Anomalous subdiffusion is a measure for cytoplasmic crowding in living cells

Biophysical Journal

Volumn 87, Issue 5, 2004, Pages 3518-3524

  Weiss, Matthias ^a   Elsner, Markus ^b   Kartberg, Fredrik ^b   Nilsson, Tommy ^b  

^a UNIVERSITY OF SOUTHERN DENMARK   (Denmark)

^b UNIVERSITY OF GOTHENBURG   (Sweden)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; COMPUTER SIMULATION; CYTOPLASM; DIFFUSION; FLUORESCENCE MICROSCOPY; HELA CELL; HUMAN; HUMAN CELL; HYDRODYNAMICS; INTRACELLULAR TRANSPORT; MACROMOLECULE; MOLECULAR DYNAMICS; TRANSPORT KINETICS; BIOLOGICAL MODEL; CHEMICAL MODEL; CHEMISTRY; COMPARATIVE STUDY; EVALUATION; METABOLISM; PARTICLE SIZE; VALIDATION STUDY;

DEXTRAN;

COMPUTER SIMULATION; CYTOPLASM; DEXTRANS; DIFFUSION; HELA CELLS; HUMANS; MACROMOLECULAR SUBSTANCES; MODELS, BIOLOGICAL; MODELS, CHEMICAL; PARTICLE SIZE;

EID: 14844331313     PISSN: 00063495     EISSN: None     Source Type: Journal    
DOI: 10.1529/biophysj.104.044263     Document Type: Article

References (39)

