Active biomolecules, particularly proteins, are increasingly used in functional nanostructures. For some applications, native proteins (i.e. proteins as they occur in nature) are not effective nanodevice components because distances between the ends of the protein and some protein functional domain exceeds some critical nanoscale distance. This problem occurs in sensing architectures that detect energy or electron transfer where native protein sizes exceed critical distances for quantum energy transfer or exceed the thickness of shielding layers of counter ions, and might be addressed by alterations of protein topography. This work describes a high-throughput recombinant DNA method rapidly to identify functional circularly permuted (cp) protein variants. When appended to a sensing device or other nanometer scale distance-dependent device using chemoselective conjugation methods, cp variants offer a potential strategy to address the nanometer size limitations of native proteins.