NMR-guided rational exploration of co-factors in boosting the Pfu DNA polymerase

With rapid developments of emerging technologies like synthetic biology, the demand for DNA polymerases with superior activities including higher thermostability and processivity has increased significantly. Thus, rational optimization of the performance of DNA polymerase is of great interest. Nuclear magnetic resonance (NMR) spectroscopy is a powerful technique used for studying protein structure and dynamics. It provides the atomic resolution information of enzymes under their functional solution environment to reveal the active sites (hot spots) of the enzyme, which could be further used for optimizing the performance of enzymes. In our previous work, we identified hot spot residues of <i>Pyrococcus furiosus</i> DNA polymerase (<i>Pfu</i> pol). We aim to employ these binding hot spots to screen for co-factors of <i>Pfu</i> pol, particularly targeting those molecules exhibiting weak intermolecular interactions. To validate this concept, we first demonstrated the feasibility of utilizing hot spot residues as screening probes for auxiliary factors by employing the well-characterized Tween-20 as a model system. Employing these hot spots as probes, two new co-factors, the heat shock protein TkHSP20 from <i>Thermococcus Kodakaraensis</i> and the chemical chaperone l-arginine, are identified to interact with <i>Pfu</i> pol to boost its performance in amplifying long DNA fragments by enhancing the thermal stability and the processivity of the <i>Pfu</i> pol. This NMR-based approach requires no prior assignment information of target enzymes, guiding the rational exploration of novel co-factors for <i>Pfu</i> pol. Moreover, our approach is not dependent on structural data or bioinformatics. Therefore, it has significant potential for application in various enzymes to expedite the progress in enzyme engineering.