Fast rational enzyme design by computational non-equilibrium alchemical transformations.

Area of Science:

• Biochemistry
• Computational Chemistry
• Enzyme Engineering

Background:

• Enzyme engineering is crucial for sustainable fine chemical production.
• Traditional experimental enzyme design methods are inefficient and labor-intensive.
• Predicting the impact of mutations on enzyme kinetics is challenging.

Purpose of the Study:

• To develop a computational workflow for predicting mutation-induced changes in enzyme activation free energy barriers.
• To enable efficient and rational enzyme design for sustainable chemical synthesis.

Main Methods:

• Utilizing non-equilibrium alchemical free energy calculations.
• Employing ab initio derived force fields for accurate predictions.
• Applying the workflow to enzymes catalyzing hydride transfer from NADPH.

Main Results:

• The computational workflow accurately predicted changes in activation free energy barriers.
• Results closely matched experimental data with minimal errors (a few kJ mol⁻¹).
• The method demonstrated low computational requirements suitable for high-throughput analysis.

Conclusions:

• The proposed computational workflow offers an efficient alternative to experimental methods for enzyme design.
• This approach aids in the rational design of enzymes for sustainable fine chemical production.
• The methodology can accelerate the discovery and optimization of biocatalysts.