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Universal Design Principle to Enhance Enzymatic Activity using the Substrate Affinity

View ORCID ProfileHideshi Ooka, View ORCID ProfileYoko Chiba, View ORCID ProfileRyuhei Nakamura
doi: https://doi.org/10.1101/2023.02.01.526728
Hideshi Ooka
1Biofunctional Catalyst Research Team, Center for Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama 351-0198 Japan
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  • For correspondence: hideshi.ooka@riken.jp
Yoko Chiba
1Biofunctional Catalyst Research Team, Center for Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama 351-0198 Japan
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Ryuhei Nakamura
1Biofunctional Catalyst Research Team, Center for Sustainable Resource Science, 2-1 Hirosawa, Wako, Saitama 351-0198 Japan
2Earth-Life Science Institute (ELSI), Tokyo Institute of Technology, 2-12-IE-1 Ookayama, Meguro-ku, Tokyo 152-8550, Japan
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ABSTRACT

Design principles to improve enzymatic activity are essential to promote energy-material conversion using biological systems. For more than a century, the Michaelis-Menten equation has provided a fundamental framework of enzymatic activity. However, there is still no concrete guideline on how the parameters should be optimized to enhance enzymatic activity. Here, we demonstrate that tuning the Michaelis-Menten constant (Km) to the substrate concentration (S) maximizes enzymatic activity. This guideline (Km = S) was obtained by applying the Brønsted (Bell)-Evans-Polanyi (BEP) principle of heterogeneous catalysis to the Michaelis-Menten equation, and is robust even with mechanistic deviations such as reverse reactions and inhibition. Furthermore, Km and S are consistent to within an order of magnitude over an experimental dataset of approximately 1000 wild-type enzymes, suggesting that even natural selection follows this principle. The concept of an optimum Km offers the first quantitative guideline towards improving enzymatic activity which can be used for highthroughput enzyme screening.

Competing Interest Statement

The authors have declared no competing interest.

Footnotes

  • Competing Interest Statement: The authors declare no competing interests.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted February 03, 2023.
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Universal Design Principle to Enhance Enzymatic Activity using the Substrate Affinity
Hideshi Ooka, Yoko Chiba, Ryuhei Nakamura
bioRxiv 2023.02.01.526728; doi: https://doi.org/10.1101/2023.02.01.526728
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Universal Design Principle to Enhance Enzymatic Activity using the Substrate Affinity
Hideshi Ooka, Yoko Chiba, Ryuhei Nakamura
bioRxiv 2023.02.01.526728; doi: https://doi.org/10.1101/2023.02.01.526728

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