Figure 4. All-Atom Molecular Simulations Identify MxB Interactions at the Tri-hexamer Interface.

(A) The all-atom model of MxB_1–35 at the tri-hexamer interface. Three dimers from different hexamers are in blue, yellow, and green (left). The MxB_1–35 peptide in red is placed above the middle of the tri-hexamer region before simulations (right).

(B) The dynamics of MxB_1–35 in tri-hexamer interface. The evolution of MxB secondary structure (top) during the simulation, computed by the STRIDE program in VMD and the root-mean-square deviation (RMSD) plot of the MxB Cα atoms (bottom).

(C) MxB_1–35 (red) binds in the tri-hexamer interface. The MxB ¹¹RRR¹³ motif is shown in magenta sticks.

(D) Molecular contacts between the MxB ¹¹RRR¹³ motif and experimentally tested CA residues are shown for R11 (left), R12 (middle), and R13 (right), with corresponding contact occupancies.

(E) In a second simulation, the MxB peptide was initially placed at the interface between two CA hexamers (blue/green). The di- and tri-hexamer interfaces are marked by an oval and a triangle, respectively.

(F) Still images from the second simulation at the beginning and after 15 μs reveal that the MxB peptide again migrates to the tri-hexamer interface. The CA-binding ¹¹RRR¹³ motif is shown in red sticks (right).

See also, Figure S5.