De novo design of proteins that bind naphthalenediimides, powerful photooxidants with tunable photophysical properties

De novo protein design provides a framework to test our understanding of protein function. Ligand binding, while simple in concept, is an ongoing challenge requiring precise placement of polar groups within a protein core. Addressing this challenge enables binding of abiological cofactors with interesting chemical properties. Here, we report the design of a helical bundle to bind naphthalenediimides (NDIs), powerful photooxidants with tunable photophysical properties. We augmented our design methods with MD simulations to assess dynamics within the binding site, including four H-bonding interactions to the NDI carbonyls. The MD simulations were validated by solution NMR which showed a helical backbone with 0.9 Å rmsd relative to the design and 19 NOEs between the NDI and the protein. We utilize two NDI cofactors in this de novo protein and use ultra-fast pump-probe spectroscopy to demonstrate light-triggered intra- and intermolecular electron transfer function. Moreover, we highlight the utility of this platform to activate molecular probes for protein proximity labeling in a light dependent manner.