Resolution of physics and deep learning-based protein engineering filters: A case study with a lipase for industrial substrate hydrolysis

Computational enzyme design remains a powerful yet imperfect tool for optimizing biocatalysts, especially when targeting non-natural substrates. Using design tools we investigated Pseudomonas aeruginosa LipA, a lipase with a flexible lid domain crucial for substrate binding and turnover, aiming to enhance its hydrolysis of the industrially relevant substrate Roche ester. We generated an initial set of single-point mutations based on structural proximity to the active site and evaluated their effects using a computational pipeline integrating molecular dynamics (MD) simulations, density functional theory (DFT) calculations, and ensemble-based energy scoring. While we identified several active variants, attempts to rank them by activity using structural features, such as hydrogen bond formation or residue flexibility, failed. Deep learning models, applied post hoc for structural analysis via AlphaFold3, produced nearly identical active site geometries across variants, irrespective of activity. Reaction pathway analysis revealed energy barriers varying by 5-15 kcal/mol depending on substrate conformation, with the nucleophile addition step consistently rate-limiting. However, these small energetic shifts, likely critical for incremental activity changes, were indistinguishable by current computational or deep learning methods. Our results highlight the limitations of existing approaches in resolving subtle functional differences and underscore the need for improved benchmarks, reactive force fields, and more sensitive ranking metrics. Advancing these areas will be essential for designing enzymes with gradual, evolution-like activity improvements and for bridging the gap between structural prediction and catalytic function.