Accelerating Enzyme Activity Enhancement: Targeting Suboptimal Residues Beyond the Binding Pocket

The pSUFER algorithm offers a rapid method for identifying suboptimal residues that hinder protein folding. These residues are crucial to enzyme stability and activity, as active sites exhibiting metastable effects and conformational changes are primarily responsible for enhancing the proteins' activity rather than their stability. Previous research has highlighted the effectiveness of the pSUFER algorithm in optimizing protein design and concentrating FuncLib design computations on suboptimal regions of underperforming enzymes, leading to increased catalytic efficiency. This study, aiming to expedite the process of enhancing enzyme activity, advocates that FuncLib design should prioritize not only residues associated with the enzyme binding pocket but also residues identified by pSUFER that are located away from the ligand. This is particularly critical for suboptimal residues situated within the loop region of the binding pocket, which exhibit greater flexibility and can significantly influence overall protein stability, as well as the entry and exit of small molecules into and out of the binding pocket.