Figure 2. The Virtual Cell predicts experimental actin comet tail characteristics at steady state if aggregate size and velocity are known. We adapted a previously published Virtual Cell model to our experimental system to test the theoretical effect of aggregate size and velocity on actin polymerization. Using this model, we show that when aggregate size and velocity are known, actin polymerization downstream of Nck SH3 aggregates can be predicted. (A) Virtual Cell reaction diagram of the simplified actin dendritic nucleation model in which N-WASp is activated on the membrane by Nck. In the Virtual Cell reaction diagram, green circles represent species that participate in reaction, yellow ovals represent biochemical reactions, lines connecting species and reactions indicate the reactants and products of each reaction, and the vertical line in the left schematic designates the separation between membrane and cytosol. The reaction scheme on the left describes membrane reactions, whereas the reaction scheme on the right describes cytosolic reactions. The detailed schematic can be found in the Virtual Cell database under the user JDitlev, model Nck Induces Actin Comet Tail Formation Single NWASP Activation of Arp2/3 Simplified Actin Dendritic Nucleation. (B) Example of an Nck-induced actin comet tail from Virtual Cell simulations at steady state. Nck SH3 domains were localized to a patch on the membrane (red membrane mesh units) inducing actin polymerization in the adjacent mesh units in the cytosol (scaled from blue ∼195 µM to red ∼1,500 µM). Actin then flowed away from the Nck SH3 patch, as indicated by the advection arrow, at a constant velocity to mimic actin propulsion of the Nck SH3 aggregate. (C) Predicted versus experimental actin comet tails induced by aggregates traveling at similar velocities (0.060–0.090 µm/s). Experimental data were divided into five groups by aggregate size (n = 2–9). The mean experimentally measured actin concentrations from linescans were compared with Virtual Cell predictions. Virtual Cell simulations qualitatively predicted experimental results at a given aggregate velocity. Error bars indicate the SEM of averaged experimental data from each group at each measured point. (D) Predicted versus experimental actin comets tails induced by aggregates with a similar number of Nck SH3 molecules (12,000–22,000 molecules). Experimental data were divided into five groups by velocity (n = 2–11). The mean experimentally measured actin concentrations from linescans were compared with Virtual Cell predictions. Virtual Cell simulations predicted experimental results at a given aggregate size. Error bars indicate the SEM of averaged experimental data from each group at each measured point. (E) Four representative comparisons chosen from 145 experimentally measured actin comet tails with corresponding simulations. The following parameters were used for simulations run with the experimentally measured size (Exp.) and velocity of individual Nck SH3 aggregates (VCell): 17,000 molecules, 0.04 µm/s (top left); 10,000 molecules, 0.050 µm/s (top right); 17,000 molecules, 0.057 µm/s (bottom left); and 17,000 molecules, 0.120 µm/s (bottom right).
Figure 2.

The Virtual Cell predicts experimental actin comet tail characteristics at steady state if aggregate size and velocity are known. We adapted a previously published Virtual Cell model to our experimental system to test the theoretical effect of aggregate size and velocity on actin polymerization. Using this model, we show that when aggregate size and velocity are known, actin polymerization downstream of Nck SH3 aggregates can be predicted. (A) Virtual Cell reaction diagram of the simplified actin dendritic nucleation model in which N-WASp is activated on the membrane by Nck. In the Virtual Cell reaction diagram, green circles represent species that participate in reaction, yellow ovals represent biochemical reactions, lines connecting species and reactions indicate the reactants and products of each reaction, and the vertical line in the left schematic designates the separation between membrane and cytosol. The reaction scheme on the left describes membrane reactions, whereas the reaction scheme on the right describes cytosolic reactions. The detailed schematic can be found in the Virtual Cell database under the user JDitlev, model Nck Induces Actin Comet Tail Formation Single NWASP Activation of Arp2/3 Simplified Actin Dendritic Nucleation. (B) Example of an Nck-induced actin comet tail from Virtual Cell simulations at steady state. Nck SH3 domains were localized to a patch on the membrane (red membrane mesh units) inducing actin polymerization in the adjacent mesh units in the cytosol (scaled from blue ∼195 µM to red ∼1,500 µM). Actin then flowed away from the Nck SH3 patch, as indicated by the advection arrow, at a constant velocity to mimic actin propulsion of the Nck SH3 aggregate. (C) Predicted versus experimental actin comet tails induced by aggregates traveling at similar velocities (0.060–0.090 µm/s). Experimental data were divided into five groups by aggregate size (n = 2–9). The mean experimentally measured actin concentrations from linescans were compared with Virtual Cell predictions. Virtual Cell simulations qualitatively predicted experimental results at a given aggregate velocity. Error bars indicate the SEM of averaged experimental data from each group at each measured point. (D) Predicted versus experimental actin comets tails induced by aggregates with a similar number of Nck SH3 molecules (12,000–22,000 molecules). Experimental data were divided into five groups by velocity (n = 2–11). The mean experimentally measured actin concentrations from linescans were compared with Virtual Cell predictions. Virtual Cell simulations predicted experimental results at a given aggregate size. Error bars indicate the SEM of averaged experimental data from each group at each measured point. (E) Four representative comparisons chosen from 145 experimentally measured actin comet tails with corresponding simulations. The following parameters were used for simulations run with the experimentally measured size (Exp.) and velocity of individual Nck SH3 aggregates (VCell): 17,000 molecules, 0.04 µm/s (top left); 10,000 molecules, 0.050 µm/s (top right); 17,000 molecules, 0.057 µm/s (bottom left); and 17,000 molecules, 0.120 µm/s (bottom right).

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