Qi, Y.; Zhang, G.; Yserentant, K.; Lee, S.; Lyubimov, A.; Ibrahim, K.; Cimicata, G.; Fraser, J. S.; Huang, B.; Kortemme, T.

In engineering, industrial design principles link geometric form with function. In nature, global protein shape, curvature, and chirality similarly drive critical processes like membrane remodeling and cellular motility. However, explicitly programming these global features remains a challenge for generative AI. Here, we integrate computer-aided design (CAD) blueprints with diffusion models, establishing protein shape as an explicit, programmable layer. We engineered diverse, tunable architectures, including single-chain shapes, scaffolds with unusual twist handedness, and superhelical assemblies, structurally validating 31 of 59 designs via X-ray crystallography or electron microscopy. To demonstrate shape-encoded function, we coupled fluid-flow-optimized helical propellers to an F1-ATPase rotor, yielding a prototype ATP-dependent molecular swimmer. This framework translates industrial design principles to the molecular scale, enabling the programmable engineering of biomimetic architecture with emergent functions.