FluoSim: simulator of single molecule dynamics for fluorescence live-cell and super-resolution imaging of membrane proteins - Computational Biology and Bioinformatics Access content directly
Journal Articles Scientific Reports Year : 2020

FluoSim: simulator of single molecule dynamics for fluorescence live-cell and super-resolution imaging of membrane proteins

Matthieu Lagardère
  • Function : Author
Ingrid Chamma
Emmanuel Bouilhol
Macha Nikolski


Fluorescence live-cell and super-resolution microscopy methods have considerably advanced our understanding of the dynamics and mesoscale organization of macro-molecular complexes that drive cellular functions. However, different imaging techniques can provide quite disparate information about protein motion and organization, owing to their respective experimental ranges and limitations. To address these issues, we present here a robust computer program, called FluoSim, which is an interactive simulator of membrane protein dynamics for live-cell imaging methods including SPT, FRAP, PAF, and FCS, and super-resolution imaging techniques such as PALM, dSTORM, and uPAINT. FluoSim integrates diffusion coefficients, binding rates, and fluorophore photo-physics to calculate in real time the localization and intensity of thousands of independent molecules in 2D cellular geometries, providing simulated data directly comparable to actual experiments. FluoSim was thoroughly validated against experimental data obtained on the canonical neurexin-neuroligin adhesion complex at cell-cell contacts. This unified software allows one to model and predict membrane protein dynamics and localization at the ensemble and single molecule level, so as to reconcile imaging paradigms and quantitatively characterize protein behavior in complex cellular environments. Critical cellular functions such as membrane adhesion, receptor-mediated signaling, or synaptic transmission, involve the diffusional trapping of specific molecules in sub-cellular compartments 1,2. To quantitatively describe such molecular dynamics in living cells, several fluorescence imaging techniques are currently available 3 4 : (1) single particle tracking (SPT) which resolves the motion of individual proteins at camera frame rate; (2) photo-activation and photo-bleaching methods, namely PhotoActivation of Fluorescence (PAF) and Fluorescence Recovery After Photobleaching (FRAP) which infer protein turnover at the population level; and (3) Fluores-cence Correlation Spectroscopy (FCS), which analyzes molecular dynamics by correlating intensity fluctuations. More recent approaches based on single molecule localization such as PhotoActivated Localization Microscopy (PALM) 5,6 , direct Stochastic Optical Reconstruction Microscopy (dSTORM) 7 , and Point Accumulation In Nano-scopic Topography (PAINT) 8 , yield images of protein distribution at improved resolution (below 50 nm), giving unprecedented information about the nanoscale organization of biological structures 9. Despite such progress in imaging power, many experimental parameters remain difficult to estimate or control , including protein expression levels, probe labeling density, potential fixation artifacts, spatial and temporal sampling of the recordings, and protein motion below the system resolution, such that results from different experimental paradigms are often difficult to reconcile 10. Thus, there is a pressing need for computer simulators that could unify those different imaging modes in a unique framework, estimate their respective biases, and serve as a predictive tool for experimenters, with the aim to quantitatively decipher protein organization and dynamics in living cells. Several particle-based packages relying on Monte Carlo simulations already exist to predict random motion and multi-state reactions of biological molecules, but either they do not integrate fluorescence properties or are limited to a specific type of imaging mode, and are usually not performing real-time visualization 11-18. In this context, we provide here fast, robust, and user-friendly software (FluoSim) that allows real time simulation of membrane protein dynamics in live-cell imaging (SPT, FRAP, PAF, and FCS) and super-resolution (PALM, dSTORM, uPAINT) modalities. We also show that FluoSim can be further used to produce large virtual data sets OPEN
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Dates and versions

hal-03010357 , version 1 (17-11-2020)



Matthieu Lagardère, Ingrid Chamma, Emmanuel Bouilhol, Macha Nikolski, Olivier Thoumine. FluoSim: simulator of single molecule dynamics for fluorescence live-cell and super-resolution imaging of membrane proteins. Scientific Reports, 2020, 10, ⟨10.1038/s41598-020-75814-y⟩. ⟨hal-03010357⟩
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