Exploring Bacterial Organelle Interactomes: A Model of the Protein-Protein Interaction Network in the Pdu Microcompartment
Figure 4
Models of N-terminal peptide extensions from different enzymes docked onto a PduA hexamer. All the models were aligned and overlaid using the PduA structure as guide.
(A) Six N-terminal peptides are docked on the concave (presumptively luminal) face of the PduA hexamer. Four of the five identified earlier as probable targeting sequences (PduC, PduD, PduE, PduP) were folded into α-helices by the flexible docking procedure (see text and Methods) and were docked in the same cleft on the PduA surface. The tail of PduL adopted a less regular conformation during the simulation. The tail from PduQ, which was not predicted to act as a targeting sequence and thereby serves as a control, exhibits an apparently spurious binding mode. To convey depth, the surface of PduA is shaded according to diffusion accessibility [106]. (B) The five targeting peptides, when docked onto the other (flat) face of the PduA shell protein, were found scattered across the surface in arrangements exhibiting poorer interaction interfaces. (C) Binding statistics are reported for all the docking simulations. In all cases, both the predicted energy score (in Rosetta Energy Units) and the buried surface at the interface yielded better values when peptides were docked onto PduA’s concave side. Because the shell protein hexamer is 6-fold symmetric, in all cases the solutions were rotated by multiples of 60° around the axis of symmetry to allow internal consistency.