Interplay of the Bacterial Ribosomal A-Site, S12 Protein Mutations and Paromomycin Binding: A Molecular Dynamics Study

doi:10.1371/journal.pone.0111811

Interplay of the Bacterial Ribosomal A-Site, S12 Protein Mutations and Paromomycin Binding: A Molecular Dynamics Study

Figure 10

The network of interactions between S12 and rRNA.

(a, b, c) Snapshots are shown of the most frequent H-bonds formed between R/A53 or R93 and other regions of the ribosome; only polar hydrogens are shown. Positions of the C 3 atoms of C1412 and A1413 are indicated. (d) The stable H-bonds between the PNSA and PGVR loops are shown, as is the most frequent H-bond of K42 (which may affect the mutual position of h27 and h44). e) This schematic interaction map for S12 and rRNA shows S12 (yellow), h44 (green), and h27 (orange). The H-bonds observed in MD simulations are denoted by dashed lines as either stable (black), broken/destabilized in some variants (red) or formed upon S12 mutation (light blue). The close neighboring h27 and h44 residues, near the decoding site, are indicated by a black arrow (see text and Fig 9a).

doi: https://doi.org/10.1371/journal.pone.0111811.g010