A number of protein complexes have been developed as nanoscale templates. These can be functionalized using peptide sequences that bind inorganic materials or by fusion to binding or catalytic proteins. In order to integrate peptides and proteins into specific positions in a protein template, we used circular permutation to relocate the amino and carboxy termini of the polypeptide chain. Additional sequences can then be joined to the protein termini. This minimizes disruption of the protein structure and reduces restrictions on size and conformation of the added sequence. We relocated the termini of a Sulfolobus shibatae chaperonin subunit to five different locations across the outside surface of the chaperonin complex (after residues 153, 267, 316, 480 and 499). These changes place the termini on the outside surface of the chaperonin complex. The permutants formed double rings and higher-order assemblies similar to those observed in the natural protein. When enhanced yellow fluorescent protein was fused to two chaperonin subunits permuted at positions 267 and 480, the resulting fusion protein was fluorescent and formed assembled double rings and higher-order structure. This approach is applicable to other nanoscale protein templates.