UiO-66 MOF Nanozymes as Affinity Columns for Proteomics Applications

Metal–organic framework (MOF) nanozymes have shown great activity toward the hydrolysis of peptide bonds in proteins, offering considerable potential to be developed as artificial proteases suitable for proteomics and other biotechnological applications. However, the adsorption of native proteins and resulting protein fragments onto MOFs has been scarcely addressed, despite the fact that it complicates their downstream analysis and hinders further applications. In this study, we treated MOFs as “stationary phases” of affinity columns and evaluated a broad range of compounds such as surfactants, organic solvents, acids, and salts to induce variations in pH and ionic strength of the “mobile phase” and facilitate the disruption of protein-MOF interactions. As a result, we developed a reliable protein elution strategy using carbonate solutions, enabling streamlined analysis of protein digests, even at low sodium carbonate concentrations and with short elution times. The newly designed elution protocol significantly improved the desorption of polypeptide fragments from the MOF structure and enabled shorter reaction times, revealing that the reported hydrolytic activity of UiO-66 is greater than previously anticipated. Cytochrome c was selected to further evaluate the efficiency of the protocol, as its hydrolysis using MOF nanozymes has not been achieved before due to its strong adsorption onto MOFs. By applying the protocol, the hydrolysis and efficient release of cytochrome c was observed, consistently yielding reproducible peptide fragments and ensuring their full recovery from the MOF. Mechanistic experiments highlighted the key role of carbonate salts in circumventing the high affinity of peptide chains for Zr(IV) sites and in disrupting the electrostatic interactions between the MOF and peptide fragments by shielding charged amino acids. This advancement contributes to further application of MOFs in proteomics and other biotechnology fields requiring efficient hydrolytic cleavage, offering a significant advantage over natural enzymes due to the potential for MOF regeneration.