Engineering an ATP Binding Pocket in the Kirbac3.1 Inward Rectifier Potassium Channel Scaffold using De Novo Design

Abstract

De novo design seeks to engineer brand-new proteins rather than modify existing ones. This specific and innovative approach allows researchers to advance medicine and biotechnology through designed proteins with unique properties (folds, functions, amino-acid sequence) absent in naturally occurring proteins. One key assumption in design is that binding sites can be engineered into any site if the underlying interactions are well understood. We sought to engineer a binding pocket for adenosine triphosphate (ATP) within the fold of the Kirbac3.1 inward rectifier potassium channel using RFDiffusion. This fold offers a great challenge because it is a membrane-bound protein we look to re-engineer into a water-soluble protein. It also has well-defined binding pockets that require transformation. We discuss the challenges in transforming a protein and the further issues in transferring binding pockets.