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

Scientific Reports
Matthieu LagardereOlivier Thoumine

Abstract

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 t...Continue Reading

References

Sep 14, 2002·Science·George H Patterson, Jennifer Lippincott-Schwartz
Oct 3, 2003·The Journal of Biological Chemistry·Davide ComolettiPalmer Taylor
Jun 3, 2004·The Journal of Cell Biology·Anne K KenworthyJennifer Lippincott-Schwartz
Jul 22, 2006·The EMBO Journal·Pierre-François LenneDidier Marguet
Aug 12, 2006·Science·Eric BetzigHarald F Hess
Oct 25, 2006·Nature Methods·Ulrich RothbauerHeinrich Leonhardt
May 5, 2007·Annual Review of Biophysics and Biomolecular Structure·Elke Haustein, Petra Schwille
Dec 20, 2007·The Journal of Biological Chemistry·Tomas D PerezW James Nelson
Jan 15, 2008·Nature Methods·Suliana ManleyJennifer Lippincott-Schwartz
Apr 12, 2008·Science·Martin HeineDaniel Choquet
Jul 23, 2008·Angewandte Chemie·Mike HeilemannMarkus Sauer
Oct 13, 2008·SIAM Journal on Scientific Computing : a Publication of the Society for Industrial and Applied Mathematics·Rex A KerrJoel R Stiles
Mar 18, 2010·BMC Systems Biology·Dominic P Tolle, Nicolas Le Novère
Aug 18, 2010·Biophysical Journal·Gregory GiannoneLaurent Cognet
Dec 15, 2010·Neuron·Adish DaniXiaowei Zhuang
Dec 28, 2010·Nature Chemical Biology·Matthieu SainlosBarbara Imperiali
Feb 15, 2012·Optics Express·I IzeddinJ B Sibarita
Feb 15, 2012·Proceedings of the National Academy of Sciences of the United States of America·Katalin CzöndörOlivier R Thoumine
Oct 2, 2012·Nature Cell Biology·Olivier RossierGrégory Giannone
Apr 9, 2013·Biophysical Journal·Fabian HeinemannPetra Schwille
Aug 9, 2013·The Journal of Neuroscience : the Official Journal of the Society for Neuroscience·Deepak NairJean-Baptiste Sibarita
Nov 5, 2013·Neuron·Daniel Choquet, Antoine Triller
Mar 1, 2014·Nature Methods·Hendrik DeschoutKevin Braeckmans
Sep 26, 2014·PLoS Computational Biology·Melanie I StefanMary B Kennedy
Jan 9, 2015·Molecular Biology of the Cell·Anaël ChazeauOlivier Thoumine
May 23, 2015·Molecular Cell·Zhe LiuEric Betzig
Jun 4, 2015·Proceedings of the National Academy of Sciences of the United States of America·Mikael GarciaOlivier Thoumine
Jul 1, 2015·Nature Methods·Mohamed El BeheiryJean-Baptiste Masson
Aug 11, 2015·Nature·Reza VafabakhshEhud Y Isacoff
Mar 2, 2016·Nature Methods·Varun VenkataramaniThomas Kuner
Aug 9, 2016·Annual Review of Cell and Developmental Biology·Michael L Dustin, Kaushik Choudhuri
Dec 7, 2017·Biophysical Journal·Marianne RennerAntoine Triller
Apr 17, 2018·Nature Biotechnology·Wei OuyangChristophe Zimmer
Apr 22, 2018·Nature Communications·Alexander BläßlePatrick Müller
Sep 17, 2018·Biophysical Journal·Jennifer Lippincott-SchwartzRobert D Phair
Nov 28, 2018·Nature Methods·Martin WeigertEugene W Myers
Apr 5, 2019·Methods in Molecular Biology·Jose-Juan TapiaJames R Faeder

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Methods Mentioned

BETA
fluorescence
Fluorescence Correlation Spectroscopy
FCS
super-resolution microscopy
PCRs
PCR
pull-down

Software Mentioned

Tracer
FERNET
dSTORM
PALM
STORM
FluoSim
- Tracer
Metamorph
uPAINT
PyFRAP

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