Micro-Aqueous Organic System: A Neglected Model in Computational Lipase Design?

• Published in: Biomolecules
• Main Authors: Shang Wang, Yan Xu, Xiao-Wei Yu
• Format: Article in Journal/Newspaper
• Language: English
• Published: MDPI AG 2021
• Subjects: lipase; molecular dynamic simulation; non-aqueous phase catalysis; Microbiology; QR1-502; Rugosa; Antarc*; Antarctica
• Online Access: https://doi.org/10.3390/biom11060848; https://doaj.org/article/e0b1a39851884d66a67a43b8e18379f5

Water content is an important factor in lipase-catalyzed reactions in organic media but is frequently ignored in the study of lipases by molecular dynamics (MD) simulation. In this study, Candida antarctica lipase B, Candida rugosa lipase and Rhizopus chinensis lipase were used as research models to explore the mechanisms of lipase in micro-aqueous organic solvent (MAOS) media. MD simulations indicated that lipases in MAOS systems showed unique conformations distinguished from those seen in non-aqueous organic solvent systems. The position of water molecules aggregated on the protein surface in MAOS media is the major determinant of the unique conformations of lipases and particularly impacts the distribution of hydrophilic and hydrophobic amino acids on the lipase surface. Additionally, two maxima were observed in the water-lipase radial distribution function in MAOS systems, implying the formation of two water shells around lipase in these systems. The energy landscapes of lipases along solvent accessible areas of catalytic residues and the minimum energy path indicated the dynamic open states of lipases in MAOS systems differ from those in other solvent environments. This study confirmed the necessity of considering the influence of the microenvironment on MD simulations of lipase-catalyzed reactions in organic media.