7-1-26 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan.
authors.forename: Yasuhiro
authors.initials: Y
authors.lastname: Matsunaga
authors.affiliation: Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan.
authors.forename: Akinori
authors.initials: A
authors.lastname: Kidera
authors.affiliation: Advanced Institute for Computational Science, RIKEN, 7-1-26 Minatojima-minamimachi, Chuo-ku, Kobe, Hyogo 650-0047, Japan.
authors.forename: Yuji
authors.initials: Y
authors.lastname: Sugita
mesh_terms: D031541:Fluorescence Resonance Energy Transfer; D056004:Molecular Dynamics Simulation; D010455:Peptides / Q000737:chemistry*; D017785:Photons
chemical_list: D010455:Peptides; C011083:polyproline