Metabolons, quinary structure, and domain motion: enzyme choreography in the cytoplasm

How do enzymes form metabolons inside cells? To answer that question, we created an all-atom model of a section of the human cytoplasm and simulated it for over 30 microseconds. Among other proteins, nucleic acids, and metabolites, the model contains three successive members of the glycolytic cycle: glyceraldehyde-3-phosphate dehydrogenase (GAPDH), phosphoglycerate kinase (PGK), and phosphoglycerate mutase (PGM). These enzymes interact to form transient, but long-lived, multi-enzyme complexes with characteristic lifetimes in the 1 to 5 μs range, thus modeling the functional metabolon structures that facilitate compartmentalization of metabolic pathways and substrate channeling in cell. We analyze the quinary structure between enzymes down to the formation of specific hydrogen-bonded interactions between side chains, together with the movement, in concert, of water molecules in or out between interacting amino acids to mediate contact formation and dissolution. We also observed large-scale enzymatic domain motion that has been proposed to convert between substrate-accessible and catalytically functional states: a direct hinge-bending motion of up to 28° changes the relative orientation of the N- and C-terminal domains of PGK, causing the initially open, and presumably inactive, conformation of PGK to sample both “semi-closed” and “closed” conformations. Although classical molecular dynamics (MD) cannot simulate enzymatic activity, closed structures are the functionally active forms of PGK, and their equilibrium with open structures opens the door for future quantum mechanics/molecular mechanics (QM/MM) and other reactive simulations of the cytoplasm.