Experiment-friendly kinetic analysis of single molecule data in and out of equilibrium

TL;DR

SMACKS is a robust maximum likelihood method for extracting detailed kinetic and thermodynamic information from single molecule data, applicable to both equilibrium and non-equilibrium conditions, demonstrated on Hsp90 protein.

Contribution

The paper introduces SMACKS, a novel analysis technique that does not require prior models or equilibrium assumptions, improving kinetic analysis of single molecule data.

Findings

Successfully analyzed Hsp90 kinetics in and out of equilibrium

Resolved all statistically relevant rates and their uncertainties

Demonstrated superior performance over existing methods

Abstract

We present a simple and robust technique to extract kinetic rate models and thermodynamic quantities from single molecule time traces. SMACKS (Single Molecule Analysis of Complex Kinetic Sequences) is a maximum likelihood approach that works equally well for long trajectories as for a set of short ones. It resolves all statistically relevant rates and also their uncertainties. This is achieved by optimizing one global kinetic model based on the complete dataset, while allowing for experimental variations between individual trajectories. In particular, neither a priori models nor equilibrium have to be assumed. The power of SMACKS is demonstrated on the kinetics of the multi-domain protein Hsp90 measured by smFRET (single molecule F\"orster resonance energy transfer). Experiments in and out of equilibrium are analyzed and compared to simulations, shedding new light on the role of Hsp90's ATPase function. SMACKS pushes the boundaries of single molecule kinetics far beyond current methods.