Multiscale simulation-guided design of enzyme bioconjugates with enhanced catalysis

Biopolymer scaffold modification is widely used to enhance enzyme catalysis. A central challenge is predicting the effects of scaffold position on enzyme properties. Here, we use a computational-experimental approach to develop a model for the effects of DNA scaffold position on enzyme kinetics. Using phosphotriesterase (PTE) modified with a 20-bp dsDNA, we demonstrate that conjugation position is as important as the scaffold's chemistry and structure. Multiscale simulations predict the effective substrate concentration increases close to the scaffold, which has mM strength binding to the substrate. Kinetic analysis shows that the effective concentration that the scaffold provides is best utilized when positioned next to, but not blocking, the active site. At similar to 5-A degrees distance between scaffold and active site, a 7-fold increase in k(cat)/K-M was achieved. A model that accounts for the substrate concentration as well as PTE-DNA geometry accurately captures the kinetic enhancements, enabling prediction of the effect across a range of DNA positions.

Automated summary

Biopolymer scaffold modification is widely used to enhance enzyme catalysis. However, predicting the effects of scaffold position on enzyme properties is a central challenge. Researchers have developed a computational-experimental approach to model the effects of DNA scaffold position on enzyme kinetics and have found that the conjugation position is as important as the scaffold's chemistry and structure. They also discovered that there is a significant enhancement in enzyme kinetics when the scaffold is positioned at a suitable distance from the active site.