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  • 1
    Keywords: SIMULATIONS ; CELLS ; CELL ; Germany ; MODEL ; DEATH ; PROTEINS ; cell line ; LINES ; COMPLEX ; COMPLEXES ; CELL-LINES ; treatment ; SPECTROSCOPY ; CELL-DEATH ; CELL-LINE ; LINE ; KINETICS ; LIVING CELLS ; FLUORESCENCE ; cell lines ; MONTE-CARLO ; TRANSLATIONAL DIFFUSION ; fluorescence correlation spectroscopy ; RE ; ENVIRONMENTS ; cell death ; ANOMALOUS DIFFUSION ; USA ; correlation ; compartment ; CYTOPLASM ; SUBDIFFUSION
    Abstract: We have used fluorescence correlation spectroscopy to determine the anomalous diffusion properties of. fluorescently tagged gold beads in the cytoplasm and the nucleus of living cells. From the extracted mean-square displacement v( t); t a, wehave determined the complex shear modulus G(v); v a for both compartments. Without treatment, all tested cell lines showed a strong viscoelastic behavior of the cytoplasm and the nucleoplasm, highlighting the crowdedness of these intracellular. fluids. We also found a similar viscoelastic response in frog egg extract, which tended toward a solely viscous behavior upon dilution. When cells were osmotically stressed, the diffusion became less anomalous and the viscoelastic response changed. In particular, the anomality changed from a approximate to 0.55 to a approximate to 0.66, which indicates that the Zimm model for polymer solutions under varying solvent conditions is a good empirical description of the material properties of the cytoplasm and the nucleoplasm. Since osmotic stress may eventually trigger cell death, we propose, on the basis of our observations, that intracellular. fluids are maintained in a state similar to crowded polymer solutions under good solvent conditions to keep the cell viable. We have used fluorescence correlation spectroscopy to determine the anomalous diffusion properties of fluorescently tagged gold beads in the cytoplasm and the nucleus of living cells. From the extracted mean- square displacement v(tau)similar to tau(alpha), we have determined the complex shear modulusG(omega)similar to omega(alpha) for both compartments. Without treatment, all tested cell lines showed a strong viscoelastic behavior of the cytoplasm and the nucleoplasm, highlighting the crowdedness of these intracellular. uids. We also found a similar viscoelastic response in frog egg extract, which tended toward a solely viscous behavior upon dilution. When cells were osmotically stressed, the diffusion became less anomalous and the viscoelastic response changed. In particular, the anomality changed from a approximate to 0.55 to a approximate to 0.66, which indicates that the Zimm model for polymer solutions under varying solvent conditions is a good empirical description of the material properties of the cytoplasm and the nucleoplasm. Since osmotic stress may eventually trigger cell death, we propose, on the basis of our observations, that intracellular. uids are maintained in a state similar to crowded polymer solutions under good solvent conditions to keep the cell viable
    Type of Publication: Journal article published
    PubMed ID: 17416631
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  • 2
    Keywords: SIMULATIONS ; PROTEIN ; DYNAMICS ; ASSOCIATION ; LIVING CELLS ; MOTION ; MONTE-CARLO ; DIFFUSION ; COEFFICIENT ; SUBDIFFUSION ; DIMENSIONS ; INTRACELLULAR ENVIRONMENTS ; NONCLASSICAL KINETICS ; RATE LAWS
    Abstract: Using particle-based simulations, we show that anomalous diffusion in two-dimensional (2D) environments induces a strongly fractal reaction kinetics, i.e. time-dependent rate coefficients. While non-classical kinetics is anticipated already for normal diffusion due to the compactness of Brownian motion in 2D, the effect is even more pronounced when particles move via subdiffusion. As a consequence, strong reactant segregation is observed. Based on these findings, we argue that the experimentally observed subdiffusion of proteins on biomembranes may serve as a means to foster biochemical reactions in well-defined "hot spots" without the need for diffusion barriers.
    Type of Publication: Journal article published
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  • 3
    Keywords: CELLS ; DYNAMICS ; LIVING CELLS ; MONTE-CARLO ; fluorescence correlation spectroscopy ; SUBDIFFUSION
    Abstract: Anomalous diffusion in crowded fluids, e. g. in the cytoplasm of living cells, is a frequent phenomenon. Despite manifold observations of anomalous diffusion with several experimental techniques, a thorough understanding of the underlying microscopic causes is still lacking. Here, we have quantitatively compared two popular techniques with which anomalous diffusion is typically assessed. Using extensive computer simulations of two prototypical random walks with stationary increments, i.e. fractional Brownian motion and obstructed diffusion, we find that single particle tracking (SPT) yields results for the diffusion anomaly that are equivalent to those obtained by fluorescence correlation spectroscopy (FCS). We also show that positional uncertainties, inherent to SPT experiments, lead to a systematic underestimation of the diffusion anomaly, regardless of the underlying random walk and measurement technique. This effect becomes particularly relevant when the position uncertainty is larger than the average positional displacement between two successive frames
    Type of Publication: Journal article published
    PubMed ID: 21613702
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  • 4
    Keywords: CELLS ; MODEL ; PROTEIN ; DYNAMICS ; SEQUENCE ; TRANSPORT ; LIVING CELLS ; SUBDIFFUSION ; COPI
    Abstract: Diffusion-mediated searching for interaction partners is an ubiquitous process in cell biology. Transcription factors, for example, search specific DNA sequences, signaling proteins aim at interacting with specific cofactors, and peripheral membrane proteins try to dock to membrane domains. Brownian motion, however, is affected by molecular crowding that induces anomalous diffusion (so-called subdiffusion) of proteins and larger structures, thereby compromising diffusive transport and the associated sampling processes. Contrary to the naive expectation that subdiffusion obstructs cellular processes, we show here by computer simulations that subdiffusion rather increases the probability of finding a nearby target. Consequently, important events like protein complex formation and signal propagation are enhanced as compared to normal diffusion. Hence, cells indeed benefit from their crowded internal state and the associated anomalous diffusion
    Type of Publication: Journal article published
    PubMed ID: 17827216
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  • 5
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    Journal of Chemical Physics 134 (16), ArtNr: 165101- 
    Keywords: SIMULATIONS ; MODEL ; MOLECULES ; LIVING CELLS ; MEMBRANES ; MONTE-CARLO ; fluorescence correlation spectroscopy ; DISSIPATIVE PARTICLE DYNAMICS ; POLYMERS ; SUBDIFFUSION
    Abstract: Transmembrane proteins frequently form (transient) oligomers on biomembranes, e. g., while participating in protein sorting and signaling events. Using coarse-grained membrane simulations we show here that transmembrane proteins show a subdiffusive motion on short time scales when being part of a linear oligomer, i.e., a flexible polymer, embedded in a two-dimensional membrane. Our results are in agreement with previous experimental observations. They further indicate that polymers of transmembrane proteins are well described by predictions from Rouse theory in two dimensions even in the presence of hydrodynamic interactions.
    Type of Publication: Journal article published
    PubMed ID: 21528980
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