Multi-parameter photon-by-photon hidden Markov modeling

Paul David Harris; Alessandra Narducci; Christian Gebhardt; Thorben Cordes; Shimon Weiss; Eitan Lerner

doi:10.1038/s41467-022-28632-x

Multi-parameter photon-by-photon hidden Markov modeling

Nat Commun. 2022 Feb 22;13(1):1000. doi: 10.1038/s41467-022-28632-x.

Authors

Paul David Harris¹, Alessandra Narducci², Christian Gebhardt², Thorben Cordes², Shimon Weiss^{3

4}, Eitan Lerner^{5

6}

Affiliations

¹ Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, Faculty of Mathematics & Science, The Edmond J. Safra Campus, The Hebrew University of Jerusalem, Jerusalem, 9190401, Israel. paul.harris@mail.huji.ac.il.
² Physical and Synthetic Biology. Faculty of Biology, Ludwig-Maximilians-Universität München, Großhadernerstr. 2-4, 82152, Planegg-Martinsried, Germany.
³ Department of Chemistry and Biochemistry, and Department of Physiology, University of California, Los Angeles, CA, USA.
⁴ CaliforniaNanoSystems Institute, University of California, Los Angeles, CA, USA.
⁵ Department of Biological Chemistry, The Alexander Silberman Institute of Life Sciences, Faculty of Mathematics & Science, The Edmond J. Safra Campus, The Hebrew University of Jerusalem, Jerusalem, 9190401, Israel. eitan.lerner@mail.huji.ac.il.
⁶ The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem, 9190401, Israel. eitan.lerner@mail.huji.ac.il.

Abstract

Single molecule Förster resonance energy transfer (smFRET) is a unique biophysical approach for studying conformational dynamics in biomacromolecules. Photon-by-photon hidden Markov modeling (H²MM) is an analysis tool that can quantify FRET dynamics of single biomolecules, even if they occur on the sub-millisecond timescale. However, dye photophysical transitions intertwined with FRET dynamics may cause artifacts. Here, we introduce multi-parameter H²MM (mpH²MM), which assists in identifying FRET dynamics based on simultaneous observation of multiple experimentally-derived parameters. We show the importance of using mpH²MM to decouple FRET dynamics caused by conformational changes from photophysical transitions in confocal-based smFRET measurements of a DNA hairpin, the maltose binding protein, MalE, and the type-III secretion system effector, YopO, from Yersinia species, all exhibiting conformational dynamics ranging from the sub-second to microsecond timescales. Overall, we show that using mpH²MM facilitates the identification and quantification of biomolecular sub-populations and their origin.

Publication types

Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't
Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

Fluorescence Resonance Energy Transfer*
Molecular Conformation
Photons*

Grants and funding

R01 GM130942/GM/NIGMS NIH HHS/United States