From biopolymers to microcompartments: A structured review of protein-based scaffolds for enzyme immobilization

Enzyme immobilization is a foundational strategy for enhancing the performance of biocatalysts in both industrial and biomedical applications. Although traditional carriers including biopolymers, organic matrices, and inorganic supports have been widely adopted in established biocatalytic processes, their ability to provide precise nanoscale spatial organization of enzymes and pathway-level reaction control remains limited, particularly in applications such as multi-enzyme cascade reactions, synthetic metabolic pathways, and cell-free systems. While challenges related to enzyme stability, reuse, and apparent reaction efficiency can often be mitigated through well-established biochemical engineering strategies (e.g., carrier functionalization, reactor design, and process optimization), these approaches do not readily enable programmable enzyme colocalization or metabolite channeling, thereby motivating the development of more advanced scaffold systems. In this review, we adopt a tiered perspective progressing from naturally derived biopolymer supports to engineered protein scaffolds, and ultimately to bacterial microcompartments (BMCs) as emerging, organelle-like platforms. We discuss the structural and functional diversity of these proteinaceous scaffolds, including self-assembling nanostructures, virus-like particles, and modular interaction systems. Special emphasis is placed on BMCs for their spatial precision, selective permeability, and ability to encapsulate multi-enzyme pathways. Recent advances in synthetic biology, from orthogonal shell engineering to modular cargo recruitment, underscore their transformative potential for pathway design and metabolic control. This synthesis of current developments aims to inform future scaffold design and broaden the scope of biocatalysis.