A computational methodology to screen activities of enzyme variants

Area of Science:

• Biochemistry
• Computational Chemistry
• Enzyme Engineering

Background:

• Enzyme activity is crucial for many biological and industrial processes.
• Predicting the impact of mutations on enzyme function is challenging and time-consuming.
• Efficient screening methods are needed to accelerate enzyme discovery and optimization.

Purpose of the Study:

• To develop a fast computational method for screening enzyme activity.
• To enable rapid estimation of mutation effects on enzyme-catalyzed reaction barrier heights.
• To facilitate the screening of numerous enzyme mutants for improved activity.

Main Methods:

• Utilized the PM6 and MOZYME methods within MOPAC2009 for calculations.
• Employed adiabatic mapping to estimate reaction barrier heights.
• Automated the generation of mutant structures and setup of semiempirical calculations.
• Validated results against high-level quantum chemical calculations (B3LYP/6-31G(d)//RHF/3-21G).

Main Results:

• The method computes mutation effects on barrier heights within 24 hours using approximately 10 processors.
• Achieved accuracy within 3 kcal/mol compared to high-level calculations for a model system.
• Demonstrated the ability to estimate effects for hundreds of mutants in weeks using high-performance computing.
• Identified specific computational parameters (convergence criteria, cutoff distances) for reliable results.

Conclusions:

• The presented computational method offers a fast and efficient way to screen enzyme activity.
• This approach can significantly accelerate the process of enzyme engineering and discovery.
• The automation and speed allow for the exploration of a large number of enzyme variants.
• The method provides reliable estimates of mutation effects on enzyme catalysis.