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dc.contributor.authorKühn, Thomas
dc.contributor.authorIhalainen, Teemu
dc.contributor.authorHyväluoma, Jari
dc.contributor.authorDross, Nicolas
dc.contributor.authorWillman, Sami
dc.contributor.authorLangowski, Jörg
dc.contributor.authorVihinen-Ranta, Maija
dc.contributor.authorTimonen, Jussi
dc.date.accessioned2011-12-19T11:20:08Z
dc.date.available2011-12-19T11:20:08Z
dc.date.issued2011
dc.identifier.citationKühn, T., Ihalainen, T., Hyväluoma, J., Dross, N., Willman, S., Langowski, J., Vihinen-Ranta, M., & Timonen, J. (2011). Protein diffusion in mammalian cell cytoplasm. <i>PLoS ONE</i>, <i>6</i>(8), e22962. <a href="https://doi.org/10.1371/journal.pone.0022962" target="_blank">https://doi.org/10.1371/journal.pone.0022962</a>
dc.identifier.otherCONVID_20696197
dc.identifier.otherTUTKAID_46614
dc.identifier.urihttps://jyx.jyu.fi/handle/123456789/37114
dc.description.abstractWe 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.
dc.language.isoeng
dc.publisherPublic Library of Science (PLoS)
dc.relation.ispartofseriesPLoS ONE
dc.relation.urihttp://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0022962
dc.subject.othersolu
dc.subject.otherproteiinin diffuusio
dc.subject.otherProteiinien kuljetus
dc.subject.otherCell
dc.subject.otherprotein diffusion
dc.subject.otherProtein transport
dc.titleProtein diffusion in mammalian cell cytoplasm
dc.typearticle
dc.identifier.urnURN:NBN:fi:jyu-2011121511804
dc.contributor.laitosBio- ja ympäristötieteiden laitosfi
dc.contributor.laitosFysiikan laitosfi
dc.contributor.laitosDepartment of Biological and Environmental Scienceen
dc.contributor.laitosDepartment of Physicsen
dc.contributor.oppiaineSolu- ja molekyylibiologiafi
dc.contributor.oppiaineSoveltava fysiikkafi
dc.contributor.oppiaineNanoscience Centerfi
dc.contributor.oppiaineCell and Molecular Biologyen
dc.contributor.oppiaineApplied Physicsen
dc.contributor.oppiaineNanoscience Centeren
dc.type.urihttp://purl.org/eprint/type/JournalArticle
dc.date.updated2011-12-15T04:30:10Z
dc.type.coarjournal article
dc.description.reviewstatuspeerReviewed
dc.format.pagerangee22962
dc.relation.issn1932-6203
dc.relation.numberinseries8
dc.relation.volume6
dc.type.versionpublishedVersion
dc.rights.copyright© 2011 Kühn et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
dc.rights.accesslevelopenAccessfi
dc.subject.ysodiffuusio
dc.subject.ysosolulima
jyx.subject.urihttp://www.yso.fi/onto/yso/p18009
jyx.subject.urihttp://www.yso.fi/onto/yso/p28857
dc.rights.urlhttps://creativecommons.org/licenses/by/2.0/
dc.relation.doi10.1371/journal.pone.0022962


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© 2011 Kühn et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
Except where otherwise noted, this item's license is described as © 2011 Kühn et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.