De novo design of light-controlled conformational protein switches

Abstract

Light-responsive proteins offer the ability to control biology at an unmatched resolution. Yet, optogenetics is limited to a relatively small number of natural and engineered photoreceptors. The design of light-responsive proteins with native-like complexity is challenging as they must incorporate a light-responsive chromophore, couple chemical changes in the chromophore to structural changes in the protein, and ultimately propagate these changes to downstream effectors. Here, we present the computational design of new light-responsive proteins entirely from the bottom-up. We design de novo proteins that accurately bind a retinal chromophore and further design a protein conformational switching motion linked to retinal isomerisation. This switch unlocks a new protein-peptide interaction, creating light-activated heterodimers with an over 30-fold increase in binding upon illumination. Moreover, we show that the designed heterodimers are customisable, with tuneable wavelengths, sensitivities, and specificities. Further, we use the designed heterodimers to control biological function, regulating intracellular protein-protein interactions and cell-signalling receptors. Finally, we use real-time light-activated NMR to demonstrate that they undergo a defined light-activated conformational change. Overall, we computationally design a new class of light-responsive proteins that may open a new optogenetics toolbox with applications in biology.