Maturation Kinetics of a Multiprotein Complex Revealed by Metabolic Labeling

All proteins interact with other cellular components to fulfill their function. While tremendous progress has been made in the identification of protein complexes, their assembly and dynamics remain difficult to characterize. Here, we present a high-throughput strategy to analyze the native assembly kinetics of protein complexes. We apply our approach to characterize the co-assembly for 320 pairs of nucleoporins (NUPs) constituting the ≈50 MDa nuclear pore complex (NPC) in yeast. Some NUPs co-assemble fast via rapid exchange whereas others require lengthy maturation steps. This reveals a hierarchical principle of NPC biogenesis where individual subcomplexes form on a minute timescale and then co-assemble from center to periphery in a ∼1 h-long maturation process. Intriguingly, the NUP Mlp1 stands out as joining very late and associating preferentially with aged NPCs. Our approach is readily applicable beyond the NPC, making it possible to analyze the intracellular dynamics of a variety of multiprotein assemblies. [Display omitted] •KARMA, an approach to characterize maturation and dynamics of protein complexes•Metabolic labeling rates reveal complex maturation time and assembly order•Nuclear pore complex maturation follows a modular principle•Nucleoporins assemble from center to periphery on a minute to hour timescale A general approach to determining assembly kinetics for large protein architectures reveals the time scale and assembly sequence for the nuclear pore complex.