Volume 22, Issue 10, Pages 1467-1477 (October 2014) Multiscale Conformational Heterogeneity in Staphylococcal Protein A: Possible Determinant of Functional Plasticity  Lindsay N. Deis, Charles W. Pemble, Yang Qi, Andrew Hagarman, David C. Richardson, Jane S. Richardson, Terrence G. Oas  Structure  Volume 22, Issue 10, Pages 1467-1477 (October 2014) DOI: 10.1016/j.str.2014.08.014 Copyright © 2014 Elsevier Ltd Terms and Conditions

Structure 2014 22, 1467-1477DOI: (10.1016/j.str.2014.08.014) Copyright © 2014 Elsevier Ltd Terms and Conditions

Figure 1 Staphylococcal Protein A and the Crystal Structures of C and B-B Domains (A) Schematic showing the organization of SpA and its five protein-binding domains. The conserved linker (green) between the E and D domains has a three-residue insertion, indicated by a star. (B) The asymmetric unit of C domain (cyan). The three helices are labeled (Hlx1-3) and the conserved linker regions are indicated (arrow) and colored dark blue. (C) The asymmetric unit of B-B domain. The two copies of B-B domain are colored in shades of green or purple. Each domain (Domain1 and Domain2) and the linker in between are depicted as a ribbon drawing, where Domain2 is rotated by 180°. See also Figure S1. Structure 2014 22, 1467-1477DOI: (10.1016/j.str.2014.08.014) Copyright © 2014 Elsevier Ltd Terms and Conditions

Figure 2 Residue-Level Conformational Heterogeneity (A) Examples of heterogeneity in C domain. Lys42 and Glu24 sidechains are solvent-exposed, and Ile34 is in the interior. The maximum distance between equivalent side chain atoms (see text) is depicted for each residue. (B) Putty-sausage diagram of C domain where the relative diameter represents the maximum distance between equivalent atoms of alternative conformations (if present) within each residue. The color coding reflects the type of heterogeneity. (C) Comparison of residue-level conformational heterogeneity of single domains in C domain and B-B structures. B-B chain and domain designations are indicated as a suffix to the protein name. For example, “X1” indicates domain1 of chain X. See also Figures S3 and S4. Structure 2014 22, 1467-1477DOI: (10.1016/j.str.2014.08.014) Copyright © 2014 Elsevier Ltd Terms and Conditions

Figure 3 Concerted Conformational Heterogeneity in B-B (A–C) Populations of Tyr114-X, Gln110-Y, and Tyr114-Y for the alt-a (A, 60%), mixed alt-a/alt-b (B, 8%), and alt-b (C, 32%) conformations. (D–F) Trp13 in Domain1 (D) and Trp113 in Domain2 (E) constrain the rotamers of nearby residues, whereas the mixed conformations of the two domains when superimposed (F) are incompatible with one another due to significant overlap of the van der Waals spheres, as indicated by red spikes. Structure 2014 22, 1467-1477DOI: (10.1016/j.str.2014.08.014) Copyright © 2014 Elsevier Ltd Terms and Conditions

Figure 4 Global Conformational Heterogeneity of Hlx1 in SpA Protein Binding Domains (A) Helix-axis orientations of sixteen different SpA domains in a coordinate system where the x axis is parallel to Hlx2, and Hlx3 lies nearly in the x-y plane. The cryogenic C domain (C) and 1Q2N Z domain (Z) structures are labeled. (B) Superposition of both C domain structures with the four individual domains of our B-B structure. (C) Superposition of Z domain (1Q2N, variant of B domain) and cryogenic C domain using Hlx2 and Hlx3 for the superposition. (D) Peel-away of interior of the Hlx1-Hlx2/3 interface, shown from both sides. Interfacial sidechains are highlighted with colored spheres. The key core residue at the interface is Ile16, which forms the pivot point for variation in the angle of Hlx1. (E) The helix differences between 1Q2N and C domain are the consequence of significant rearrangements in the interhelical knob packing for all three helices. Residues and spheres are colored as in (B), which represent structure affiliation. The pivot, marked in the figure, consists of Ile16. Structure 2014 22, 1467-1477DOI: (10.1016/j.str.2014.08.014) Copyright © 2014 Elsevier Ltd Terms and Conditions

Figure 5 Coordination of Backbone and Side Chain Conformational Changes with Binding of Fc (A and B) All-atom contacts at binding interfaces. (A) Well-fit, cognate interface of Fc with SpA B domain (low-angle helix 1-2 orientation), in PDB file 1FC2; (B) Poorly fit, noncognate interface of Fc with superimposed high-helix-angle conformation of C domain from 4NPD. Green and blue dots show good van der Waals contact or H bonds, and clusters of red spikes show steric clashes. (C and D) Correlation of changes in helix-helix angle with concerted rotamer changes in a network of seven side chains (bold colors) for (C) two low helix-angle structures (B-B domain 1 for both chains), similar to the B domain in 1FC2, and for (D) two high helix-angle structures (C domain and B-B chain Y Domain2). Switching only side chain network conformations on the superimposed, high-angle, noncognate C model from (B) can eliminate most clashes but neither recreates good van der Waals packing nor any H-bonds. However, the high-angle domain structures each form an extensive, well-packed contact with another SpA-domain partner in the crystal. See also Table S1. Structure 2014 22, 1467-1477DOI: (10.1016/j.str.2014.08.014) Copyright © 2014 Elsevier Ltd Terms and Conditions

Figure 6 Conformational Compatibility of B-B with Antibody Binding (A) Tyr114 alt-a (blue) adopts the same conformation as seen in the Fc/B domain complex (1FC2, magenta), but Tyr114 alt-b (cyan) is incompatible. The Tyr alt-a side chain is posed for interaction with Leu432 from Fc. (B) The Asp36 conformation in Domain1 is able to bind Arg2519 of Fab (as it does in the structure of Fab in complex with D domain, 1DEE), but the Asp136 conformation in Domain2 is not possible due to a steric clash with the Fab molecule. (C and D) Functional relevance of interdomain orientation. (C) The crystallographic interdomain conformation of B-B is incompatible with Fc binding because when Domain1 is posed as in 1FC2, the second domain clashes with the Fc molecule. To bind to Fc, B-B must adopt another interdomain conformation. (D) The interdomain orientation of B-B is compatible with binding two Fab molecules, when superimposed with 1DEE. Structure 2014 22, 1467-1477DOI: (10.1016/j.str.2014.08.014) Copyright © 2014 Elsevier Ltd Terms and Conditions