Molecular insights into particular mutations impact on Taq polymerase dynamics and structure: a molecular dynamics simulation study

Taq DNA polymerase (Taq pol), a useful enzyme in biotechnology, has been the subject of an extensive investigation to create enzymes with altered characteristics, notably the enhancement of Taq pol's thermostability, But the demand for such enzymes remains unmet. In this study, we aimed to introduce several mutations to the Taq pol structure to improve its structural stability. We combined the sequence-based and structure-based rational design mutagenesis techniques to incorporate five mutations into the Taq pol structure. The impact of the mutations on the enzyme was examined by the utilization of molecular dynamics simulations. All mutant enzymes exhibited a more compact structure and a greater abundance of internal hydrogen bonds and secondary structure contents. While the mutants TaqG389E and TaqS290K|A353K|L365E|N384E|G389E demonstrated the least structural dynamics, the other mutant enzymes displayed higher or comparable flexibility compared to the wild-type. Furthermore, a reduction in the distance between mutation positions and neighboring charged amino acids was observed in most of the mutant structures. The enhancement of non-bonded interactions resulted in the evaluation of structure stability. Based on this fact, all of the suggested mutations had positive effects on the stability of the Taq pol structure. Additionally, a decrease in structural flexibility led to a more stable structure; hence, TaqG389E and TaqS290K|A353K|L365E|N384E|G389E mutants were considered more stable compared to wild-type Taq pol. The mutants TaqG389E and TaqS290K|A353K|L365E|N384E|G389E exhibited excellent performance in terms of reduced structural flexibility, evaluated internal hydrogen bonds, and the capacity to establish multiple stabilizable interactions when compared to the wild-type.