Discovering and designing multistate protein assemblies

Abstract

Evolved protein assemblies exploit multiple weak interfaces to package cargo, facilitate metabolism, and direct cell movement, often through architectures that depart from strict geometric symmetry. Designed protein assemblies can also break symmetry through conformational flexibility or strain-based defects, but have generally lacked the capacity for large-scale structural rearrangements characteristic of evolved systems. Here, we characterize the structures and biophysical properties of emergent protein assemblies and establish a strategy for designing quasisymmetric materials that switch between assembly states. Rather than relying on intrinsic flexibility, our approach programs multiple self-assembling interfaces onto rigid oligomers. Using multistate design and ensemble predictions, we generate assemblies in which protomers can adopt alternative designed interface modes, enabling identical amino acid sequences to form distinct configurations depending on assembly pathway and environmental conditions. As a proof of principle, we construct quasisymmetric capsids that transition into micron-scale 2D arrays in response to temperature. This work establishes a strategy for encoding alternative assembly geometries within a single protein sequence and provides a foundation for engineering materials with environmentally tunable properties.