Open and closed states of Mrlip1 DAG lipase revealed by molecular dynamics simulation

ABSTRACT

The lid and flap domains control the catalytic activity of lipase through the opening and closing motion. However, this gating mechanism of diacylglycerol (DAG) lipase is poorly understood due to the lack of 3D structures in open conformations. In this study, the opening and closing states of Mrlip1 DAG lipase are revealed by the homology modelling and molecular dynamic simulations. It was found that the active residues (Ser₁₇₁, His₂₈₁ and Asp₂₂₈) in the catalytic pocket of Mrlip1 DAG lipase are covered by the lid domain in the closed conformation, and exposed to the solvent in the open conformation. The role of residues Phe₂₇₈ and Gln₂₈₂ in the flap domain, as well as that of Thr₁₀₁ and Thr₁₀₇ in the lid domains are also identified in gating mechanism. The site-directed mutagenesis have been carried out to illustrate the putative alterations of enzyme specificity. Our results suggest that the substrate specificity is achieved by these two key residues Phe₂₇₈ and Gln₂₈₂, and the irreversible conversion from DAG to TAG (Triacylglycerol) lipase are enabled by the two-point mutations.

KEYWORDS:

• Lipase
• catalytic triad
• gating mechanism
• computational modelling
• mutation analysis

Acknowledgements

Authors would like to thank Professor Dong-Qing Wei, SJTU (Shanghai Jiao Tong University) for providing computational resource.

Disclosure statement

No potential conflict of interest was reported by the authors .

ORCID

Shahid Ali http://orcid.org/0000-0002-4724-5086

Faez Iqbal Khan http://orcid.org/0000-0001-9088-0723

Additional information

Funding

This work was supported by the National Outstanding Youth Science Foundation of China [grant number 31725022]; Molecular Enzyme and Engineering International Cooperation Base of South China University of Technology [grant number 2017A050503001]; The PhD start-up Fund of Natural Science Foundation of Guangdong Province of China [grant number 2015A030310381].