2020/08/27 by Marijn de Boer, de Boer, Marijn
Biochemistry, Genetics and Molecular Biology · Physics and Astronomy · #Advanced Fluorescence Microscopy Techniques #Biological Physics (physics.bio-ph) #DNA and Nucleic Acid Chemistry #FOS: Biological sciences #FOS: Physical sciences #Protein Structure and Dynamics #Quantitative Methods (q-bio.QM) #Spectroscopy and Quantum Chemical Studies
paper · pdf · doi:10.48550/arxiv.2008.12278
openalex publication_date 2020/08/27 · openalex created_date 2022/07/26 · openalex updated_date 2026/07/28
Measuring the F "orster resonance energy transfer (FRET) efficiency of\nfreely diffusing single molecules provides information about the sampled\nconformational states of the molecules. Under equilibrium conditions, the\ndistribution of the conformational states is independent of time, whereas it\ncan vary over time under non-equilibrium conditions. In this work, we consider\nthe problem of parameter inference on non-equilibrium solution-based\nsingle-molecule FRET data. With a non-equilibrium model for the conformational\ndynamics and a model for the conformation-dependent FRET efficiency\ndistribution, the likelihood function could be constructed. The model\nparameters, such as the rate constants of the non-equilibrium conformational\ndynamics model and the average FRET efficiencies of the different\nconformational states, have been estimated from the data by maximizing the\nappropriate likelihood function via the Expectation-Maximization algorithm. We\nillustrate the likelihood method for a few simple non-equilibrium models and\nvalidated the method by simulations. The likelihood method could be applied to\nstudy protein folding, macromolecular complex formation, protein conformational\ndynamics and other non-equilibrium processes at the single-molecule level and\nin solution.\n