Protein modification: convergence of artificial intelligence, synthetic biology, and nano-assembly

The extensive application of biosynthetically produced proteins in advanced food systems remains limited because of functional deficiencies, including poor solubility, inadequate emulsifying activity, and low in vitro digestibility. To address this gap, this study aimed to critically examine recent advances in the functional enhancement of biosynthetically produced proteins. It highlights emerging strategies that integrate computational design, artificial intelligence-guided protein engineering, and genetic code expansion to enable precise molecular-level customization. Additionally, the study emphasizes the synergistic benefits of combining chemical, enzymatic, and physical field-assisted modification techniques with macro-scale approaches such as multicomponent self-assembly and nanofabrication. These integrated modification strategies have demonstrated substantial functional gains, including markedly improved thermal stability, substantially enhanced biosynthetic yields, and significantly strengthened antimicrobial activity under food-relevant conditions. In summary, this cross-disciplinary synthesis underscores a transformative pathway toward the development of sustainable, high-performance protein ingredients through closed-loop AI-guided protein design.