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. 2016 Apr 8;5:e14119. doi: 10.7554/eLife.14119

Figure 3. Computational model.

(A) Schematic illustration of the computational model. FG domains are represented as end-grafted polymers anchored at 5.5 pmol/cm2 (i.e., 3.3 molecules per 100 nm2) to the bottom of a 100 nm diameter cylinder, and modeled as strings of beads, where each bead has equal bond length and diameter (two amino acids, 0.76 nm). The number of polymer beads was set to match the length of experimentally used FG domains. NTF2 dimers and Impβ are represented as spherical colloids of 4.0 and 6.0 nm diameter, respectively. (B) Matching of the computational model with experimental data for FG domain films in the absence of NTRs. Horizontal lines represent the experimentally determined film thickness per amino acid for different FG domains (black line - Nsp1 at 4.9 pmol/cm2; blue line - Nup98-glyco at 5.4 pmol/cm2; orange line - reg-FSFG at 6.1 pmol/cm2), with shaded areas in matching colors indicating confidence intervals. Symbols represent the thickness as predicted by the computational model as a function of εpp for the different FG domains (at 5.5 pmol/cm2; colors match experimental data). The data points and the upper and lower ends of the vertical lines refer to the effective thicknesses where the densities have dropped to 5%, 1% and 10% of the maximal densities in the film, respectively. Symbols for Nsp1 and Nup98-glyco are translated along the x axis by +0.1 kBT and -0.1 kBT, respectively, to improve their visibility. Dashed lines through the symbols are cubic interpolations (the black dashed line is for Nsp1 and Nup98-glyco). Full computational details are available in ‘Materials and methods’ and Figure 3—figure supplements 1–5.

DOI: http://dx.doi.org/10.7554/eLife.14119.014

Figure 3.

Figure 3—figure supplement 1. Scheme illustrating how computational modeling data is presented in the form of maps of the polymer and colloid packing fractions.

Figure 3—figure supplement 1.

Maps are cross-sections along the axis of the modeled cylinder (with polymers grafted at the bottom; cf. Figure 3A). The bottom part of the cylinder at full width (100 nm) is shown, with horizontal and vertical dimensions to scale. The left half of each map shows the polymer packing fraction as a heat map (with scale bar in the bottom right) and the colloid packing fraction as iso-density lines; the right half shows the colloid packing fraction as a heat map and the polymer packing fraction as iso-density lines.
DOI: http://dx.doi.org/10.7554/eLife.14119.015
Figure 3—figure supplement 2. Computational modeling data for a polymer length equivalent to Nsp1 and colloids of 4.0 nm diameter (equivalent to NTF2 homodimers).

Figure 3—figure supplement 2.

(A) Maps of the polymer and colloid packing fractions at 10 μM colloid in solution, presented as described in figure supplement 1, for selected sets of εpc (rows, as indicated on left side) and εpp (columns, as indicated on bottom). (B-C) Areal density of colloids in the film and film thickness, respectively, as a function of colloid concentration in solution for selected sets of εpp (as indicated on top) and εpc (as indicated in the graphs). The data covers the full parameter space computed. The lines and upper and lower ends of the vertical bars in (C) correspond to effective thicknesses where the densities have dropped to 5%, 1% and 10% of the maximal densities in the film, respectively (see Figure 3 and Materials and methods).
DOI: http://dx.doi.org/10.7554/eLife.14119.016
Figure 3—figure supplement 3. Computational modeling data for a polymer length equivalent to Nup98-glyco and colloids of 4.0 nm diameter (equivalent to NTF2 homodimers).

Figure 3—figure supplement 3.

Data are displayed analogous to Figure 3—figure supplement 2.
DOI: http://dx.doi.org/10.7554/eLife.14119.017
Figure 3—figure supplement 4. Computational modeling data for a polymer length equivalent to reg-FSFG and colloids of 4.0 nm diameter (equivalent to NTF2 homodimers).

Figure 3—figure supplement 4.

Data are displayed analogous to Figure 3—figure supplement 2.
DOI: http://dx.doi.org/10.7554/eLife.14119.018
Figure 3—figure supplement 5. Computational modeling data for a polymer length equivalent to Nsp1 and colloids of 6.0 nm diameter (equivalent to Impβ).

Figure 3—figure supplement 5.

Data are displayed analogous to Figure 3—figure supplement 2.
DOI: http://dx.doi.org/10.7554/eLife.14119.019