Protein diffusion in mammalian cell cytoplasm

PLoS ONE

Volumn 6, Issue 8, 2011, Pages

  Kühn, Thomas ^a   Ihalainen, Teemu O ^a   Hyväluoma, Jari ^a,b   Dross, Nicolas ^c   Willman, Sami F ^a   Langowski, Jörg ^c   Vihinen Ranta, Maija ^a   Timonen, Jussi ^a  

^a UNIVERSITY OF JYVÄSKYLÄ   (Finland)

^b FINNISH FOREST RESEARCH INSTITUTE   (Finland)

^c GERMAN CANCER RESEARCH CENTER DKFZ   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CELL NUCLEOPLASM; CELL NUCLEUS; CELL NUCLEUS MEMBRANE; CELLS AND CELL COMPONENTS; CONTROLLED STUDY; CYTOPLASM; CYTOSOL; DIFFUSION COEFFICIENT; FEMALE; FLUORESCENCE CORRELATION SPECTROSCOPY; FLUORESCENCE RECOVERY AFTER PHOTOBLEACHING; HUMAN; HUMAN CELL; INTERMETHOD COMPARISON; MAMMAL CELL; MATHEMATICAL ANALYSIS; MOLECULAR IMAGING; NONHUMAN; NUCLEOSOL; POROSITY; PROTEIN DIFFUSION; PROTEIN TRANSPORT; ANIMAL; BIOLOGICAL MODEL; CAT; CELLS; COMPUTER SIMULATION; CONFOCAL MICROSCOPY; DIFFUSION; FLUORESCENCE MICROSCOPY; HELA CELL; IMAGE PROCESSING; MAMMAL; METABOLISM; REPRODUCIBILITY;

MAMMALIA;

BACTERIAL PROTEIN; PHOTOPROTEIN; PROTEIN; YELLOW FLUORESCENT PROTEIN, BACTERIA;

ANIMALS; BACTERIAL PROTEINS; CATS; CELLS; COMPUTER SIMULATION; CYTOPLASM; DIFFUSION; FLUORESCENCE RECOVERY AFTER PHOTOBLEACHING; HELA CELLS; HUMANS; IMAGE PROCESSING, COMPUTER-ASSISTED; LUMINESCENT PROTEINS; MAMMALS; MICROSCOPY, CONFOCAL; MICROSCOPY, FLUORESCENCE; MODELS, BIOLOGICAL; POROSITY; PROTEINS; REPRODUCIBILITY OF RESULTS;

EID: 84855602279     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0022962     Document Type: Article

References (39)

