Exploring particulate methane monooxygenase (pMMO) proteins using experimentation and computational molecular docking

Abstract

Researchers had difficulty studying pure full-length pMMO due to the solubility problem and loss of enzymatic activity after its elimination from the native membrane. To study pMMO, we performed several bioinformatics tools to analyze the entire structure of it available in the PDB database. We also carried out molecular docking studies to prove that quinone and duroquinone can bind to several sites of eight pMMO proteins. However, some sites in the orientation are not required by the catalysis process. Furthermore, molecular docking was done for predicting the binding affinity of P450 with target enzymes. Interestingly, our analysis illustrated that pMMO can produce methanol in the presence of quinone and duroquinone and the absence of Cu. Moreover, pmoB1 can interact with P450. Consequently, our findings highlight, for the first time, the significance of studying the membrane of pMMO to provide valuable insights into its functions.

Keywords

• Methanol
• Molecular docking
• Particulate methane monooxygenase
• Quinone
• Duroquinone