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Molecular Modeling and Optimization of Type II E.coli l-Asparginase Activity by in silico Design and in vitro Site-directed Mutagenesis

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Abstract

Introduction

L-asparaginase (also known as L-ASNase) is a crucial therapeutic enzyme that is widely used in treatment of ALL (acute lymphoblastic leukemia) as a chemotherapeutic drug. Besides, this enzyme is used in the food industry as a food processing reagent to reduce the content of acrylamide in addition to the clinical industry. The improvement of activity and kinetic parameters of the L-ASNase enzyme may lead to higher efficiency resulting in practical achievement. In order to achieve this goal, we chosen glycine residue in position 88 as a potential mutation with advantageous outcomes.

Method

In this study, firstly to find the appropriate mutation on glycine 88, various in silico analyses, such as MD simulation and molecular docking, were carried out. Then, the rational design was adopted as the best strategy for molecular modifications of the enzyme to improve its enzymatic properties.

Result

Our in silico findings show that the four mutations G88Q, G88L, G88K, and G88A may be able to increase L-ASNase’s asparaginase activity. The catalytic efficiency of each enzyme (kcat/Km) is the most important feature for comparing the catalytic activity of the mutants with the wild type form. The laboratory experiments showed that the kcat/Km for the G88Q mutant is 36.32% higher than the Escherichia coli K12 ASNase II (wild type), which suggests that L-ASNase activity is improved at lower concentration of L-ASN. Kinetic characterization of the mutants L-ASNase activity confirmed the high turnover rate (kcat) with ASN as substrate relative to the wild type enzyme.

Conclusion

In silico analyses and laboratory experiments demonstrated that the G88Q mutation rather than other mutation (G88L, G88K, and G88A) could improve the kinetics of L-ASNase.

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Acknowledgements

We thank our colleagues from “NIGEB and Applied Microbiology Research Center” who provided insight and expertise that greatly assisted our research.

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Authors and Affiliations

  1. Department of Systems Biotechnology, Institute of Industrial and Environmental Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), Shahrake- Pajoohesh Blvd., 15th Km, Tehran-Karaj Highway, P.O. Box 14965-161, Tehran, Iran

    Mahdieh Mahboobi & Bijan Bambai

  2. Applied Microbiology Research Center, Systems Biology and Poisonings Institute, Baqiyatallah University of Medical Sciences, Tehran, Iran

    Mahdieh Mahboobi & Hamid Sedighian

  3. Department of Agricultural Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), Shahrake- Pajoohesh Blvd., 15th Km, Tehran-Karaj Highway, P.O. Box 14965-161, Tehran, Iran

    Ali-Hatef Salmanian

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  1. Mahdieh Mahboobi
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  3. Hamid Sedighian
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  4. Bijan Bambai
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Contributions

MM Conceptualization, Methodology, Validation, formal analysis, Investigation, wrote the manuscript draft, Visualization. AHS and BB, Conceptualization, Writing review & editing and supervision. MM and HS revized the manuscript and bioinformatic analysis. All authors read and approved the final manuscript.

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Correspondence to Ali-Hatef Salmanian or Bijan Bambai.

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Mahboobi, M., Salmanian, AH., Sedighian, H. et al. Molecular Modeling and Optimization of Type II E.coli l-Asparginase Activity by in silico Design and in vitro Site-directed Mutagenesis. Protein J 42, 664–674 (2023). https://doi.org/10.1007/s10930-023-10149-x

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