Fig. 1.

A general method to create arbitrary protein shapes using a library of designed junctions. (A) Building blocks: (Left, with different numbers of repeat units indicated in parentheses) DHRs, (Middle) homo-oligomers made from DHRs (9), and (Right) an ankyrin. (B) Junctions can be made by superimposing helices by overlapping six residues (red) in terminal repeats (gray). The nearby residues are then redesigned (red sticks). (C) Junctions can also be made by building additional protein backbone (gold) as a contiguous chain with Rosetta fragment assembly. Following removal of a helix (gray) and/or one to four terminal helix residues (black), the sequence near the interface is redesigned (red sticks). (D) Designs from both fusion methods are filtered to ensure they are lower in energy than other conformations in the energy landscape, contain two or more helices in contact throughout the junction, and there are no buried unsatisfied residues. To check that the design is the lowest energy we used either Rosetta@home to model the energy landscape or a machine-learning approximation to the Rosetta@home simulation (SI Appendix, Discussion S2). (E) The junction library is then used to sculpt proteins into various shapes. In this case, a repeat protein shown in dark blue is connected first to a repeat protein in cyan followed by a repeat protein in light blue. Junctions are shown in gold. REU, Rosetta energy units.