Assembly of Nsp1 Nucleoporins Provides Insight into Nuclear Pore Complex Gating (original) (raw)
Figure 6
Structural features of bundle regions and cross-linking regions observed in coarse-grained and all-atom molecular simulations.
(a) Probability of amino acids to form inter-chain backbone-backbone hydrogen bonds (HB) when located inside the bundle regions (brown bars) or inside the cross-linking regions (blue bars). Shown are the results obtained from the all-atom simulation. All amino acids located outside the bundle regions are considered to be inside the cross-linking regions. The bars labelled FG and FxFG denote the probabilities for the first phenylalanine residues in FG and FxFG motifs, respectively. (b) Solvent accessible surface area (SASA) of the first phenylalanine residues that are located either inside the bundle regions (labeled “bundle regions”) or inside the cross-linking regions (labeled “cross-linking regions”). SASA values from CG simulations wild-type_ring, random_array and random_bath (summarized in Table 1) are compared with SASA values from the all-atom simulation fragment_AA (Table 1) which comprises of eleven Nsp1-FG fragments of the final cross-linked bundle structure resulting from the CG simulation wild-type_ring.