Expectation-maximization of the potential of mean force and diffusion coefficient in Langevin dynamics from single molecule FRET data photon by photon.
The dynamics of a protein along a well-defined coordinate can be formally projected onto the form of an overdamped Lagevin equation. Here, we present a comprehensive statistical-learning framework for simultaneously quantifying the deterministic force (the potential of mean force, PMF) and the stochastic force (characterized by the diffusion coefficient, D) from single-molecule Förster-type resonance energy transfer (smFRET) experiments. The likelihood functional of the Langevin parameters, PMF and D, is expressed by a path integral of the latent smFRET distance that follows Langevin dynamics and realized by the donor and the acceptor photon emissions. The solution is made possible by an eigen decomposition of the time-symmetrized form of the corresponding Fokker-Planck equation coupled with photon statistics. To extract the Langevin parameters from photon arrival time data, we advance the expectation-maximization algorithm in statistical learning, originally developed for and mostly used in discrete-state systems, to a general form in the continuous space that allows for a variational calculus on the continuous PMF function. We also introduce the regularization of the solution space in this Bayesian inference based on a maximum trajectory-entropy principle. We use a highly nontrivial example with realistically simulated smFRET data to illustrate the application of this new method.
Department of Chemical and Biomolecular Engineering, University of California-Berkeley , Berkeley, California 94720, United States.
Kevin R
KR
Haas
Haw
H
Yang
Jhih-Wei
JW
Chu
D000465:Algorithms; D001426:Bacterial Proteins / Q000737:chemistry / Q000378:metabolism; D001499:Bayes Theorem; D004058:Diffusion; D031541:Fluorescence Resonance Energy Transfer; D009169:Mycobacterium tuberculosis / Q000201:enzymology / Q000378:metabolism; D017785:Photons; D017027:Protein Tyrosine Phosphatases / Q000737:chemistry / Q000378:metabolism
D001426:Bacterial Proteins; D017027:Protein Tyrosine Phosphatases