Alien Proteomics Reveals Physical Rules for Diffusion through the Nuclear Pore

The separation of proteins between the nucleus and cytoplasm is key to many eukaryotic processes. This partitioning results from regulated diffusion through nuclear pores, but it is still unclear how protein size and surface properties govern these diffusion rates. In our experiments, we injected "alien" bacterial lysate into the cytoplasm of frog oocytes. We quantified the nucleocytoplasmic partitioning for ~1000 bacterial proteins at various times after injection using mass spectrometry. The proteome-wide data suggests a polymer physics-based diffusion model for passage through the nuclear pore complex. In this model, the free-energy cost of a protein entering the pore depends on the excluded volume and the interactions between the protein's surface and nucleoporins. We further improved this model by taking into account the diffusion throughout the cytoplasm and nucleus. This study demonstrates the integration of biochemical measurements with physical insight to predict cellular biology on a systems level.