Figure 3. Radial density distribution and conductance data for Nsp1 and Nsp1-S biomimetic pores.

(A) Radial protein density distribution for biomimetic nuclear pores with pore diameters of 22 nm, 45 nm, and 60 nm, for pores coated with Nsp1 (blue) and Nsp1-S (green). All data are taken within the height of the cylinder (20 nm; −10 nm <z < 10 nm) that is divided into 20 equally spaced discs of thickness 1 nm each. Each of the 20 curves represented in each panel shows the radial density distribution for that specific z location. (B) Modeling results for the conductance as a function of pore diameter for Nsp1-coated pores (blue) and Nsp1-S-coated pores (green). The dashed lines are linear guides to the eye. The inset shows a comparison between the computed and the experimental conductance. (C) Conductance versus pore diameter for the experimental (open symbols) and modeling data (closed symbols). For Nup-coated pores, the conductance is low (G < 4 nS) for small diameters, but it increases strongly with a non-linear dependence on pore diameter beyond ~40 nm for Nsp1 and beyond ~20 nm for Nsp1-S. At larger diameters the conductance increases almost linearly with a slope slightly smaller than that of the bare pore, with G-values of tens of nS. The red solid line corresponds to Equation (1) for the bare pore and the green and blue solid lines correspond to Equation (2) with the conductivities for the access and pore regions obtained by fitting the numerical results using sigmoidal functions (see Figure 3—figure supplement 2 ).

Figure 3—figure supplement 1. Conductance as a function of pore diameter below 40 nm.

The conductance change is plotted versus the diameter of Nsp1 coated pores. The measured conductance of the NPC falls in the range of 0.3–2 nS for monovalent salt (Bustamante et al., 1995; Tonini et al., 1999), which is comparable to the values measured here (0.2–4 nS) for pore sizes in the range from 5 to 40 nm.

Figure 3—figure supplement 2. The conductivity in the pore region (${\sigma }_{\mathrm{p}\mathrm{o}\mathrm{r}\mathrm{e}})$) and access region (${\sigma }_{\mathrm{a}\mathrm{c}\mathrm{c}\mathrm{e}\mathrm{s}\mathrm{s}})$) for the simulated nanopores lined with Nsp1 (blue circles; panel A) and Nsp1-S (green circles; panel B) plotted as a function of pore diameter.

For ${\sigma }_{\mathrm{p}\mathrm{o}\mathrm{r}\mathrm{e}}$the density distribution is integrated over the pore region |z| < 10 nm according to Equation 3 in the main text. For the conductivity in the access region ${\sigma }_{\mathrm{a}\mathrm{c}\mathrm{c}\mathrm{e}\mathrm{s}\mathrm{s}}$ the density distribution in the range 10 nm < |z| < 40 nm is considered, as the l/d ratio for the nanopore is comparable to 1.5 (Hyun et al., 2012). These serve as input to the conductance relation G(d) in Equation 2 of the main text. The solid lines are sigmoidal fits to the data. The sigmoid function is of the form $S\left(x\right)=d+\left(\left(-d\right)/\left(1+{\left(x/c\right)}^b\right)\right)$. The R² values of ${\sigma }_{\mathrm{p}\mathrm{o}\mathrm{r}\mathrm{e}}$ and ${\sigma }_{\mathrm{a}\mathrm{c}\mathrm{c}\mathrm{e}\mathrm{s}\mathrm{s}}$ are 0.85, 0.96 in Nsp1 and 0.98, 0.99 for Nsp1-S.

Figure 3—figure supplement 3. The conductivity and conductance for the simulated nanopores lined with Nup98 as a function of pore diameter.

(A) Based on the radial density distributions $\rho \left(r\right)$ of the Nup98 pore (Figure 2—figure supplement 2, bottom row), we calculated the pore conductivities ${\sigma }_{\mathrm{p}\mathrm{o}\mathrm{r}\mathrm{e}}$ and ${\sigma }_{\mathrm{a}\mathrm{c}\mathrm{c}\mathrm{e}\mathrm{s}\mathrm{s}}$ (black circles) for each diameter using Equation 3 of the main text, with ${\rho }_{crit}$=85 mg/ml as fitted to the Nsp1 and Nsp1-S data. For the access region the density distribution in the range 10 nm < |z| < 40 nm is considered, as the l/d ratio for the nanopore is comparable to 1.5 (Hyun et al., 2012). The solid lines are sigmoidal fits to the data. The sigmoid function is of the form $S\left(x\right)=d+\left(\left(-d\right)/\left(1+{\left(x/c\right)}^b\right)\right)$. The R² values of ${\sigma }_{\mathrm{p}\mathrm{o}\mathrm{r}\mathrm{e}}$ and ${\sigma }_{\mathrm{a}\mathrm{c}\mathrm{c}\mathrm{e}\mathrm{s}\mathrm{s}}$ are both equal to 0.99. (B) The conductance G of the Nup98-coated pores (black) and bare pores (red) plotted as a function of the pore diameter. The open squares represent experimental data (Kowalczyk et al., 2011b), while the closed circles represent the results of the MD simulations. The solid lines are predictions of the conductance relation that describes the conductance G as a function of diameter d for the bare pore (red, see Equation 1 in the main text with l = 20 nm), resulting in a fitted value of ${\sigma }_{\mathrm{b}\mathrm{a}\mathrm{r}\mathrm{e}}$ = 2.13 ± 0.05 nS/nm (with an R² value of 0.93). The conductivity results from panel A (${\sigma }_{\mathrm{p}\mathrm{o}\mathrm{r}\mathrm{e}}$ and ${\sigma }_{\mathrm{a}\mathrm{c}\mathrm{c}\mathrm{e}\mathrm{s}\mathrm{s}})$ are taken as input for the conductance relation of Equation 2 resulting in the solid black line for the Nup98-coated pores in panel B, showing excellent agreement with the experiments (R² = 0.93).

Figure 3—figure supplement 4. Computed conductance vs the experimentally measured conductance, for (A) Nsp1 (blue circles) and Nsp1-S (green circles), and (B) Nup98 (black circles).

The solid lines have a slope of 1, representing a perfect match between experiment and model.