Cavity Formation in Protein@Metal-Organic Frameworks Through Late-Stage Crystal Dissolution

Proteins are increasingly used to guide the crystallization of metal-organic frameworks (MOFs), yielding protein@MOFs (p@MOFs) that encapsulate fragile biomacromolecules within stable crystalline hosts. These biohybrid materials offer tunable porosity and spatial organization that are difficult to achieve with conventional synthesis. Despite their growing importance, the mechanisms by which proteins influence MOF nucleation, crystal growth, and defect formation remain poorly understood. Here, we use a distributed electron microscopy approach to follow the full crystallization pathway of ferritin@ZIF-8 (Fn@ZIF-8). The method combines cryogenic transmission electron microscopy (cryo-TEM), cryogenic electron tomography (cryo-ET), and liquid-phase TEM (LP-TEM) to capture structural transitions over time. Using the ferritin iron oxide core as an intrinsic nanoscale tracer, we visualize the transformation of protein-rich amorphous precursors into crystalline particles that ripen, aggregate, and develop large, surface-accessible cavities. These cavities emerge only during later stages of growth, where localized dissolution and recrystallization restructure the framework. Concurrently, proteins become enriched near the crystal periphery and depleted from cavity-rich regions. Our results suggest that protein organization and dissolution-driven restructuring both contribute to defect formation. This work provides a mechanistic framework for understanding how hierarchical porosity develops in p@MOFs and establishes distributed electron microscopy as an approach for investigating biohybrid crystallization pathways.