Figure 5. Coarse-grained modeling of Nsp1-coated pores.

(A) One-bead-per-residue representation of an Nsp1-coated nanopore. (B) Top views of the Nsp1 meshwork in pores of 50 nm, 60 nm, and 80 nm diameter (for a grafting density of 1 Nsp1 per 300 nm²). For pores with a diameter below 60 nm, the Nsp1 meshwork was closed throughout the entire simulation, while for pores with diameters ≈ 60 nm transient openings were observed in the center of the pore, which were persistent for diameters ≥80 nm. (C) Calculated event rate of BSA as a function of pore diameter for open pores (cyan filled dots) and Nsp1-coated pores (purple dots) of 1 Nsp1 per 300 nm². The calculated event rates are in good agreement with the experimental event rates (open squares). Solid lines are fits to the calculated event rates using the quadratic function given in (2) for open pores and (3) for Nsp1-coated pores. (D) Calculated selectivity versus pore diameter, showing that the selectivity is lost for Nsp1-coated pores with increasing diameter. The average selectivity for open pores is shown as a green dashed line. The effect of grafting density on the apparent selectivity is indicated by the purple dotted lines that depict the results for grafting densities of 1 Nsp1 per 200 nm² and 1 Nsp1 per 400 nm² (see Appendix 10—figure 3). (E) Axi-radial and time-averaged protein density distributions inside Nsp1-coated pores of 50 nm, 60 nm, and 80 nm diameter at a grafting density of 1 Nsp1 per 300 nm². For pore diameters below 60 nm, we observed the highest protein density along the pore axis, while for diameters ≥60 nm, the highest density was found near the pore walls. This observation was valid for each of the probed Nsp1 grafting densities (see Appendix 10—figure 4). (F) Axi-radial and time-averaged void distributions inside Nsp1-coated pores of 50 nm, 60 nm, and 80 nm diameter at a grafting density of 1 Nsp1 per 300 nm². The void distributions suggest that for pores of 50 nm diameter there is no preferred pathway for the BSA proteins, while for larger pores the translocations happen mostly along the central axis.

Figure 5—video 1. Video of the top view of the pores presented in Figure 5B for 40 ns of the simulation.

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