Fig. 4: Accurate de novo design of a high-affinity cyclic peptide binder against the predicted structure of RbtA from A. baumannii.
From: Accurate de novo design of high-affinity protein-binding macrocycles using deep learning
a, AfCycDesign prediction of design RBB_D10 (violet cartoon) bound to the AF2-predicted β-helix domain of RbtA shown as gray surface. Hotspot residues from RbtA used during the backbone design step are shown in green. b, SPR sensorgram from nine-point single-cycle kinetics experiment (fivefold dilution, highest concentration: 20 µM). The Kd determined from the SPR experiment is also denoted on the plot. c, Close agreement of the RF2-predicted structure of RbtA (gray) with the X-ray structure (gold) of the RbtA N-terminal domain determined here confirms the predicted structure of the target used for the macrocycle design calculations. d, Alignment of the design model of RbtA-bound RBB_D10 (violet and gray) to the X-ray structure (gold) shows a close match between the design model and the experimentally determined structure (Cɑ r.m.s.d. for macrocycle: 1.4 Å). Close-up view of the RbtA-bound RBB_D10 with side chains shown as sticks. e, Overlay of RBB_D10 design model (after the AfCycDesign prediction step) aligned to the X-ray structure without RbtA demonstrates a nearly identical match for backbone coordinates and side-chain rotamers (Cɑ r.m.s.d.: 0.4 Å). The design model and X-ray structure are shown in violet and gold, respectively. f, Close-up view of the macrocycle-bound RbtA structure and design model showing polar side chain-to-backbone interactions mediated by RBB_D10 residue Asn12 at the interface. g, Close-up view of the polar side chain-to-side chain interactions mediated by RBB_D10 residue Asp6 at the interface. h, Close-up view of the hydrophobic interactions between RbtA and RBB_D10 at the binding interface.
