title: Empirical Bayes methods enable advanced population-level analyses of single-molecule FRET experiments.
abstract: Many single-molecule experiments aim to characterize biomolecular processes in terms of kinetic models that specify the rates of transition between conformational states of the biomolecule. Estimation of these rates often requires analysis of a population of molecules, in which the conformational trajectory of each molecule is represented by a noisy, time-dependent signal trajectory. Although hidden Markov models (HMMs) may be used to infer the conformational trajectories of individual molecules, estimating a consensus kinetic model from the population of inferred conformational trajectories remains a statistically difficult task, as inferred parameters vary widely within a population. Here, we demonstrate how a recently developed empirical Bayesian method for HMMs can be extended to enable a more automated and statistically principled approach to two widely occurring tasks in the analysis of single-molecule fluorescence resonance energy transfer (smFRET) experiments: 1), the characterization of changes in rates across a series of experiments performed under variable conditions; and 2), the detection of degenerate states that exhibit the same FRET efficiency but differ in their rates of transition. We apply this newly developed methodology to two studies of the bacterial ribosome, each exemplary of one of these two analysis tasks. We conclude with a discussion of model-selection techniques for determination of the appropriate number of conformational states. The code used to perform this analysis and a basic graphical user interface front end are available as open source software.
authors.affiliation: Department of Statistics, Columbia University, New York, New York.
authors.forename: Jan-Willem
authors.initials: JW
authors.lastname: van de Meent
authors.affiliation: Department of Chemistry, Columbia University, New York, New York.
authors.forename: Jonathan E
authors.initials: JE
authors.lastname: Bronson
authors.affiliation: Department of Applied Physics and Applied Mathematics, Columbia University, New York, New York.
authors.forename: Chris H
authors.initials: CH
authors.lastname: Wiggins
authors.affiliation: Department of Chemistry, Columbia University, New York, New York. Electronic address: rlg2118@columbia.edu.
authors.forename: Ruben L
authors.initials: RL
authors.lastname: Gonzalez
mesh_terms: D001499:Bayes Theorem; D031541:Fluorescence Resonance Energy Transfer / Q000379:methods*; D008390:Markov Chains; D054680:Ribosome Subunits, Small, Bacterial / Q000737:chemistry