QuantiTrack: A unified software to study protein dynamics in living cells

Linking the spatiotemporal dynamics of proteins in live cells to physiological functions is a fundamental challenge in biology and robust quantification of protein dynamics is a major step towards this endeavor. Single molecule tracking (SMT) has emerged as a powerful technique to investigate protein dynamics at the single molecule level in living cells. Most SMT analyses require familiarity with biophysical models and programming and the results from different analyses cannot be easily integrated. To mitigate these shortcomings, we developed QuantiTrack – a MATLAB-based SMT analysis software that can be operated from a simple graphical user interface. This provides a much-needed end-to-end solution where a user can load a movie, track single molecules, and perform a range of analyses. In addition to a detailed user guide with step-by-step instructions, QuantiTrack includes quality control metrics that can be used to systematically determine tracking parameters. As a practical example, we address by QuantiTrack a question relevant to hormonal therapy: How does the glucocorticoid receptor (GR), a hormone-regulated transcription factor (TF), respond to treatment and washout of its cognate hormone. Hormone washout results in rapid (in minutes) downregulation of GR target genes to basal levels. We observe dynamics of the Halo tagged GR (Halo-GR) and by integrating several analyses, show that hormone washout results in a substantially lower bound fraction of GR, reduced occupancy in the mobility state associated with GR activation, and shorter GR dwell times. These analyses showcase QuantiTrack as a convenient tool for comprehensive SMT analysis for a wide range of biologists.