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Multiscale simulation-guided design of enzyme bioconjugates with enhanced catalysis
Xiao Hong1, Timothy Cholko2, Chia-En A Chang2
1Department of Biochemistry, University of California-Riverside, Riverside, CA, 92521.
Chem Catalysis
|December 26, 2022
Summary
DNA scaffold position significantly impacts enzyme catalysis. Optimal positioning near the active site, without blocking it, maximizes catalytic efficiency, offering a 7-fold increase in enzyme kinetics.
Area of Science:
- Biochemistry
- Biotechnology
- Computational Biology
Background:
- Biopolymer-scaffold modification is a key strategy for enhancing enzyme catalysis.
- Predicting how scaffold position affects enzyme properties remains a significant challenge.
Purpose of the Study:
- To develop a predictive model for DNA scaffold position effects on enzyme kinetics.
- To understand how scaffold conjugation position influences enzyme properties.
Main Methods:
- Utilized a computational-experimental approach combining multiscale simulations and kinetic analysis.
- Employed phosphotriesterase (PTE) modified with a 20 base pair (bp) double-stranded DNA (dsDNA) scaffold.
- Investigated the impact of scaffold-enzyme geometry on catalytic efficiency.
Main Results:
- Demonstrated that DNA scaffold conjugation position is critical, comparable to scaffold chemistry and structure.
- Multiscale simulations predicted increased effective substrate concentration near the scaffold.
- Achieved a 7-fold enhancement in enzyme kinetics (kcat/KM) when the scaffold was optimally positioned (~5Å from the active site).
Conclusions:
- Scaffold positioning is crucial for maximizing enzyme catalytic enhancement.
- A predictive model incorporating substrate concentration and PTE-DNA geometry accurately captures kinetic improvements.
- This model enables prediction of kinetic effects across various DNA scaffold positions.
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