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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: CELLS ; tumor ; CELL ; Germany ; PROTEIN ; PROTEINS ; cell line ; LINES ; CONTRAST ; BIOLOGY ; CELL-LINES ; MOLECULAR-BIOLOGY ; METASTASIS ; CELL-LINE ; LINE ; NUCLEUS ; MAMMALIAN-CELLS ; NETHERLANDS ; LIVING CELLS ; BEHAVIOR ; cell lines ; DIFFUSION ; fluorescence correlation spectroscopy ; molecular biology ; molecular ; RE ; SCALE ; SIZE ; ANOMALOUS DIFFUSION ; LATERAL DIFFUSION ; cell size ; compartment ; CYTOPLASM ; ANOMALOUS SUBDIFFUSION ; ARCHIPELAGO ; FLUIDS ; FORCE MICROSCOPY ; macromolecular crowding ; viscoelastic ; VISCOELASTICITY
    Abstract: Macromolecular crowding provides the cytoplasm and the nucleoplasm with strongly viscoelastic properties and renders the diffusion of soluble proteins in both fluids anomalous. Here, we have determined the nanoscale viscoelasticity of the cytoplasm and the nucleoplasm in different mammalian cell lines. In contrast to the cell-specific response on the macroscale the nanoscale viscoelasticity (i.e. the behavior on length scales about 100-fold smaller than the cell size) only showed minor variations between different cell types. Similarly, the associated anomalous diffusion properties varied only slightly. Our results indicate a conserved state of macromolecular crowding in both compartments for a variety of mammalian cells with the cytoplasm being somewhat more crowded than the nucleus. (C) 2007 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved
    Type of Publication: Journal article published
    PubMed ID: 17923125
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  • 3
    Keywords: SIMULATIONS ; Germany ; MICROSCOPY ; MODEL ; ENZYMES ; DYNAMICS ; SIMULATION ; WATER ; ACID ; MEMBRANE ; fatty acids ; KINETICS ; molecular ; FATTY-ACID ; RE ; PHOSPHOLIPIDS ; SI ; LIPASE ; ENZYME ; DISSIPATIVE PARTICLE DYNAMICS ; ELASTICITY ; ENZYMATIC-ACTIVITY ; HYDROLYSIS ; LIPID-BILAYERS ; phospholipid ; SURFACE-TENSION ; VESICLE
    Abstract: Phospholipases are a class of molecular machines that are involved in the active remodelling processes of biological membranes. These lipases are interfacially activated enzymes and in the specific case of phospholipase A(2) (PLA(2))the enzyme catalyses the hydrolysis of di-acyl phospholipids into products of lysolipids and fatty acids, that dramatically change the physical properties of lipid membrane substrates. Using dissipative particle dynamics simulations on a simple coarse-grained bead-spring model of a fluid lipid bilayer in water, the mechanical and diffusive properties of the bilayer in the pure state and after the action of PLA(2) have been calculated. It is found that, in response to hydrolysis, the lipid membrane. becomes mechanically softened and the various in-plane and trans-bilayer diffusional modes become enhanced. The results compare favourably with available experimental data
    Type of Publication: Journal article published
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  • 4
    Keywords: CELL ; Germany ; MICROSCOPY ; MODEL ; PATHWAY ; SITE ; SITES ; PROTEIN ; PROTEINS ; COMPONENTS ; RESOLUTION ; COMPLEXES ; DOMAIN ; DYNAMICS ; BINDING ; BIOLOGY ; TRANSPORT ; MEMBRANE ; NUMBER ; PREDICTION ; KINETICS ; LIVING CELLS ; systems biology ; FLUORESCENCE ; SPATIAL-ORGANIZATION ; ORGANIZATION ; DOMAINS ; ENDOPLASMIC-RETICULUM ; ER ; RE ; PATTERN ; VESICLES ; INCREASE ; LEADS ; FLUORESCENCE MICROSCOPY ; COPII ; endoplasmic reticulum ; EXPORT ; PREDICTS ; ENGLAND ; PREDICT ; AGREEMENT ; PICHIA-PASTORIS ; TURNOVER ; SECRETORY PATHWAY ; CELL BIOLOGY ; biophysical modelling ; COOPERATIVE BINDING ; COPII-COATED VESICLE ; domain formation ; membrane traffic
    Abstract: Exit sites (ES) are specialized domains of the endoplasmic reticulum (ER) at which cargo proteins of the secretory pathway are packaged into COPII-coated vesicles. Although the essential COPII proteins (Sar1p, Sec23p-Sec24p, Sec13p-Sec31p) have been characterized in detail and their sequential binding kinetics at ER membranes have been quantified, the basic processes that govern the self-assembly and spatial organization of ERES have remained elusive. Here, we have formulated a generic computational model that describes the process of formation of ERES on a mesoscopic scale. The model predicts that ERES are arranged in a quasi-crystalline pattern, while their size strongly depends on the cargo-modulated kinetics of COPII turnover - that is, a lack of cargo leads to smaller and more mobile ERES. These predictions are in favorable agreement with experimental data obtained by fluorescence microscopy. The model further suggests that cooperative binding of COPII components, for example mediated by regulatory proteins, is a key factor for the experimentally observed organism-specific ERES pattern. Moreover, the anterograde secretory flux is predicted to grow when the average size of ERES is increased, whereas an increase in the number of (small) ERES only slightly alters the flux
