Mechanism of Protein-Directed Biomimetic Mineralization in Metal–Organic Frameworks

Protein@metal-organic frameworks (MOFs) have emerged as promising biohybrid materials with diverse applications in catalysis, drug delivery, and biosensing. Their capability to protect proteins─particularly enzymes─under harsh conditions, enhance catalytic performance, and facilitate the spatial organization of multiple biomolecules has garnered great attention. Despite the growing adoption of protein@MOF, a fundamental question remains: how are proteins encapsulated within MOFs during nucleation or crystal growth? Herein, we combine molecular dynamics simulations and experiments to elucidate the detailed mechanism of protein encapsulation during biomimetic mineralization, using the zeolitic imidazolate framework (ZIF-8) as a model system. Simulations reveal that stable protein-metal-ligand complexes do not form directly in precursor solutions. Instead, proteins influence ZIF-8 nucleation and crystal growth through negatively charged or metal-coordinating residues, which bind partially positive Zn²⁺ sites on the amorphous phase or nascent nuclei. In this way, proteins promote particle aggregation or act as capping agents, facilitating nucleation or crystal growth processes while simultaneously enabling protein encapsulation. In contrast, positively charged proteins experience electrostatic repulsion, limiting their encapsulation. Experimental results corroborate this mechanism by studying the growth kinetics of protein@MOF formation. Furthermore, leveraging this mechanism enables the construction of hierarchical assemblies containing multiple proteins with spatial organization. These findings enhance our understanding of how protein surface properties guide MOF assembly, providing a foundation for the rational design of protein@MOF composites with tailored morphologies and improved functionalities for diverse biorelevant applications.