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  • 1
    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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  • 2
    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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  • 3
    Keywords: TRANSPORT ; SOFT ; HAMILTONIAN-SYSTEMS ; POINCARE RECURRENCES ; QUANTUM CHAOS ; CAVITIES ; GRAPHS
    Abstract: Abstract: We study the signatures of a classical mixed phase space for open quantum systems. We find the scaling of the break time up to which quantum mechanics mimics the classical staying probability and derive the distribution of resonance widths. Based on these results we explain why for mixed systems two type of conductance fluctuations were found: quantum mechanics divides the hierarchically structured chaotic component of phase space into two parts -one yields fractal conductance fluctuations while the other causes isolated resonances. In general, both type appear together, but on different energy scales.
    Type of Publication: Journal article published
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  • 4
    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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  • 5
    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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  • 6
    Keywords: SIMULATIONS ; Germany ; MODEL ; PATHWAY ; PROTEIN ; PROTEINS ; SIMULATION ; BIOLOGY ; TRANSPORT ; EXPERIENCE ; MEMBRANE ; LOCALIZATION ; Golgi apparatus ; cholesterol ; NETHERLANDS ; MEMBRANES ; ENDOPLASMIC-RETICULUM ; CHEMISTRY ; SCALE ; SCIENCE ; PHASE ; endoplasmic reticulum ; RETENTION ; SECRETORY PATHWAY ; biophysical modelling ; INCLUSIONS ; MEMBRANE-INDUCED INTERACTIONS ; GOLGI ENZYMES ; Hydrophobic mismatch ; KIN RECOGNITION ; Membrane simulations ; Protein sorting
    Abstract: Sorting of transmembrane proteins is a central task of the secretory pathway. Due to the lack of an organizing mastermind, the decision whether a protein participates in anterograde/retrograde transport or rather stays in its compartment has to be made by a self-organization process on the molecular scale. Minimizing the hydrophobic mismatch between a protein and the surrounding lipid bilayer has been shown to be an important determinant of protein localization. It has remained elusive, however, how mislocalized proteins sense that remote organelles may provide a better lipid environment, i.e. how proteins differentially control their journey along the secretory pathway. Here we show by coarse-grained membrane simulations that proteins partition into the lipid phase with the smallest hydrophobic mismatch on heterogeneous membranes while they cluster and even segregate as homo-oligomers according to their hydrophobic mismatch on a homogeneous bilayer. We propose that protein sorting is facilitated by stabilizing coat proteins at clusters of mislocalized proteins that experience a hydrophobic mismatch.
    Type of Publication: Journal article published
    PubMed ID: 20537786
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