Abstract
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.
Highlights
Lipases catalyze the synthesis and hydrolysis of ester bonds of lipids [1,2]
Several commonly used models in the lipase catalysis industry were selected, including Candida antarctica lipase B (CALB), Candida rugosa lipase (CRL) and Rhizopus chinensis lipase (RCL), as models for studies of molecular dynamics (MD) simulations run under water, non-aqueous organic solvent (n-heptane or toluene) and micro-aqueous organic solvent (MAOS) solvent conditions
Bank entries 1TCA, 1TRH and 6A0W, respectively. All three of these enzymes exhibited ester synthesis activity. In these X-ray crystal structures, the active pockets are covered by different types of lids. (CALB is excluded because it is classified as a lidless lipase [13].) The tautomeric and protonation states of residues at pH 7.0 were assigned with PROPKA [14]
Summary
Lipases (triacylglycerol acyl hydrolases, EC 3.1.1.3) catalyze the synthesis and hydrolysis of ester bonds of lipids [1,2]. MD simulations of MAOS-like systems (224 water:2289 chloroform, mol/mol) were performed by Pleiss et al [12]. We hope to construct a model in a MD simulation to demonstrate the conformational differences of lipases existing between the MAOS system and non-aqueous organic solvent systems; this, the authors believe, will provide additional insights into our understanding of lipase catalysis in organic systems. Several commonly used models in the lipase catalysis industry were selected, including Candida antarctica lipase B (CALB), Candida rugosa lipase (CRL) and Rhizopus chinensis lipase (RCL), as models for studies of MD simulations run under water, non-aqueous organic solvent (n-heptane or toluene) and MAOS solvent conditions. This study confirms the necessity of considering the influence of a small amount of water in MD simulations of lipase-catalyzed reactions in organic media
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