Challenges in Inferring the Directionality of Active Molecular Processes from 
Single-Molecule Fluorescence Resonance Energy Transfer Trajectories

Godec, Aljaz; Makarov, Dmitrii E.

doi:10.1021/acs.jpclett.2c03244

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Challenges in Inferring the Directionality of Active Molecular Processes from Single-Molecule Fluorescence Resonance Energy Transfer Trajectories

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Godec, Aljaz
Research Group of Mathematical Biophysics, Max Planck Institute for Multidisciplinary Sciences, Max Planck Society;

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Citation

Godec, A., & Makarov, D. E. (2023). Challenges in Inferring the Directionality of Active Molecular Processes from Single-Molecule Fluorescence Resonance Energy Transfer Trajectories. The Journal of Physical Chemistry Letters, 14(1), 49-56. doi:10.1021/acs.jpclett.2c03244.

Cite as: https://hdl.handle.net/21.11116/0000-000C-739A-5

Abstract

We discuss some of the practical challenges that one faces in using stochastic thermodynamics to infer directionality of molecular machines from experimental single-molecule trajectories. Because of the limited spatiotemporal resolution of single-molecule experiments and because both forward and backward transitions between the same pairs of states cannot always be detected, differentiating between the forward and backward directions of, e.g., an ATP-consuming molecular machine that operates periodically, turns out to be a nontrivial task. Using a simple extension of a Markov-state model that is commonly employed to analyze single-molecule transition-path measurements, we illustrate how irreversibility can be hidden from such measurements but in some cases can be uncovered when non-Markov effects in low-dimensional single-molecule trajectories are considered.