Allosteric inhibition of complement function by a staphylococcal immune evasion protein

Abstract

The complement system is a major target of immune evasion by Staphylococcus aureus. Although many evasion proteins have been described, little is known about their molecular mechanisms of action. Here we demonstrate that the extracellular fibrinogen-binding protein (Efb) from S. aureus acts as an allosteric inhibitor by inducing conformational changes in complement fragment C3b that propagate across several domains and influence functional regions far distant from the Efb binding site. Most notably, the inhibitor impaired the interaction of C3b with complement factor B and, consequently, formation of the active C3 convertase. As this enzyme complex is critical for both activation and amplification of the complement response, its allosteric inhibition likely represents a fundamental contribution to the overall immune evasion strategy of S. aureus.

Fig. 1.

Changes in HDX levels of C3b in presence of Efb-C. (A and B) Domain organization of C3b as sequence (A) and arrangement representation (B). The ANA domain, which does not exist in C3b, is marked in gray. (C) Relative distribution of HDX changes in the C3b domains as represented by the number of altered peptides per domain (colored according to legend). (D) Sequence coverage of each domain of C3b in the presence of wild-type Efb-C (Lower) or its RANA mutant (Upper). Segments identified by HDX-MS are marked in green, of which peptides showing significantly altered HDX are highlighted in blue (≤ -10%) and orange (≥10%); unidentified sequences are in gray. (E and F) Localization of HDX peptides on the crystal structure of unbound C3b (23), visualized as cartoons (E) and surface-accessible surface (F) with color coding as in D.

Fig. 2.

Efb-C-induced changes in C3b as revealed by SAXS. (A) Experimental scattering curves for free C3b (black) and C3b/Efb-C (blue) were fit to either a single (red) or minimal ensemble search model (MES; green). Guinier plots (Inset) for the SAXS profile of the highest protein concentration with linear fit (red) in the range q × R_G < 1.6. (B) Pair-distribution functions [P(r)] indicate conformational changes between C3b (black) and C3b/Efb-C (blue), where broadening of P(r) for C3b/Efb-C is consistent with reorientation of CUB-TED. P(r) from the atomic MES models are shown as a green-dashed line. Individual SAXS profiles are shown in the Kratky plot (Inset), wherein significant differences are highlighted by red arrows. (C) Comparison of R_G for the two predominant MES conformers of either C3b (black) or C3b/Efb-C (blue) as obtained by molecular dynamics conformational sampling with their maximal dimensions (D_max). Dot sizes represent the fraction ratio of the two conformers in each group. Rigid body modeling-derived C3b conformers are shown in gray with Efb-C highlighted in red. (D and E) Superposition of the SAXS/BILBOMD-derived conformers of free C3b (D, magenta and green) and C3b/Efb-C (E, blue/red) with the crystal structure of C3b (gray). The inset shows a schematic representation of the proposed domain rearrangements.

Fig. 3.

Effect of Efb-C on the ligand-binding pattern of C3b as assessed by SPR. (A and B) The cocrystal structures of (A) C3b/fH1-4 (25), C3b/CRIg (24), and C3c/Compstatin (analog 4W9A, ref. 34), and (B) C3b/Bb/SCIN (7), and CVF/fB (14) were superimposed with the crystal structure of free C3b (23). (C–L) Compstatin (C), CRIg (D), SCIN (E), and fH1-4 (F) were injected to either immobilized C3b (blue) or C3b/Efb-C (red). (G–L) Contact residues for each ligand (magenta) were determined from the corresponding cocrystal structures shown in A and B using LIGPLOT (42) and mapped on the crystal structure of C3b. The binding area of each ligand is marked by dashed circles. In the case of SCIN, both binding sites on C3b were analyzed. A more detailed binding site analysis can be found in Fig. S8 A–E. Differential HDX is marked using the color code described in Fig. 1.

Fig. 4.

Effect of Efb-C on fB binding and C3 convertase formation. (A and B) The binding of fB (A) and its fragment Ba (B) to C3b (blue) or C3b/Efb-C (red) was analyzed by SPR as in Fig. 3. (C) Formation of the C3 convertase was monitored using SPR by injecting a 1∶1 mixture of fB and fD onto either C3b (blue) or C3b/Efb-C (red). Regular convertase decay was followed for 3 min and fH was injected to accelerate decay. (D) Contact residues for fB were determined on the cocrystal structure of CVF/fB (14) and transferred on the structure of C3b (23). Peptides of differential HDX are visualized using the color code in Fig. 1 and binding areas for the Ba and Bb segments are marked with circles. A detailed binding site analysis can be found in Fig. S8F.