Highly dynamic assemblies of glycolytic enzymes by quinary determinants

Molecular channelling has long since been proposed as an amenable solution to efficiently drive sequential enzymatic reactions in the cell. Nonetheless, metabolic channelling in central pathways such as glycolysis is still a matter of debate and plausible underlying mechanisms are not known. Here we use correlation spectroscopy and proximity labelling methods to uncover extremely dynamic interactions among enzymes of the glycolysis pathway in yeast and human cells. The resulting transient protein assemblies, tentatively named as protein flocks, form in the cytoplasm with a lifetime shorter than 10 ms. Compared to other metabolic pathways, glycolytic enzymes display a greater similarity in the electrochemical properties of surface atoms, pointing to quinary structural features as molecular determinants of protein flocks. We observe a remarkable negative correlation between the spatiotemporal coincidence by correlation spectroscopy and the Euclidean distance in surface atom configuration within multiple protein pairs, including a collection of surface variants generated from a de novo designed protein framework. By underlying protein flock formation from yeast to human, quinary determinants would provide enzymes with higher efficiency and specificity in glycolysis but, perhaps more important to human cells, would limit intermediate concentrations and prevent their inherent toxic effects.