Bioinformatics Study of Methane Monooxygenase and Its Mutagenesis to Improve Enzymatic Function

Abstract

Introduction: The sMMO enzymes contain three common components: a hydroxylase, a reductase, and a regulatory protein. In addition to its potential role in converting methane to methanol, the sMMO enzyme oxidizes a wide range of hydrophobic molecules. The main aim of this study is to improve the stability of the sMMO enzyme by altering its amino acid sequence using bioinformatics techniques.

Methods: The ClusPro web server was used for docking the hydroxylase and reductase subunits. The interactions between amino acid subunits were identified by LigPlot software. Mutagenesis was generated by Molegro Virtual Docker software based on evolutionary trends and mCSM-PP12 server predictions. The ∆G value of wild-type enzymes and mutant variants was obtained using the PRODIGY server.

Results: In the Q83L, N161H, K43M, and N101S mutants, the value of ∆G was more negative than in the wild-type MMOH-2MMOB complex. The results of the LigPlot analysis showed that the hydrogen bonds present in the wild-type enzyme were preserved in the Q83L and N161H mutants and that these mutations increased the stability of the enzyme. Besides, The D29T and H37F mutants cause a more negative ∆G value than the wild-type hydroxylase-reductase complex. The results of LigPlot analysis show that these mutations form a new hydrogen bond between the reductase and hydroxylase subunits, which is highly consistent with the ∆G value and increases the stability of the enzyme.

Conclusion: It is concluded that changing the non-polar amino acids on the protein surface to polar ones can significantly improve the stability of enzymes.