Fig. 6: Binding sites of Api137, Api88, and other PrAMPs co-localize with solvent-exposed nucleobases. | Nature Communications

Fig. 6: Binding sites of Api137, Api88, and other PrAMPs co-localize with solvent-exposed nucleobases.

From: Multimodal binding and inhibition of bacterial ribosomes by the antimicrobial peptides Api137 and Api88

Fig. 6

a All solvent-exposed nucleobases (red) within the PET and Api137 in binding sites 1 and 2 are shown. Api137 (yellow) co-localizes with these 23S rRNA residues. The PET is shown as the simulated map at 10 Å resolution. b Solvent-exposed bases at the PTC site are shown in red. Simulated surface maps of Api137 (yellow) and its surrounding residues are simulated 4 Å and are shown as transparent volumes. c–i Stacking interactions to specific rRNA bases by residues of c Api137 (yellow); d Api88 conf. I (salmon); e Api88 conf. II (orange); f Api88 conf. III (light red); g Bac7(1-16) (light brown), PDB: 5F8K27,28; h (PR)20 dipeptide (pink), PDB: 7TOS 30; i Dro (green), PDB: 8ANA29,. Views in c-i are slightly adapted to increase visibility.

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