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Protein–metal–organic frameworks (p-MOFs) are a prototypical example of how synthetic biological hybrid systems can be used to develop next-generation materials. Controlling p-MOF formation enables the design of hybrid materials with enhanced biological activity and high stability. However, such control is yet to be fully realized due to an insufficient understanding of the governing nucleation and growth mechanisms in p-MOF systems. The structural evolution of p-MOFs was probed by cryo-transmission electron microscopy, revealing nonclassical pathways via dissolution–recrystallization of highly hydrated amorphous particles and solid-state transformation of a protein-rich amorphous phase. On the basis of these data, we propose a general description of p-MOF crystallization which is best characterized by particle aggregation and colloidal theory for future synthetic strategies.