Extending the Protein-Engineering Continuum: Cross-Kingdom Chimeric Proteins from Evolutionarily Divergent Components

Abstract

Protein engineering has evolved from modifying naturally occurring proteins toward modular, computational, and AI-assisted approaches for designing new molecular functions. Chimeric and fusion protein engineering has demonstrated that functional elements from different proteins can be reorganized into novel architectures, while advances in computational design, structure prediction, and artificial intelligence have expanded the sequence and structural space accessible to engineering. Building on these developments, this review examines cross-kingdom chimeric protein engineering as a proposed extension of modular protein engineering in which functionally relevant elements from evolutionarily distant biological systems are deliberately integrated into a single protein architecture. The scientific rationale, potential opportunities, and major design challenges are discussed, with emphasis on protein folding and stability, domain and interface compatibility, linker architecture, regulatory and cellular context, and unintended molecular interactions. The review further considers computational and AI-assisted approaches for donor selection, sequence and structural analysis, architecture design, candidate prioritization, and iterative optimization. However, computational plausibility alone cannot establish biological function experimental validation therefore remains essential, progressing from biochemical and structural characterization to cellular and functional evaluation with appropriate controls. The review also examines India’s capabilities relevant to advanced protein design, including computational biology, structural biology, protein engineering, synthetic biology, and related bio manufacturing, while identifying interdisciplinary integration and specialized expertise as important opportunities. Finally, a framework is proposed to strengthen design build test learn capabilities in India and support systematic investigation of cross-kingdom protein engineering as a scientifically testable research direction.