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  • DYNAMICS  (7)
  • DISSIPATIVE PARTICLE DYNAMICS  (5)
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  • 1
    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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  • 2
    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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  • 3
    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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  • 4
    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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  • 5
    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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  • 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: 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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  • 8
    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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  • 9
    Keywords: SYSTEMS ; DYNAMICS ; DISORDER ; ORGANIZATION ; SYNCHRONIZATION ; NONLINEAR OSCILLATORS ; SPATIOTEMPORAL CHAOS ; SEMICONDUCTOR-LASERS
    Abstract: The effect of impurities in a two-dimensional lattice of coupled nonlinear chaotic oscillators and their ability to control the dynamical behavior of the system are studied. We show that a single impurity can produce synchronized spatiotemporal patterns, even though all oscillators and the impurity are chaotic when uncoupled. When a small number of impurities is arranged in a way, that the lattice is divided into two disjoint parts, synchronization is enforced even for small coupling. The synchronization is not affected as the size of the lattice increases, although the impurity concentration tends to zero.
    Type of Publication: Journal article published
    PubMed ID: 11414994
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  • 10
    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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