Figure 6. A coarse-grained model... | Rockefeller University Press

Figure 6.

$A coarse-grained model explains how PLCγ1 nonmonotonically regulates LAT clustering.(A) Sketch of the model in which the proteins are represented as 2D particles decorated by interaction patches. All bonds possible in the system, based on biochemical data, are illustrated with colored lines. (B) Top: The average cluster size displays nonmonotonic dependence on the PLCγ1 concentration (gray circles). This behavior is well captured by the likelihood for cluster coalescence (black squares). Error bars represent statistical errors on the average size over 10 different realizations of the simulation, shown are mean ± SEM. Bottom: Snapshots of typical clusters in simulations, for relative PLCγ1:LAT concentrations of 0.075, 0.75, and 3 (these clusters contain, respectively, 19, 30, and 10 LAT molecules, and with reference to D, their compactness is 0.23, 0.39, and 0.48). (C) Breakdown of the coalescence likelihood per type of possible bond. The gray and pink areas represent available bonds involving a LAT or a Sos1 molecule, respectively; blue and yellow-orange bars represent bonds involving Grb2 and PLCγ1, respectively. (D) Compactness (gray circles, see Materials and methods) and fraction of terminal nodes (black squares), as a function of PLCγ1 concentration. Shown are mean ± SD; n = 10 realizations. (E) Fraction of LAT, PLCγ1, Sos1, and Grb2 molecules per cluster, as a function of PLCγ1 concentration, shaded according to the number of other molecules they are bound to.$

A coarse-grained model explains how PLCγ1 nonmonotonically regulates LAT clustering. (A) Sketch of the model in which the proteins are represented as 2D particles decorated by interaction patches. All bonds possible in the system, based on biochemical data, are illustrated with colored lines. (B) Top: The average cluster size displays nonmonotonic dependence on the PLCγ1 concentration (gray circles). This behavior is well captured by the likelihood for cluster coalescence (black squares). Error bars represent statistical errors on the average size over 10 different realizations of the simulation, shown are mean ± SEM. Bottom: Snapshots of typical clusters in simulations, for relative PLCγ1:LAT concentrations of 0.075, 0.75, and 3 (these clusters contain, respectively, 19, 30, and 10 LAT molecules, and with reference to D, their compactness is 0.23, 0.39, and 0.48). (C) Breakdown of the coalescence likelihood per type of possible bond. The gray and pink areas represent available bonds involving a LAT or a Sos1 molecule, respectively; blue and yellow-orange bars represent bonds involving Grb2 and PLCγ1, respectively. (D) Compactness (gray circles, see Materials and methods) and fraction of terminal nodes (black squares), as a function of PLCγ1 concentration. Shown are mean ± SD; n = 10 realizations. (E) Fraction of LAT, PLCγ1, Sos1, and Grb2 molecules per cluster, as a function of PLCγ1 concentration, shaded according to the number of other molecules they are bound to.