AlphaFold-multimer and interface energetic analysis illuminate the co-translational folding process

Protein-protein interactions are at the heart of all biological processes in the cell. However, the mechanisms by which proteins assemble into complexes are still poorly understood. Here we present a new methodology for the study of protein complexes which combines existing structural data, AlphaFold complex prediction and the computation of accurate energetics for protein interfaces by pyDock, together with molecular biology and ribosome profiling data. We will show the usefulness of this method on the the yeast 6-phosphofructokinase complex, which catalyzes the phosphorylation of fructose 6-phosphate to fructose 1,6-bisphosphate. While there is experimental structural data for this complex (PDB 3o8o), this data is incomplete, our methodology can fill the structural gap and provide a more complete structural and mechanistic understanding of the co-translational process of this complex, enabling a rapid characterization of regions driving complex formation.