Figure 1.
(A) The correlation of motion of each residue during the YU2 simulation.
Blue represents anticorrelated motion, while red represents correlated motion. The residue numbering is HXB2. The subdomains are mapped in a gp120 core structure (B). Magenta represents the β-sandwich (region 1 in (A)), brown represents the αβ-bundle (region 2), green represents the bridging sheet (region 3), ice blue represents the 7-stranded barrel (region 4), red represents the 6-stranded barrel and α2 helix (region 5), and pink represents the V4 loop (region 6).
Figure 2.
The coupling of motions along (A) PC1 and (B) PC3.
Residues that are flexible in the corresponding PC are shown in red, while rigid regions are shown in blue. Regions that display moderate motion in the corresponding PC are shown in white. The histogram of displacement along (C) PC1 and (D) PC3 are also shown.
Figure 3.
The coupling of motion along PC2 (A).
Colors are as defined in Figure 4. The histogram of displacement along PC2 for each simulation is shown in (B).
Figure 4.
The optimal (blue) and suboptimal paths (green) for communication from the CD4 binding loop to the C-terminus end of the α2 helix for the (A) YU2 (B) HXB2 and (C) CAP210 networks.
Table 1.
The residues along the optimal path for communication in the three networks.
Table 2.
The path distance of the shortest path in a particular network is shown for all three networks.
Figure 5.
The modules or communities in the network for (A) YU2, (B) HXB2, and (C) CAP210 networks.
The color represents the community that the residue belongs to (bridging sheet – green, αβ-bundle – brown, β-sandwich – magenta, parts of 6-stranded barrel – blue, V4 and α2 helix – red, 6- stranded barrel – white, interface of the two barrels in outer domain – lime).
Table 3.
Comparison of the YU2 and CAP210 networks to the HXB2 network based on the subdomains in the protein.