Ca-BPDC Immobilization Redistributes Regional Proteolytic Preference of Serine Proteases

Proteases cleave peptide bonds and generate shorter polypeptide products, finding broad applications. For applications in peptide sequencing, protein mapping, and production of bioactive polypeptides, control over where proteolysis initiates and how it proceeds is critical. Natural proteolytic selectivity primarily originates from local recognition of short amino-acid motifs. However, higher-order or regional selectivity (i.e., cleavage biased toward specific termini or domains) remains difficult even with sophisticated protein engineering or complex multi-enzyme, cascade proteolytic design. We recently reported that trypsin@Ca-BPDC preferentially cleaved the N-terminus of T4 phage lysozyme (T4L) [ACS Appl. Mater. Interfaces 2023, 15 (7), 8927-8936], indicating a promising alternative to introduce directional or regional proteolysis through enzyme immobilization via a unique MOF, Ca-BPDC. To confirm such preference, as a follow-up of that work, here, we extend the MOF-based immobilization to two commercial serine proteases (mixture products with unreported compositions). Our time-resolved electron paramagnetic resonance (EPR) shows that, despite differing or weakly defined selectivity in solution, both commercial proteases exhibit a consistent shift toward N-terminal cleavage of T4L upon immobilized in Ca-BPDC through co-crystallization. Control experiments indicate negligible adsorption of the substrate to the Ca-BPDC alone, suggesting that directional selectivity arises from the coupled MOF-protease environment rather than substrate-MOF interactions. These results indicate that Ca-BPDC may be able to impose an additional, material-derived layer of proteolytic selection on commercial serine proteases. Thus, it may offer a practical way for directional or programmable proteolysis without enzyme chemical or genetic modification. Our immobilization platform also offers a reusable matrix compatible with real-time mechanistic analysis. This approach opens opportunities for controlled peptide generation, proteolytic selectivity tuning, and design of programmable proteolytic bioreactors.