Computational design and experimental verification of a symmetric protein homodimer

Significance Computational protein design tools use a bottom-up approach that allows for the testing of hypotheses on the relationships between amino acid sequence, protein structure and stability, and biological function. Here, we exploited two computational methods, protein docking and protein sequence optimization, to create a favorable protein–protein interaction between two identical proteins, resulting in a novel homodimer. A stepwise approach proved useful: scaffold stabilization followed by interface design to achieve homodimerization. Our results suggest that for some proteins, stabilization may be required for the successful design of functionality.