Figure 1.
Zinc-finger motif of Vif showing tetrahedral coordination between residues C115, C134, H140 and H109 and average bond length between the atoms from Cys and His residues and the zinc ion computed after 10 ns molecular dynamics and the crystallographic structure of BC-box motif in blue (PDB ID code: 3DCG, chain E) aligned with the Vif model showed a satisfactory structures superposition.
Figure 2.
Vif theoretical structure showing the binding sites to the proteins of E3 ubiquitin ligase complex and to the A3G and A3F.
The PPLP motif is located away from the hydrophobic region of HCCH domain and the BC-box exhibit the SLQ(Y/F)LA motif.
Figure 3.
Assembled complex of Vif-EloBC-A3G N-CDA. Panels show interactions of Vif with A3G, EloC, EloB and (in the clockwise direction).
In the first panel, the residues L146 and L149 from Vif BC-box are involved in EloC interaction (Vif is in cyan and EloC in orange). The second panel shows that in the N-terminal region, Vif interact via hydrogen bonding with A3G (Vif is in cyan and A3G in red). Last panel shows residues L161 and P162 from Vif Cullin-box interacting by hydrophobic interaction with the residue E97 and P96 from the C-terminal end of EloB (Vif is in cyan and EloB in green).
Figure 4.
The average atomic B-factor per residue is plotted as function of the residue number and was obtained after 10ns of molecular dynamics simulation.
These figure information have been adapted from Wissing et al., [87] to the Vif sequence modeled.
Figure 5.
Root-mean-square deviation (RMSD) values of the Vif backbone in unbound state (black line) and its structure interacting with the EloBC-A3G complex (red line).
In both cases the values were calculated over the 10