Tuning Selectivity in CalA Lipase: Beyond Tunnel Engineering

Selective production of functional sn-1,3-diacylglycerol by microbial lipases: A comprehensive review

Since early 1990s, diacylglycerol (DAG) has drawn a continuous trending interest among researchers and oil industries/markets as part of a reduced-energy diet due to its functions to prevent and manage obesity. With the accumulated knowledge, a stereoisomer of sn-1,3-DAG is regarded as the sole compound to contribute to DAG's functions. sn-1,3-DAG can be produced by direct esterification of free fatty acids and glycerol, partial hydrolysis of TAGs/edible oils, and glycerolysis of TAGs/edible oils with glycerol using the regioselective microbial lipases as the catalyst. However, the specific microbial lipases with high efficiency to produce sn-1,3-DAG and their catalytic mechanisms are still a mystery. Herein, we provide an overview of metabolic fates of three stereoisomers of DAGs including sn-1,3-DAG, sn-1,2-DAG and/or sn-2,3-DAG, and synthesis process for sn-1,3-DAG, and critically outline the microbial lipases to selectively produce sn-1,3-DAG, and their pathways and mechanisms, which hopefully presents a reasonable full picture of functions, synthesis schemes, and catalytic performance to improve regioselectivity and catalytic efficiency for sn-1,3-DAG production with high yield.

Simultaneously Enhancing the Catalytic Activity and Thermostability of Pseudomonas aeruginosa Aminopeptidase via Structure-based Design

Aminopeptidases are crucial hydrolases in the food and pharmaceutical industries. This study addresses the need to enhance the catalytic performance of Pseudomonas aeruginosa aminopeptidase (PaAps) through a multifaceted computational design strategy. We introduced single-site mutations followed by combinatorial mutations to develop a mutant library, identifying the optimal mutant S112D, which demonstrated a 5.19-fold increase in catalytic activity and nearly doubled the thermostability compared to the wild type. The kinetic parameters (kcat, kcat/Km, and Vmax) of S112D were found to be 4.36, 6.52, and 4.36 times greater than those of the wild type, respectively. Molecular dynamics (MD) simulations revealed that the S112D mutant induced global conformational changes, resulting in a more open active pocket that facilitated better binding with the substrate, thereby improving conformational stability. Additionally, the S112D mutant exhibited a closer nucleophilic attack distance and stronger hydrogen bonding interactions, further boosting catalytic efficiency. Remarkably, mutant S112D, as well as the wild type, showed hydrolytic activity on both corn and soybean proteins. The hydrolysis rate of corn protein by S112D was approximately 1.92 times that of PaAps, and for soybean protein, it is roughly 1.84 times. These findings offered valuable insights for developing more efficient enzyme modification strategies.

Promoted expression of a lipase for its application in EPA/DHA enrichment and mechanistic insights into its substrate specificity

Expanding toolkits of EPA/DHA enrichment from natural sources is essential for better satisfying increasing demands for them. Lipase K80, from Proteus vulgaris K80, showed an application potential in EPA/DHA enrichment, whereas no desired heterologous expression in generally regarded as safe (GRAS) hosts restricted its relevant applications. In this study, expression of lipase K80 in a well-reputed GRAS host, Pichia pastoris, was achieved and further enhanced via combining disruption of its C-terminal KKL motif with co-expression of N-Acetyltransferase Mpr1, with a cumulative increment of nearly 200% in the secretion level and the volumetric activity. Its application in EPA/DHA enrichment from fish oil was thereafter obtained with merits of low temperature and much less time, yielding an increase of ~31% in their total percentage. To gain mechanistic insights into its substrate chain-length specificity, we performed molecular dynamics simulation and revealed the substrate-dependent significant yet divergent conformational shifts of predominantly distal surface-exposed regions, suggesting a predominant long-range modulation mechanism. Together, this work provided in-depth insights into substrate specificity of lipase K80 and an alternate engineering site, the C-terminal KKL motif, for its expression optimization in P. pastoris, as well as extended toolboxes of EPA/DHA enrichment and application scopes of lipase K80.

Learning from Protein Engineering by Deconvolution of Multi-Mutational Variants

This review analyzes a development in biochemistry, enzymology and biotechnology that originally came as a surprise. Following the establishment of directed evolution of stereoselective enzymes in organic chemistry, the concept of partial or complete deconvolution of selective multi-mutational variants was introduced. Early deconvolution experiments of stereoselective variants led to the finding that mutations can interact cooperatively or antagonistically with one another, not just additively. During the past decade, this phenomenon was shown to be general. In some studies, molecular dynamics (MD) and quantum mechanics/molecular mechanics (QM/MM) computations were performed in order to shed light on the origin of non-additivity at all stages of an evolutionary upward climb. Data of complete deconvolution can be used to construct unique multi-dimensional rugged fitness pathway landscapes, which provide mechanistic insights different from traditional fitness landscapes. Along a related line, biochemists have long tested the result of introducing two point mutations in an enzyme for mechanistic reasons, followed by a comparison of the respective double mutant in so-called double mutant cycles, which originally showed only additive effects, but more recently also uncovered cooperative and antagonistic non-additive effects. We conclude with suggestions for future work, and call for a unified overall picture of non-additivity and epistasis.

