Metal Organic Framework Nanomaterial-Based Extraction and Proteome Analysis of Membrane and Membrane-Associated Proteins

Membrane proteins (MPs) play a key role in various biological processes, while difficulties still exist in the extraction because of their inherent low abundance and poor solubility caused by high hydrophobicity. Metal organic framework (MOF) materials with good hydrophobic properties have the ability to absorb MPs, especially zeolitic imidazolate framework (ZIF) materials. Here, two MOF materials (ZIF-8 and ZIF-67) were compared for MP extraction, and our results revealed that higher yield was obtained with ZIF-67. After method development, the optimal enrichment effect was obtained when the mass ratio of proteins and ZIF-67 reached 1:20 with 100 mM NaCl in 20% ethanol at 4 °C and pH 9.0. When compared with a commercial kit, the extraction yield increased by 88.11% and the average number of identified MPs elevated by 29.17% with the developed ZIF method. Normal lung cell MRC5 was employed to verify the effectiveness of the ZIF method. Results showed 45.13% increase in yield and 22.88% increase in average number of identified MPs by the ZIF method. Our method was further applied to the enrichment of MPs for high-metastatic (95D) and low-metastatic (95C) human lung cancer cells. A total of 1732 (95D) and 1711 (95C) MPs were identified, among which 710 MPs were dysregulated significantly; 441 upregulated MPs in 95D cells were found to be closely related to the growth, proliferation, and migration of lung cancer cells. Our results collectively demonstrated that ZIF-67 was an ideal material for MP extraction, which might be helpful for analysis of cancer proteomics and discovery of cancer migration associated MPs.