Anomalous subdiffusion is a measure for cytoplasmic crowding in living cells.

Macromolecular crowding dramatically affects cellular processes such as protein folding and assembly, regulation of metabolic pathways, and condensation of DNA. Despite increased attention, we still lack a definition for how crowded a heterogeneous environment is at the molecular scale and how this manifests in basic physical phenomena like diffusion. Here, we show by means of fluorescence correlation spectroscopy and computer simulations that crowding manifests itself through the emergence of anomalous subdiffusion of cytoplasmic macromolecules. In other words, the mean square displacement of a protein will grow less than linear in time and the degree of this anomality depends on the size and conformation of the traced particle and on the total protein concentration of the solution. We therefore propose that the anomality of the diffusion can be used as a quantifiable measure for the crowdedness of the cytoplasm at the molecular scale.

[1]  G. Warren,et al.  Rapid, endoplasmic reticulum-independent diffusion of the mitotic Golgi haze. , 2004, Molecular biology of the cell.

[2]  Judith Herzfeld,et al.  Life in a crowded world , 2004, EMBO reports.

[3]  Mehran Kardar,et al.  Anomalous dynamics of forced translocation. , 2003, Physical review. E, Statistical, nonlinear, and soft matter physics.

[4]  Tommy Nilsson,et al.  Spatiotemporal dynamics of the COPI vesicle machinery , 2003, EMBO reports.

[5]  Matthias Weiss,et al.  Stabilizing Turing patterns with subdiffusion in systems with low particle numbers. , 2003, Physical review. E, Statistical, nonlinear, and soft matter physics.

[6]  Allen P. Minton,et al.  Cell biology: Join the crowd , 2003, Nature.

[7]  Damien Hall,et al.  Macromolecular crowding: qualitative and semiquantitative successes, quantitative challenges. , 2003, Biochimica et biophysica acta.

[8]  J. Klafter,et al.  When translocation dynamics becomes anomalous. , 2003, Biophysical journal.

[9]  Tommy Nilsson,et al.  Anomalous protein diffusion in living cells as seen by fluorescence correlation spectroscopy. , 2003, Biophysical journal.

[10]  I. Vattulainen,et al.  How would you integrate the equations of motion in dissipative particle dynamics simulations , 2003, cond-mat/0302454.

[11]  W. Webb,et al.  Focal volume optics and experimental artifacts in confocal fluorescence correlation spectroscopy. , 2002, Biophysical journal.

[12]  Hugues Berry,et al.  Monte carlo simulations of enzyme reactions in two dimensions: fractal kinetics and spatial segregation. , 2002, Biophysical journal.

[13]  Y. Cheng,et al.  Diffusion of Mesoscopic Probes in Aqueous Polymer Solutions Measured by Fluorescence Recovery after Photobleaching , 2002 .

[14]  M. Saxton,et al.  Anomalous subdiffusion in fluorescence photobleaching recovery: a Monte Carlo study. , 2001, Biophysical journal.

[15]  R. Ellis Macromolecular crowding : obvious but underappreciated , 2022 .

[16]  D. Mastronarde,et al.  Organellar relationships in the Golgi region of the pancreatic beta cell line, HIT-T15, visualized by high resolution electron tomography , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[17]  J. Klafter,et al.  The random walk's guide to anomalous diffusion: a fractional dynamics approach , 2000 .

[18]  J Langowski,et al.  Anomalous diffusion of fluorescent probes inside living cell nuclei investigated by spatially-resolved fluorescence correlation spectroscopy. , 2000, Journal of molecular biology.

[19]  M. Vacher,et al.  Translational diffusion of globular proteins in the cytoplasm of cultured muscle cells. , 2000, Biophysical journal.

[20]  D. Zanette,et al.  Experimental evidence of power-law trapping-time distributions in porous media. , 1999, Physical review. E, Statistical physics, plasmas, fluids, and related interdisciplinary topics.

[21]  J. Korlach,et al.  Fluorescence correlation spectroscopy with single-molecule sensitivity on cell and model membranes. , 1999, Cytometry.

[22]  H Schindler,et al.  Single-molecule microscopy on model membranes reveals anomalous diffusion. , 1997, Biophysical journal.

[23]  A. Verkman,et al.  Translational Diffusion of Macromolecule-sized Solutes in Cytoplasm and Nucleus , 1997, The Journal of cell biology.

[24]  G. Phillips,et al.  The molecular structure of green fluorescent protein , 1996, Nature Biotechnology.

[25]  W. Webb,et al.  Constrained diffusion or immobile fraction on cell surfaces: a new interpretation. , 1996, Biophysical journal.

[26]  J. Haseloff,et al.  Molecular Characterization of Recombinant Green Fluorescent Protein by Fluorescence Correlation Microscopy , 1995 .

[27]  A. V. Grimstone Molecular biology of the cell (3rd edn) , 1995 .

[28]  T. Hirano,et al.  Conformation of (2→1)-β-d-fructan in aqueous solution , 1994 .

[29]  E. Nordmeier,et al.  Static and dynamic light-scattering solution behavior of pullulan and dextran in comparison , 1993 .

[30]  M. Saxton,et al.  Lateral diffusion in an archipelago. Dependence on tracer size. , 1993, Biophysical journal.

[31]  S. Havlin,et al.  Diffusion in disordered media , 1991 .

[32]  J. Bouchaud,et al.  Anomalous diffusion in disordered media: Statistical mechanisms, models and physical applications , 1990 .

[33]  D. Taylor,et al.  Hindered diffusion of inert tracer particles in the cytoplasm of mouse 3T3 cells. , 1987, Proceedings of the National Academy of Sciences of the United States of America.

[34]  D. Taylor,et al.  Probing the structure of cytoplasm , 1986, The Journal of cell biology.

[35]  A. Fulton,et al.  How crowded is the cytoplasm? , 1982, Cell.

[36]  M. Saxton,et al.  Lateral diffusion in an archipelago. Effects of impermeable patches on diffusion in a cell membrane. , 1982, Biophysical journal.

[37]  J. Mullins,et al.  Production of large numbers of mitotic mammalian cells by use of the reversible microtubule inhibitor nocodazole. Nocodazole accumulated mitotic cells. , 1980, Experimental cell research.

[38]  P. Nikunena,et al.  How would you integrate the equations of motion in dissipative particle dynamics simulations ? , 2003 .

[39]  A. Verkman Solute and macromolecule diffusion in cellular aqueous compartments. , 2002, Trends in biochemical sciences.

[40]  Michael J. Saxton,et al.  Chemically limited reactions on a percolation cluster , 2002 .