Fig. 4: Molecular dynamic (MD) simulations of nsP1 protein-lipid membrane interaction. | Nature Communications

Fig. 4: Molecular dynamic (MD) simulations of nsP1 protein-lipid membrane interaction.

From: Saddle curvature association of nsP1 facilitates the replication complex assembly of Chikungunya virus in cells

Fig. 4

a Snapshots of all-atom MD simulation showing the interaction of a single nsP1 protein with a planar membrane at initial (left) and equilibrated (right) states. Protein atoms are colored by residue type (acidic: red; basic: blue; hydrophobic: white; and polar: green). Lipid atoms are shown as carbon (C; cyan), oxygen (O; red), phosphorus (P; green), nitrogen (N; blue), and hydrogen (H; white). b Simulation snapshots showing the temporal evolution of nsP1 dodecamer binding to a planar membrane. The top panels show side cutaway views of nsP1 dodecamer-membrane interaction at different time points; the bottom panels highlight the number of nsP1 ring subunits inserted into the membrane. Lipid head beads (PO4, NC3, and CNO) were colored in tan, glycerol linkages (GL1 and GL2) in pink, lipid tail beads in cyan, and only PO4 beads were shown in the top views. Protein beads in the top panels were colored as in (a). The inserted protein beads shown in the bottom panels were rendered in such a way that each color refers to a particular subunit of the dodecamer structure. A zoomed-in box shows the insertion of nsP1 MA loop 2 into the membrane. c Top view of the planar membrane-bound nsP1 dodecamer (left) and the corresponding color map for mean membrane curvature (right). d, e Simulation snapshots showing the temporal evolution of the interaction of the nsP1 dodecamer with a flat supported membrane (d) and a supported membrane with a radius of curvature of 100 nm (e). f Comparison in the area per lipid between planar (n = 100) and curved (n = 191452) membranes. Mean ± SD. g Comparison in the total interaction energy of the nsP1 dodecamer with planar (n = 981) and curved (n = 501) membranes. Mean ± SD. h Comparison in the maximum insertion depth of nsP1 subunits (averaged over all inserted sub-units) into planar and curved membranes (n = 100). Mean ± SD. Statistical analysis: two-tailed unpaired t test. Source data are provided as a Source Data file.

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