Unusual catalytic strategy by non-heme Fe(ii)/2-oxoglutarate-dependent aspartyl hydroxylase AspH

Biocatalytic C-H oxidation reactions are of important synthetic utility, provide a sustainable route for selective synthesis of important organic molecules, and are an integral part of fundamental cell processes. The multidomain non-heme Fe(ii)/2-oxoglutarate (2OG) dependent oxygenase AspH catalyzes stereoselective (3R)-hydroxylation of aspartyl- and asparaginyl-residues. Unusually, compared to other 2OG hydroxylases, crystallography has shown that AspH lacks the carboxylate residue of the characteristic two-His-one-Asp/Glu Fe-binding triad. Instead, AspH has a water molecule that coordinates Fe(ii) in the coordination position usually occupied by the Asp/Glu carboxylate. Molecular dynamics (MD) and quantum mechanics/molecular mechanics (QM/MM) studies reveal that the iron coordinating water is stabilized by hydrogen bonding with a second coordination sphere (SCS) carboxylate residue Asp721, an arrangement that helps maintain the six coordinated Fe(ii) distorted octahedral coordination geometry and enable catalysis. AspH catalysis follows a dioxygen activation-hydrogen atom transfer (HAT)-rebound hydroxylation mechanism, unusually exhibiting higher activation energy for rebound hydroxylation than for HAT, indicating that the rebound step may be rate-limiting. The HAT step, along with substrate positioning modulated by the non-covalent interactions with SCS residues (Arg688, Arg686, Lys666, Asp721, and Gln664), are essential in determining stereoselectivity, which likely proceeds with retention of configuration. The tetratricopeptide repeat (TPR) domain of AspH influences substrate binding and manifests dynamic motions during catalysis, an observation of interest with respect to other 2OG oxygenases with TPR domains. The results provide unique insights into how non-heme Fe(ii) oxygenases can effectively catalyze stereoselective hydroxylation using only two enzyme-derived Fe-ligating residues, potentially guiding enzyme engineering for stereoselective biocatalysis, thus advancing the development of non-heme Fe(ii) based biomimetic C-H oxidation catalysts, and supporting the proposal that the 2OG oxygenase superfamily may be larger than once perceived.

Structure of dimeric lipoprotein lipase reveals a pore adjacent to the active site

Lipoprotein lipase (LPL) hydrolyzes triglycerides from circulating lipoproteins, releasing free fatty acids. Active LPL is needed to prevent hypertriglyceridemia, which is a risk factor for cardiovascular disease (CVD). Using cryogenic electron microscopy (cryoEM), we determined the structure of an active LPL dimer at 3.9 Å resolution. This structure reveals an open hydrophobic pore adjacent to the active site residues. Using modeling, we demonstrate that this pore can accommodate an acyl chain from a triglyceride. Known LPL mutations that lead to hypertriglyceridemia localize to the end of the pore and cause defective substrate hydrolysis. The pore may provide additional substrate specificity and/or allow unidirectional acyl chain release from LPL. This structure also revises previous models on how LPL dimerizes, revealing a C-terminal to C-terminal interface. We hypothesize that this active C-terminal to C-terminal conformation is adopted by LPL when associated with lipoproteins in capillaries.

Structure of Dimeric Lipoprotein Lipase Reveals a Pore for Hydrolysis of Acyl Chains

Lipoprotein lipase (LPL) hydrolyzes triglycerides from circulating lipoproteins, releasing free fatty acids. Active LPL is needed to prevent hypertriglyceridemia, which is a risk factor for cardiovascular disease (CVD). Using cryogenic electron microscopy (cryoEM), we determined the structure of an active LPL dimer at 3.9 Ã… resolution. This is the first structure of a mammalian lipase with an open, hydrophobic pore adjacent to the active site. We demonstrate that the pore can accommodate an acyl chain from a triglyceride. Previously, it was thought that an open lipase conformation was defined by a displaced lid peptide, exposing the hydrophobic pocket surrounding the active site. With these previous models after the lid opened, the substrate would enter the active site, be hydrolyzed and then released in a bidirectional manner. It was assumed that the hydrophobic pocket provided the only ligand selectivity. Based on our structure, we propose a new model for lipid hydrolysis, in which the free fatty acid product travels unidirectionally through the active site pore, entering and exiting opposite sides of the protein. By this new model, the hydrophobic pore provides additional substrate specificity and provides insight into how LPL mutations in the active site pore may negatively impact LPL activity, leading to chylomicronemia. Structural similarity of LPL to other human lipases suggests that this unidirectional mechanism could be conserved but has not been observed due to the difficulty of studying lipase structure in the presence of an activating substrate. We hypothesize that the air/water interface formed during creation of samples for cryoEM triggered interfacial activation, allowing us to capture, for the first time, a fully open state of a mammalian lipase. Our new structure also revises previous models on how LPL dimerizes, revealing an unexpected C-terminal to C-terminal interface. The elucidation of a dimeric LPL structure highlights the oligomeric diversity of LPL, as now LPL homodimer, heterodimer, and helical filament structures have been elucidated. This diversity of oligomerization may provide a form of regulation as LPL travels from secretory vesicles in the cell, to the capillary, and eventually to the liver for lipoprotein remnant uptake. We hypothesize that LPL dimerizes in this active C-terminal to C-terminal conformation when associated with mobile lipoproteins in the capillary.