Protein diffusion in mammalian cell cytoplasm.

We introduce a new method for mesoscopic modeling of protein diffusion in an entire cell. This method is based on the construction of a three-dimensional digital model cell from confocal microscopy data. The model cell is segmented into the cytoplasm, nucleus, plasma membrane, and nuclear envelope,...

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Autores principales:	Thomas Kühn, Teemu O Ihalainen, Jari Hyväluoma, Nicolas Dross, Sami F Willman, Jörg Langowski, Maija Vihinen-Ranta, Jussi Timonen
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2011
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/45966f16aa314dd2919ac0b530383fa0
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spelling	oai:doaj.org-article:45966f16aa314dd2919ac0b530383fa02021-11-18T06:47:38ZProtein diffusion in mammalian cell cytoplasm.1932-620310.1371/journal.pone.0022962https://doaj.org/article/45966f16aa314dd2919ac0b530383fa02011-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/21886771/?tool=EBIhttps://doaj.org/toc/1932-6203We introduce a new method for mesoscopic modeling of protein diffusion in an entire cell. This method is based on the construction of a three-dimensional digital model cell from confocal microscopy data. The model cell is segmented into the cytoplasm, nucleus, plasma membrane, and nuclear envelope, in which environment protein motion is modeled by fully numerical mesoscopic methods. Finer cellular structures that cannot be resolved with the imaging technique, which significantly affect protein motion, are accounted for in this method by assigning an effective, position-dependent porosity to the cell. This porosity can also be determined by confocal microscopy using the equilibrium distribution of a non-binding fluorescent protein. Distinction can now be made within this method between diffusion in the liquid phase of the cell (cytosol/nucleosol) and the cytoplasm/nucleoplasm. Here we applied the method to analyze fluorescence recovery after photobleach (FRAP) experiments in which the diffusion coefficient of a freely-diffusing model protein was determined for two different cell lines, and to explain the clear difference typically observed between conventional FRAP results and those of fluorescence correlation spectroscopy (FCS). A large difference was found in the FRAP experiments between diffusion in the cytoplasm/nucleoplasm and in the cytosol/nucleosol, for all of which the diffusion coefficients were determined. The cytosol results were found to be in very good agreement with those by FCS.Thomas KühnTeemu O IhalainenJari HyväluomaNicolas DrossSami F WillmanJörg LangowskiMaija Vihinen-RantaJussi TimonenPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 6, Iss 8, p e22962 (2011)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Thomas Kühn Teemu O Ihalainen Jari Hyväluoma Nicolas Dross Sami F Willman Jörg Langowski Maija Vihinen-Ranta Jussi Timonen Protein diffusion in mammalian cell cytoplasm.
description	We introduce a new method for mesoscopic modeling of protein diffusion in an entire cell. This method is based on the construction of a three-dimensional digital model cell from confocal microscopy data. The model cell is segmented into the cytoplasm, nucleus, plasma membrane, and nuclear envelope, in which environment protein motion is modeled by fully numerical mesoscopic methods. Finer cellular structures that cannot be resolved with the imaging technique, which significantly affect protein motion, are accounted for in this method by assigning an effective, position-dependent porosity to the cell. This porosity can also be determined by confocal microscopy using the equilibrium distribution of a non-binding fluorescent protein. Distinction can now be made within this method between diffusion in the liquid phase of the cell (cytosol/nucleosol) and the cytoplasm/nucleoplasm. Here we applied the method to analyze fluorescence recovery after photobleach (FRAP) experiments in which the diffusion coefficient of a freely-diffusing model protein was determined for two different cell lines, and to explain the clear difference typically observed between conventional FRAP results and those of fluorescence correlation spectroscopy (FCS). A large difference was found in the FRAP experiments between diffusion in the cytoplasm/nucleoplasm and in the cytosol/nucleosol, for all of which the diffusion coefficients were determined. The cytosol results were found to be in very good agreement with those by FCS.
format	article
author	Thomas Kühn Teemu O Ihalainen Jari Hyväluoma Nicolas Dross Sami F Willman Jörg Langowski Maija Vihinen-Ranta Jussi Timonen
author_facet	Thomas Kühn Teemu O Ihalainen Jari Hyväluoma Nicolas Dross Sami F Willman Jörg Langowski Maija Vihinen-Ranta Jussi Timonen
author_sort	Thomas Kühn
title	Protein diffusion in mammalian cell cytoplasm.
title_short	Protein diffusion in mammalian cell cytoplasm.
title_full	Protein diffusion in mammalian cell cytoplasm.
title_fullStr	Protein diffusion in mammalian cell cytoplasm.
title_full_unstemmed	Protein diffusion in mammalian cell cytoplasm.
title_sort	protein diffusion in mammalian cell cytoplasm.
publisher	Public Library of Science (PLoS)
publishDate	2011
url	https://doaj.org/article/45966f16aa314dd2919ac0b530383fa0
work_keys_str_mv	AT thomaskuhn proteindiffusioninmammaliancellcytoplasm AT teemuoihalainen proteindiffusioninmammaliancellcytoplasm AT jarihyvaluoma proteindiffusioninmammaliancellcytoplasm AT nicolasdross proteindiffusioninmammaliancellcytoplasm AT samifwillman proteindiffusioninmammaliancellcytoplasm AT jorglangowski proteindiffusioninmammaliancellcytoplasm AT maijavihinenranta proteindiffusioninmammaliancellcytoplasm AT jussitimonen proteindiffusioninmammaliancellcytoplasm
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Protein diffusion in mammalian cell cytoplasm.

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