PT - JOURNAL ARTICLE AU - Schmid, Sonja AU - Götz, Markus AU - Hugel, Thorsten TI - Experiment-friendly kinetic analysis of single molecule data in and out of equilibrium AID - 10.1101/054577 DP - 2016 Jan 01 TA - bioRxiv PG - 054577 4099 - http://biorxiv.org/content/early/2016/05/23/054577.short 4100 - http://biorxiv.org/content/early/2016/05/23/054577.full AB - 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 Förster 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.