TY - JOUR T1 - Simulating Freely-diffusing Single-molecule FRET Data with Consideration of Protein Conformational Dynamics JF - bioRxiv DO - 10.1101/2021.01.19.427359 SP - 2021.01.19.427359 AU - James Losey AU - Michael Jauch AU - Axel Cortes-Cubero AU - Haoxuan Wu AU - Roberto Rivera AU - David S. Matteson AU - Mahmoud Moradi Y1 - 2021/01/01 UR - http://biorxiv.org/content/early/2021/09/16/2021.01.19.427359.abstract N2 - Single molecule Förster resonance energy transfer experiments have added a great deal to the understanding of conformational states of biologically important molecules. While great progress has been made in studying structural dynamics of biomolecular systems, much is still unknown for systems with conformational heterogeneity particularly those with high flexibility. For instance, with currently available techniques, it is difficult to work with intrinsically disordered proteins, particularly when freely diffusing smFRET experiments are used. Simulated smFRET data allows for the control of the underlying process that generates the data to examine if a given smFRET data analysis technique can detect these underlying differences. Here, we extend the PyBroMo software that simulates freely diffusing smFRET data to include a distribution of inter-dye distances generated using Langevin dynamics in order to model proteins with conformational flexibility within a given state. We compare standard analysis techniques for smFRET data to validate the new module relative to the base PyBroMo software and observe qualitative agreement in the results of standard analysis for the two timestamp generation methods. The Langevin dynamics module provides a framework for generating timestamp data with an known underlying heterogeneity of inter-dye distances that will be necessary for the development of new analysis techniques that study flexible proteins or other biomolecular systems.Graphical TOC Entry Competing Interest StatementThe authors have declared no competing interest. ER -