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  • PROTEIN  (11)
  • DYNAMICS  (7)
  • 1
    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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  • 2
    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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  • 3
    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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  • 4
    Keywords: CELLS ; CELL ; Germany ; MODEL ; PATHWAY ; SYSTEM ; PROTEIN ; METABOLISM ; COMPLEX ; DYNAMICS ; BIOLOGY ; TRANSPORT ; NUMBER ; PHENOTYPE ; LIVING CELLS ; ENDOPLASMIC-RETICULUM ; ER ; FEATURES ; SIZE ; TECHNOLOGY ; VESICLE ; MEMBRANE-FUSION ; EXIT SITES ; TIMES ; CISTERNAL MATURATION
    Abstract: The dynamic compartmentalization of eukaryotic cells is a fascinating phenomenon that is not yet understood. A prominent example of this challenge is the Golgi apparatus, the central hub for protein sorting and lipid metabolism in the secretory pathway. Despite major advances in elucidating its molecular biology, the fundamental question of how the morphogenesis of this organelle is organized on a system level has remained elusive. Here, we have formulated a coarse-grained computational model that captures key features of the dynamic morphogenesis of a Golgi apparatus. In particular, our model relates the experimentally observed Golgi phenotypes, the typical turnover times, and the size and number of cisternae to three basic, experimentally accessible quantities: the rates for material influx from the endoplasmic reticulum, and the anterograde and retrograde transport rates. Based on these results, we propose which molecular factors should be mutated to alter the organelle's phenotype and dynamics
    Type of Publication: Journal article published
    PubMed ID: 20550896
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  • 5
    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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  • 6
    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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  • 7
    Keywords: CELLS ; CELL ; MODEL ; SUPPORT ; NEW-YORK ; SITE ; SITES ; PROTEIN ; RESPONSES ; SIMULATION ; BIOLOGY ; MOLECULAR-BIOLOGY ; SIGNAL ; ALPHA ; NUMBER ; FUSION ; EFFICIENT ; OVEREXPRESSION ; ORGANIZATION ; ENDOPLASMIC-RETICULUM ; molecular biology ; molecular ; INCREASE ; COPII ; LEVEL ; endoplasmic reticulum ; EVENTS ; USA ; BIOGENESIS ; INCREASES ; SECRETORY PATHWAY ; CELL BIOLOGY ; PROTEIN-1 ; BREFELDIN-A ; COPII COAT ; DE-NOVO FORMATION ; ER EXPORT ; GOLGI PROTEINS ; phosphatidylinositol-4 kinase III alpha ; Sec16 ; unfolded protein response ; XBP1
    Abstract: The biogenesis of endoplasmic reticulum (ER) exit sites (ERES) involves the formation of phosphatidylinositol-4 phosphate (PI4) and Sec16, but it is entirely unknown how ERES adapt to variations in cargo load. Here, we studied acute and chronic adaptive responses of ERES to an increase in cargo load for ER export. The acute response (within minutes) to increased cargo load stimulated ERES fusion events, leading to larger but less ERES. Silencing either PI4-kinase III alpha (PI4K-III alpha) or Sec16 inhibited the acute response. Overexpression of secretory cargo for 24 h induced the unfolded protein response (UPR), upregulated COPII, and the cells formed more ERES. This chronic response was insensitive to silencing PI4K-III alpha, but was abrogated by silencing Sec16. The UPR was required as the chronic response was absent in cells lacking inositol-requiring protein 1. Mathematical model simulations further support the notion that increasing ERES number together with COPII levels is an efficient way to enhance the secretory flux. These results indicate that chronic and acute increases in cargo load are handled differentially by ERES and are regulated by different factors
    Type of Publication: Journal article published
    PubMed ID: 18650939
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  • 8
    Keywords: PATHWAY ; DISEASE ; PROTEIN ; PROTEINS ; MOLECULES ; TRANSPORT ; Drosophila ; MEMBRANE ; KAPPA-B ; ER ; signalling ; p24 proteins ; protein transporting ; RETROMER COMPLEX ; WINGLESS SECRETION ; Wnt secretion ; WNTLESS
    Abstract: During development and disease, the exocytosis of signalling molecules, such as Wnt ligands, is essential to orchestrate cellular programs in multicellular organisms. However, it remains a largely unresolved question whether signalling molecules follow specialized transport routes through the exocytic pathway. Here we identify several Drosophila p24 proteins that are required for Wnt signalling. We demonstrate that one of these p24 proteins, namely Opossum, shuttles in the early secretory pathway, and that the Drosophila Wnt proteins are retained in the absence of p24 proteins. Our results indicate that Wnt secretion relies on a specialized anterograde secretion route with p24 proteins functioning as conserved cargo receptors.
    Type of Publication: Journal article published
    PubMed ID: 22094269
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  • 9
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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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  • 10
    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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