1. Zeskind BJ, Jordan CD, Timp W, Trapani L, Waller G, et al. (2007) Nucleic acid and protein mass mapping by live-cell deep-ultraviolet microscopy. Nat Methods 4: 567-569.
2. Guigas G, Kalla C, Weiss M, (2007) Probing the nanoscale viscoelasticity of intracellular fluids in living cells. Biophys J 93: 316-323.
3. Ellis RJ, (2001) Macromolecular crowding: an important but neglected aspect of the intracellular environment. Current Opinion in Structural Biology 11: 114-119.
4. Marsh BJ, Mastronarde DN, Buttle KF, Howell KE, McIntosh JR, (2001) Organellar relationships in the Golgi region of the pancreatic beta cell line, HIT-T15, visualized by high resolution electron tomography. Proc Natl Acad Sci U S A 98: 2399-2406.
5. Puhka M, Vihinen H, Joensuu M, Jokitalo E, (2007) Endoplasmic reticulum remains continuous and undergoes sheet-to-tubule transformation during cell division in mammalian cells. J Cell Biol 179: 895-909.
6. Luby-Phelps K, (2000) Cytoarchitecture and physical properties of cytoplasm: volume, viscosity, diffusion, intracellular surface area. Int Rev Cytol 192: 189-221.
7. Wachsmuth M, Waldeck W, Langowski J, (2000) Anomalous diffusion of fluorescent probes inside living cell nuclei investigated by spatially-resolved fluorescence correlation spectroscopy. J Mol Biol 298: 677-689.
8. Hinde E, Cardarelli F, Digman MA, Gratton E, (2010) In vivo pair correlation analysis of egfp intranuclear diffusion reveals dna-dependent molecular flow. Proc Natl Acad Sci U S A 107: 16560-16565.
9. Schuldt A, (2010) The dynamic nucleus. Nat Rev Mol Cell Biol 11: 678-679.
10. Phair RD, Misteli T, (2000) High mobility of proteins in the mammalian cell nucleus. Nature 404: 604-609.
11. Lippincott-Schwartz J, Altan-Bonnet N, Patterson GH, (2003) Photobleaching and photoactivation: following protein dynamics in living cells. Nat Cell Biol Suppl: S7-14.
12. Axelrod D, Koppel DE, Schlessinger J, Elson E, Webb WW, (1976) Mobility measurement by analysis of fluorescence photobleaching recovery kinetics. Biophys J 16: 1055-1069.
13. Soumpasis DM, (1983) Theoretical analysis of fluorescence photobleaching recovery experiments. Biophys J 41: 95-97.
14. Sprague BL, Pego RL, Stavreva DA, McNally JG, (2004) Analysis of binding reactions by fluorescence recovery after photobleaching. Biophys J 86: 3473-3495.
15. Braga J, Desterro JM, Carmo-Fonseca M, (2004) Intracellular macromolecular mobility measured by fluorescence recovery after photobleaching with confocal laser scanning microscopes. Mol Biol Cell 15: 4749-4760.
16. Mueller F, Wach P, McNally JG, (2008) Evidence for a common mode of transcription factor interaction with chromatin as revealed by improved quantititive fluorescence recovery after photobleacing. Biophys J 94: 3323-3339.
17. Kang M, Day CA, Drake K, Kenworthy AK, DiBenedetto E, (2009) A generalization of theory for two-dimensional fluorescence recovery after photobleaching applicable to confocal laser scanning microscopes. Biophys J 97: 1501-1511.
18. Kubitscheck U, Wedekind P, Peters R, (1994) Lateral diffusion measurement at high spatial resolution by scanning microphotolysis in a confocal microscope. Biophys J 67: 948-956.
19. Meyvis TK, De Smedt SC, Van Oostveldt P, Demeester J, (1999) Fluorescence recovery after photobleaching: a versatile tool for mobility and interaction measurements in pharmaceutical research. Pharm Res 16: 1153-1162.
20. Siggia ED, Lippincott-Schwartz J, Bekiranov S, (2000) Diffusion in inhomogeneous media: theory and simulations applied to whole cell photobleach recovery. Biophys J 79: 1761-1770.
21. Beaudouin J, Mora-Bermúdez F, Klee T, Daigle N, Ellenberg J, (2006) Dissecting the contribution of diffusion and interactions to the mobility of nuclear proteins. Biophys J 90: 1878-1894.
22. Sbalzarini IF, Mezzacasa A, Helenius A, Koumoutsakos P, (2005) Effects of organelle shape on fluorescence recovery after photobleaching. Biophys J 89: 1482-1492.
23. Dross N, Spriet C, Zwerger M, Müller G, Waldeck W, et al. (2009) Mapping egfp oligomer mobility in living cell nuclei. PLoS One 4: e5041.
24. Braeckmans K, Remaut K, Vandenbroucke RE, Lucas B, De Smedt SC, et al. (2007) Line frap with the confocal laser scanning microscope for diffusion measurements in small regions of 3-d samples. Biophsy J 92: 1482-1492.
25. Parrish CR, Burtonboy G, Carmichael LE, (1988) Characterization of a nonhemagglutinating mutant of canine parvovirus. Virology 163: 230.
26. Rojo M, Emery G, Marjomki V, McDowall AW, Parton RG, et al. (2000) The transmembrane protein p23 contributes to the organization of the golgi apparatus. J Cell Sci 113: 1043.
27. Jeon JH, Tejedor V, Burov S, Barkai E, Selhuber-Unkel C, et al. (2011) In vivo anomalous diffusion and weak ergodicity breaking of lipid granules. Phys Rev Lett 106: 048103.
28. Weber SC, Spakowitz AJ, Theriot JA, (2010) Bacterial chromosomal loci move subdiffusively through a viscoelastic cytoplasm. Phys Rev Lett 104: 238102.
29. Bronstein I, Israel Y, Kepten E, Mai S, Shav-Tal Y, et al. (2009) Transient anomalous diffusion of telomeres in the nucleus of mammalian cells. Phys Rev Lett 103: 018102.
30. Metzler R, Klafter J, (2000) The random walk's guide to anomalous diffusion: a fractional dynamics approach. Phys Rep 339: 1.
31. Burov S, Jeon JH, Metzler R, Barkai E, (2011) Single particle tracking in systems showing anomalous diffusion: the role of weak ergodicity breaking. Phys Chem Chem Phys 13: 1800.
32. Abramoff MD, Magelhaes PJ, Ram SJ, (2004) Image processing with imagej. Biopotonics International 11: 36-42.
33. Ihalainen TO, Niskanen EA, Jylhävä J, Turpeinen T, Rinne J, et al. (2007) Dynamics and interactions of parvoviral ns1 protein in the nucleus. Cell Microbiol 9: 1946-1959.
34. Wachsmuth M, (2001) Fluorescence fluctuation microscopy: design of a prototype, theory and mea-surements of the mobility of biomolecules in the cell nucleus. Ph.D. thesis, Ruprecht-Karls-Universität, Heidelberg.
35. Tewes M, Langowski J, (2001) Fluorescence correlation spectroscopy module for a microscope. European patent no 0941470.
36. Kaviany M, (1995) Principles of Heat Transfer in Porous Media. Springerverlag, New York.
37. Succi S, (2001) The Lattcie Boltzmann Equation for Fluid Dynamics and Beyond. Oxford University Press, New York.
38. Wolf-Gladrow D, (1995) A lattice boltzmann equation for diffusion. Journal of Statistical Physics 79: 1023-1032.
39. Schaff J, Fink CC, Slepchenko B, Carson JH, Loew LM, (1997) A general computational framework for modeling cellular structure and function. Biophys J 73: 1135-1146.