Fig. 5: Modeling of the inward-open state of AmpG. | Nature Communications

Fig. 5: Modeling of the inward-open state of AmpG.

From: Cryo-EM characterization of the anydromuropeptide permease AmpG central to bacterial fitness and β-lactam antibiotic resistance

Fig. 5: Modeling of the inward-open state of AmpG.

AmpG in the experimental outward open conformation (a) compared to the AlphaFold335 modeled inward open conformation (b), shown with Coulombic electrostatic potential surface (above) calculated with ChimeraX35,65 and evolutionary coupled sets of resides (below). Residue pairs on the periplasmic side of the protein, Lys47 and Glu377 (green), are strongly coupled. They are separated ~30 Å in the outward structure but form close contacts in the inward model. At the cytoplasmic side, Asp134 and Ser350 (gold) are also evolutionarily coupled. c Interaction of evolutionary coupled residues E377 and K47 in the modeled inward state. d Structural alignment of N- and C-terminal helical bundles of the experimental outward and modeled inward (gray) states. TM1-TM6 (residues 1–195) RMSD was 1.7 Å, and TM7-TM12 (residues 223-413) RMSD was 1.1 Å.

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