Multi-parameter Photon-by-photon Hidden Markov Modeling

Overview

Journal Nat Commun

Specialty Biology

Date 2022 Feb 23

PMID 35194038

Authors

Paul David Harris

Alessandra Narducci

Christian Gebhardt

Thorben Cordes

Shimon Weiss

Eitan Lerner

Affiliations

Soon will be listed here.

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 (HMM) 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 HMM (mpHMM), which assists in identifying FRET dynamics based on simultaneous observation of multiple experimentally-derived parameters. We show the importance of using mpHMM 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 mpHMM facilitates the identification and quantification of biomolecular sub-populations and their origin.

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