    Type of Publication: Journal article published
    PubMed ID: 18073241
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  • 5
    Keywords: Germany ; statistics ; LOCALIZATION ; RE ; PROBABILITY-DISTRIBUTION ; FLUCTUATIONS ; ANDERSON TRANSITION ; DISORDERED-SYSTEMS ; ENERGY-LEVELS ; INVERSE PARTICIPATION RATIO ; MOBILITY EDGE ; QUANTUM CHAOTIC SCATTERING
    Abstract: We study the distribution of resonance widths P(Gamma) for three-dimensional (3D) random scattering media and analyze how it changes as a function of the randomness strength. We are able to identify in P(Gamma) the system-inherent fingerprints of the metallic, localized, and critical regimes. Based on the properties of resonance widths, we also suggest a criterion for determining and analyzing the metal-insulator transition. Our theoretical predictions are verified numerically for the prototypical 3D tight-binding Anderson model
    Type of Publication: Journal article published
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  • 6
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    Biophysical Journal 91 (7), 2393-2398 
    Keywords: SIMULATIONS ; Germany ; MICROSCOPY ; PROTEIN ; PROTEINS ; DOMAIN ; CONTRAST ; SIMULATION ; MOTION ; DOMAINS ; DIFFUSION ; CONSTANTS ; RE ; DEPENDENCE ; SIZE ; DISSIPATIVE PARTICLE DYNAMICS ; PREDICTS ; CELL-MEMBRANES ; FLUID ; LATERAL DIFFUSION ; LIPID BILAYERS ; MODEL MEMBRANES ; ROTATIONAL DIFFUSION
    Abstract: Experimentally determined diffusion constants are often used to elucidate the size and oligomeric state of membrane proteins and domains. This approach critically relies on the knowledge of the size-dependence of diffusion. We have used mesoscopic simulations to thoroughly quantify the size-dependent diffusion properties of membrane inclusions. For small radii R, we find that the lateral diffusion coefficient D is well described by the Saffman-Delbruck relation, which predicts a logarithmic decrease of D with R. However, beyond a critical radius R-c approximate to h(eta m)/(2(eta c)) (h, bilayer thickness; eta(m/c), viscosity of the ;membrane/surrounding solvent) we observe significant deviations and the emergence of an asymptotic scaling D similar to 1/R-2. The latter originates from the asymptotic hydrodynamics and the inclusion's internal degrees of freedom that become particularly relevant on short timescales. In contrast to the lateral diffusion, the size dependence of the rotational diffusion constant D-r follows the predicted hydrodynamic scaling D-r similar to 1/R-2 over the entire range of sizes studied here
    Type of Publication: Journal article published
    PubMed ID: 16829562
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  • 7
    Keywords: IN-VITRO ; Germany ; IN-VIVO ; MODEL ; VITRO ; VIVO ; PROTEIN ; PROTEINS ; DOMAIN ; SIMULATION ; MOBILITY ; MEMBRANE ; PREDICTION ; LIPID RAFTS ; MOTION ; EQUATIONS ; CLUSTERS ; DOMAINS ; CLUSTER ; DIFFUSION ; RE ; USA ; DISSIPATIVE PARTICLE DYNAMICS ; CELL-MEMBRANES ; RAFTS
    Abstract: The observation of membrane domains in vivo and in vitro has triggered a renewed interest in the size-dependent diffusion of membrane inclusions (e.g., clusters of transmembrane proteins and lipid rafts). Here, we have used coarse-grained membrane simulations to quantify the influence of a hydrophobic mismatch between the inclusion's transmembrane portion and the surrounding lipid bilayer on the diffusive mobility of the inclusion. Our data indicate only slight changes in the mobility (〈 30%) when altering the hydrophobic mismatch, and the scaling of the diffusion coefficient D is most consistent with previous hydrodynamic predictions, i.e., with the Saffman-Delbruck relation and the edgewise motion of a thin disk in the limit of small and large radii, respectively
    Type of Publication: Journal article published
    PubMed ID: 18502792
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