Thermal profiling maps the dynamic interactome in malaria parasites

Protein complexes are central to all cellular processes and their regulation. Here, we introduce the meltome-assisted profiling of protein complexes (MAP-X) that maps the complexome through thermal proteome profiling in the native environment. Applied across blood stages of malaria parasite P. falciparum, MAP-X resolved conserved protein complexes, reproduced previously identified interactions and found new associations. Among those, we discovered the missing subunits of the RNA exosome and reconstructed its structure, and further experimentally validated the interactions of the exported protein PF3D7_1149100; putative subunits of MON1-CCZ1 complex and its regulator; and promiscuous interactions between proteins Alba 1-4. Finally, we found that malaria protein complexes undergo distinct dynamic alterations across the blood stages and predicted their moonlighting subunits. Altogether, MAP X represents a highly efficient and operational method for characterizing protein complexes in intact cells that can be rapidly deployed to study cellular physiology proteome-wide in various cellular systems and conditions.