Computational design of a protein that binds polar surfaces has not been previously accomplished. In a Journal of Molecular Biology publication entitled Computational design of a protein-based enzyme inhibitor, Dr. Erik Procko and collaborators in the Baker group describe the computational design of a protein-based enzyme inhibitor that binds the polar active site of hen egg lysosome (HEL). A hot spot design approach first identified key, conserved interaction residues that contribute to much of the binding energy to HEL within a large interface. Rosetta software then identified a protein scaffold that supported the hot spots while also optimizing contact with surrounding surfaces to obtain a high affinity protein binder.
Construction of a HEL-binding protein by transplanting hot spot residues and computationally designing the surrounding interface. (a) Schematic of the design process. Hot spot residues R100 and Y101 (magenta sticks) were taken from shark VNAR (cyan cartoon) bound to HEL (green cartoon) (i). Rotamers for the disembodied hot spot residues compatible with the binding geometry are enumerated (ii). Then, protein scaffolds are docked against the target surface using PatchDock and ROSETTA with a modified energy function that biases towards backbone overlap between scaffold and hot spots. Inverse hot spot rotamers are placed sequentially on the scaffold backbone (iii), and the surrounding surface of the scaffold in contact with HEL is redesigned with ROSETTA to minimize the total energy (iv). Designs are filtered by multiple criteria to assess interface quality.