Reconfigurable asymmetric protein assemblies through implicit negative design

Asymmetric multi-protein complexes that undergo subunit exchange play central roles in biology, but present a challenge for design since the components must contain interfaces enabling reversible association but be stable and well behaved in isolation. We use implicit negative design to generate beta sheet mediated heterodimers which can be assembled into a wide variety of complexes. The designs are stable, folded and soluble in isolation and rapidly assemble upon mixing, and crystal structures are close to the computational models. We construct linearly arranged hetero-oligomers with up to 6 unique components, branched hetero-oligomers, closed C4-symmetric two-component rings, and hetero-oligomers assembled on a cyclic homo-oligomeric central hub, and demonstrate such complexes can readily reconfigure through subunit exchange. Our approach provides a general route to designing asymmetric reconfigurable protein systems.