Design and designability of protein-based assemblies

Design of protein-based assemblies is an exciting frontier in molecular engineering. It can be seen as an extension of the protein design problem, but with some added hurdles. In recent years, much of the focus in the field has been on patterning existing protein structural units (proteins, oligomers, or structural motifs) to design diverse assembly geometries, focusing on symmetry to encode both “infinite” lattices and finite-sized supramolecular particles. Despite impressive successes, several key challenges remain. Among these are the specificity problem the need to engineer preference for the intended assembly geometry over all alternatives, and the folding problem - understanding what thermodynamic or kinetic features of assembly subunits and inter-subunit interfaces lead to successfully folding superstructures and how to encode these in the amino-acid sequence. Here we focus on recent results in the context of these two problems, summarizing commonalities in successful approaches. We find that natural designability of assembly elements (i.e., their compatibility with diverse populations of natural amino-acid sequences) may be a unifying property of successful designs.