QUANTIFYING DIFFUSION RATES THROUGH THE NUCLEAR PORE USING ALIEN PROTEOMICS

Abstract

In eukaryotic cells, the distribution of proteins between the cytoplasm and nucleus plays a key role in determining many important cellular processes, and defects in protein partitioning can result in developmental defects or cancer. This partitioning is achieved via a combination of passive diffusion and active transport, though passive diffusion is the more predominant factor. To better understand the protein properties that affect passive diffusion, I quantified the diffusion of E. coli proteins into the nucleus of Xenopus oocytes. With the help of a new entropy-based model, I was able to show that proteins with native sizes of up to ~100 kDa can passively diffuse through the nuclear pore. By extending the entropy model to incorporate information about surface residue frequencies, I found that proteins with higher surface frequencies of lysine and alanine tended to diffuse slower, while other hydrophobic residues, histidine, and arginine correlated with faster diffusion. My work demonstrates the importance of both protein size and surface properties in predicting passive diffusion rates. Additionally, I have reviewed the current state of mass spectrometry-based proteomics techniques, some of which I have used in my project on quantifying passive diffusion. I also contributed to a review about how the nucleocytoplasmic partitioning of proteins is affected by both passive diffusion and active transport. Finally, I performed some mathematical derivations explaining how the Arrhenius Equation can be extended to sequences of multiple reactions, which greatly helped explain why complex developmental processes follow the Arrhenius Equation.