1. Alberts, B., D. Bray, J. Lewis, M. Raff, K. Roberts, and J. D. Watson. 1994. Molecular Biology of the Cell, 3rd ed. Garland Publishing, New York.
2. Arrio-Dupont, M., G. Foucault, M. Vacher, P. F. Devaux, and S. Cribier. 2000. Translational diffusion of globular proteins in the cytoplasm of cultured muscle cells. Biophys. J. 78:901-907.
3. Axelsson, M. A., and G. Warren. 2004. Rapid, ER-independent diffusion of the mitotic Golgi haze. Mol. Biol. Cell. 15:1843-1852.
4. Berry, H. 2002. Monte Carlo simulations of enzyme reactions in two dimensions: fractal kinetics and spatial segregation. Biophys. J. 83:1891-1901.
5. Bouchaud, J. P., and A. Georges. 1990. Anomalous diffusion in disordered media-statistical mechanisms, models, and physical applications. Physics Rep. 195:127-293.
6. Cheng, Y., R. K. Prud'homme, and J. L. Thomas. 2002. Diffusion of mesoscopic probes in aqueous polymer solutions measured by fluorescence recovery after photobleaching. Macromolecules. 35:8111-8121.
7. Doi, M. 1996. Introduction to Polymer Physics. Clarendon Press, Oxford.
8. Drazer, G., and D. H. Zanette. 1999. Experimental evidence of power-law trapping-time distributions in porous media. Phys. Rev. E. 60:5858-5864.
9. Ellis, R. J. 2001. Macromolecular crowding: obvious but underappreciated. Trends Biochem. Sci. 26:597-604.
10. Ellis, R. J., and A. P. Minton. 2003. Cell biology: join the crowd. Nature. 425:27-28.
11. Elsner, M., H. Hashimoto, J. C. Simpson, D. Cassel, T. Nilsson, and M. Weiss. 2003. Spatiotemporal dynamics of the copi vesicle machinery. EMBO Rep. 4:1000-1004.
12. Feder, T. J., I. Brust-Mascher, J. P. Slattery, B. Baird, and W. W. Webb. 1996. Constrained diffusion or immobile fraction on cell surfaces: a new interpretation. Biophys. J. 70:2767-2773.
13. Fulton, A. B. 1982. How crowded is the cytoplasm? Cell. 30:345-347.
14. Hall, D., and A. P. Minton. 2003. Macromolecular crowding: qualitative and semiquantitative successes, quantitative challenges. Biochim. Biophys. Acta. 1649:127-139.
15. Havlin, S., and D. Ben-Avraham. 1987. Diffusion in disordered media. Adv. Phys. 36:695-798.
16. Hess, S. T., and W. W. Webb. 2002. Focal volume optics and experimental artifacts in confocal fluorescence correlation spectroscopy. Biophys. J. 83:2300-2317.
17. Kantor, Y., and M. Kardar. 2004. Anomalous dynamics of forced translocation. Phys. Rev. E. 69:021806.
18. Kitamura, S., T. Hirano, K. Takeo, M. Mimura, K. Kajiwara, T. Stokke, and T. Harada. 1994. Conformation of (2 → 1)-β-d-fructan in aqueous solution. Int. J. Biol. Macromol. 16:313-317.
19. Luby-Phelps, K., P. E. Castle, D. L. Taylor, and F. Lanni. 1987. Hindered diffusion of inert tracer particles in the cytoplasm of mouse 3t3 cells. Proc. Natl. Acad. Sci. USA. 84:4910-4913.
20. Luby-Phelps, K., D. L. Taylor, and F. Lanni. 1986. Probing the structure of cytoplasm. J. Cell Biol. 102:2015-2022.
21. Marsh, B. J., D. N. Mastronarde, K. F. Buttle, K. E. Howell, and J. R. McIntosh. 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. USA. 98:2399-2406.
22. Metzler, R., and J. Klafter. 2000. The random walk's guide to anomalous diffusion: a fractional dynamics approach. Physics Rep. 339:1-77.
23. Metzler, R., and J. Klafter. 2003. When translocation dynamics becomes anomalous. Biophys. J. 85:2776-2779.
24. Nikunen, P., M. Karttunen, and I. Vattulainen. 2003. How would you integrate the equations of motion in dissipative particle dynamics simulations? Comp. Phys. Comm. 153:407-423.
25. Nordmeier, E. 1993. Static and dynamic light-scattering solution behavior of pullulan and dextran in comparison. J. Phys. Chem. 97:5770-5785.
26. Rivas, G., F. Ferrone, and J. Herzfeld. 2004. Life in a crowded world. EMBO Rep. 5:23-27.
27. Saxton, M. J. 1993. Lateral diffusion in an archipelago. Dependence on tracer size. Biophys. J. 64:1053-1062.
28. Saxton, M. J. 2001. Anomalous subdiffusion in fluorescence photobleaching recovery: a Monte Carlo study. Biophys. J. 81:2226-2240.
29. Saxton, M. J. 2002. Chemically limited reactions on a percolation cluster. J. Chem. Phys. 116:203-208.
30. Schutz, G. J., H. Schindler, and T. Schmidt. 1997. Single-molecule microscopy on model membranes reveals anomalous diffusion. Biophys. J. 73:1073-1080.
31. Schwille, P., J. Korlach, and W. W. Webb. 1999. Fluorescence correlation spectroscopy with single-molecule sensitivity on cell and model membranes. Cytometry. 36:176-182.
32. Seksek, O., J. Biwersi, and A. S. Verkman. 1997. Translational diffusion of macromolecule-sized solutes in cytoplasm and nucleus. J. Cell Biol. 138:131-142.
33. Terry, B. R., E. K. Matthews, and J. Haseloff. 1995. Molecular characterization of recombinant green fluorescent protein by fluorescence correlation microscopy. Biochem. Biophys. Res. Commun. 217:21-27.
34. Verkman, A. S. 2002. Solute and macromolecule diffusion in cellular aqueous compartments. Trends Biochem. Sci. 27:27-33.
35. Wachsmuth, M., W. Waldeck, and J. Langowski. 2000. Anomalous diffusion of fluorescent probes inside living cell nuclei investigated by spatially-resolved fluorescence correlation spectroscopy. J. Mol. Biol. 298:677-689.
36. Weiss, M. 2003. Stabilizing turing patterns with subdiffusion in systems with low particle numbers. Phys. Rev. E. 68:036213.
37. Weiss, M., H. Hashimoto, and T. Nilsson. 2003. Anomalous protein diffusion in living cells as seen by fluorescence correlation spectroscopy. Biophys. J. 84:4043-4052.
38. Yang, F., L. G. Moss, and G. N. Phillips. 1996. The molecular structure of green fluorescent protein. Nat. Biotechnol. 14:1246-1251.
39. Zieve, G. W., D. Turnbull, J. M. Mullins, and J. R. McIntosh. 1980. Production of large numbers of mitotic mammalian cells by use of the reversible microtubule inhibitor nocodazole. Nocodazole accumulated mitotic cells. Exp. Cell Res. 126:397-405.