Purinosome Unmasked: Exploring the Molecular-Scale Structure of a Purinosome Complex In Silico

The de novo synthesis of purines, activated when purine levels are low, is ensured by the assembly of the purinosome, a multienzyme complex constituted by the six enzymes participating in the reaction. Experimentally, there is evidence that this metabolon facilitates substrate channeling between enzymes during the 10 reaction steps of the purine synthesis. In this work, we provide the first molecular view of the purinosome organization and dynamics using coarse-grained simulations. Based on three different ideal initial organizations of the enzymes, we explored their relaxation at different time scales, ∼1-10² μs, and constructed protein-protein contact maps. Our simulations, together with kinetic analysis of the participating enzymes, provide support for cluster channeling as the dominant channeling mechanism involved in the purinosome. Finally, via a multiscale strategy, we studied the complex formation process of the purinosome characterizing enzyme clustering, the protein-protein interaction maps, and the relevant time scales for their assembly.