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Updated: Sep 5, 2025

Protein WISDOM: A Workbench for In silico De novo Design of BioMolecules
Published on: July 25, 2013
A preorganization oriented computational method for de novo design of Kemp elimination enzymes
Shengyu Zhang1, Jun Zhang2, Wenjia Luo3
1College of Life Science and Technology, Beijing University of Chemical Technology, Beijing 100029, China; Department of Chemical Engineering, Tsinghua University, Beijing 100084, China.
Abstract:
A preorganization oriented computational strategy for de novo enzyme design based on computational enzyme design tool PRODA was developed and demonstrated by the creation of Kemp elimination enzymes. A pre-organized active site model of proton transfer from carbon with a low energy barrier was proposed and then anchored into the scaffold 3AOF, the endoglucanase from Thermotoga maritima, which was selected from the protein structural database. The low-energy amino acid sequences at the binding pocket to stabilize the catalytic productive geometry were computationally generated via the iterative protein redesign and molecular dynamics simulation. The designed variant (3AOF-KE03) bearing 17 mutations was experimentally confirmed to afford catalytic activity (kcat/KM=14.04M-1s-1) towards Kemp elimination, with measured rate (kcat=0.033s-1) enhancement of up to 104-fold. This computational strategy is general, and we anticipate the creation of a wide range of artificial enzymes to catalyze reactions with industrial significance in the future.
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