In this study, we highlight the role of nitrogen-enriched surface groups on proteins in directing topological transformations of metal-organic frameworks (MOFs). Using a modified-protein-directed MOFs template synthesis (mDTS) strategy, we demonstrate that these surface modifications on cytochrome c (Cyt c) selectively induce the formation of leaf-like zeolitic imidazolate frameworks (ZIF-L). This approach not only enables a structural transition from ZIF-8 to a more open ZIF-L framework but also substantially enhances Cyt c's catalytic activity and loading beyond traditional immobilization methods. Adjusting the concentration of surface modifier allows for precise tuning of Cyt c's activity, allowing optimal enzyme function at specific modifier levels. Furthermore, our results reveal surface modifications of a variety of proteins can facilitate the formation of ZIF-L, emphasizing the broad applicability of the mDTS method. This approach offers significant promise for developing highly efficient protein-MOFs composites, offering transformative potential for industrial catalysis and biotechnological applications.