The evolution of multiple active site configurations in a designed enzyme

Area of Science:

• Biochemistry
• Computational Chemistry
• Enzyme Engineering

Background:

• Enzyme de novo design and optimization are advanced by computational chemistry, bioinformatics, and laboratory evolution.
• Studying designed enzymes offers insights into catalytic mechanisms and enzyme evolution.

Purpose of the Study:

• To investigate conformational sampling, electrostatic preorganization, and quantum tunneling during the evolution of a designed Kemp eliminase.
• To understand the relationship between conformational plasticity and enzyme evolvability.

Main Methods:

• Computational chemistry simulations
• Bioinformatics analysis
• Laboratory evolution experiments
• Analysis of designed Kemp eliminase (KE07) evolution

Main Results:

• Instability in the designed Kemp eliminase KE07 active site led to the emergence of multiple active site configurations.
• Evolutionary conformational selection stabilized the most efficient configuration, enhancing enzyme performance.
• Residues distant from the active site were found to significantly influence active site conformation and catalytic efficiency.

Conclusions:

• Conformational plasticity is intrinsically linked to enzyme evolvability.
• Enzyme evolution can be guided by stabilizing specific active site conformations.
• Remote residues play a critical role in shaping enzyme active sites for optimal catalysis.