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. 2018 Feb 14;7:e31510. doi: 10.7554/eLife.31510

Figure 2. Coarse-grained molecular dynamics results of Nup density distributions in Nsp1 and Nsp1-S pores of varying diameter.

(A) Coarse-grained one-bead-per-amino-acid representation of Nsp1; the different colors of the beads represent the 20 different amino acids. The collapsed-coil N-terminal ‘head’ region is visible at the top right. (B) Multiple Nsp1s tethered inside a cylindrical pore of height 20 nm and a diameter of 45 nm with anchor points spaced according to a fully triangulated (close-packed) distribution with a spacing of 5.7 nm. (C) Time-averaged r-z density distribution of Nsp1-coated nanopores (top row) with diameters 22 nm, 45 nm and 60 nm; and similarly for Nsp1-S (bottom row). These data show denser structures for the smaller pores and much lower densities for Nsp1-S compared to the wildtype Nsp1. The nups are coated on the inner surface of the cylindrical nanopores at a close-packed triangular spacing of 5.7 nm.

Figure 2.

Figure 2—figure supplement 1. Top: The configuration of Nsp1 consists of a ‘collapsed coil’ head (in blue) and a ‘extended coil’ stalk region (multi-colored; each color represents a different amino acid).

Figure 2—figure supplement 1.

Bottom: Two-dimensional r-z density distribution of the mass density of the head-region (1-172) of Nsp1, for nanopores with diameters 22 nm, 45 nm and 60 nm (first row). The second row shows the same pores but coated with the Nsp1-S mutant. These data show the much more center-pore localized mass density for the wildtype Nsp1 compared to the Nsp1 mutant.
Figure 2—figure supplement 2. Simulation results for the density distribution in Nup98-coated biomimetic pores.

Figure 2—figure supplement 2.

Top panel: Two-dimensional r-z density distribution of Nup98-coated pores with diameters 22 nm, 45 nm, and 65 nm. Bottom panel: the corresponding radial density distributions. 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.