Composition analysis of positional isomers of phosphatidylinositol by high-performance liquid chromatography

Analysis of positional isomers of 2-3-4-alkoxyphenylcarbamic acid derivatives by a combination of TLC and IMS

In this study, we have demonstrated a separation of positional isomers of some derivatives of alkoxyphenylcarbamic acid. These compounds belong to drugs with local anesthetics activity. The low volatility compounds were analysed by a Thin Layer Chromatography (TLC) and Ion Mobility Spectrometry (IMS) using diode laser desorption for sample introduction to IMS. This combined approach allowed the identification of compounds. Also, we have carried out IMS studies of all compounds and determined their ion mobilities The ion mobilities were increasing with the geometry change from position ortho to para of alkoxy chain, which is in agreement with their different collision cross section (CCS).

Structures of an engineered phospholipase D with specificity for secondary alcohol transphosphatidylation: insights into plasticity of substrate binding and activation

Phospholipase D (PLD) is an enzyme useful for the enzymatic modification of phospholipids. In the presence of primary alcohols, the enzyme catalyses transphosphatidylation of the head group of phospholipid substrates to synthesise a modified phospholipid product. However, the enzyme is specific for primary alcohols and thus the limitation of the molecular size of the acceptor compounds has restricted the type of phospholipid species that can be synthesised. An engineered variant of PLD from Streptomyces antibioticus termed TNYR SaPLD was developed capable of synthesising 1-phosphatidylinositol with positional specificity of up to 98%. To gain a better understanding of the substrate binding features of the TNYR SaPLD, crystal structures have been determined for the free enzyme and its complexes with phosphate, phosphatidic acid and 1-inositol phosphate. Comparisons of these structures with the wild-type SaPLD show a larger binding site able to accommodate a bulkier secondary alcohol substrate as well as changes to the position of a flexible surface loop proposed to be involved in substrate recognition. The complex of the active TNYR SaPLD with 1-inositol phosphate reveals a covalent intermediate adduct with the ligand bound to H442 rather than to H168, the proposed nucleophile in the wild-type enzyme. This structural feature suggests that the enzyme exhibits plasticity of the catalytic mechanism different from what has been reported to date for PLDs. These structural studies provide insights into the underlying mechanism that governs the recognition of myo-inositol by TNYR SaPLD, and an important foundation for further studies of the catalytic mechanism.

Preparation and Application of 13C-Labeled myo-Inositol to Identify New Catabolic Products in Inositol Metabolism in Lactobacillus casei

myo-Inositol (mI) is widely distributed in all domains of life and is important for several cellular functions, including bacterial survival. The enzymes responsible for the bacterial catabolism of mI, encoded in the iol operon, can vary from one organism to another, and these pathways have yet to be fully characterized. We previously identified a new scyllo-inositol dehydrogenase (sIDH) in the iol operon of Lactobacillus casei that can oxidize mI in addition to the natural substrate, scyllo-inositol, but the product of mI oxidation was not determined. Here we report the identification of these metabolites by monitoring the reaction with ¹³C nuclear magnetic resonance. We prepared all six singly ¹³C-labeled mI isotopomers through a biocatalytic approach and used these labeled inositols as substrates for sIDH. The use of all six singly labeled mI isotopomers allowed for metabolite characterization without isolation steps. sIDH oxidation of mI produces 1l-5-myo-inosose preferentially, but also two minor products, 1d-chiro-inosose and 1l-chiro-inosose. Together with previous crystal structure data for sIDH, we were able to rationalize the observed oxidation preference. Our relatively simple procedure for the preparation of isotopically labeled mI standards can have broad applications for the study of mI biotransformations.

Directing positional specificity in enzymatic synthesis of bioactive 1-phosphatidylinositol by protein engineering of a phospholipase D

Phosphatidylinositol (PI) holds a potential of becoming an important dietary supplement due to its effects on lipid metabolism in animals and humans manifested as a decrease of the blood cholesterol and lipids, and relief of the metabolic syndrome. To establish an efficient, enzymatic system for PI production from phosphatidylcholine and myo-inositol as an alcohol acceptor, our previous study started with the wild-type Streptomyces antibioticus phospholipase D (SaPLD) as a template for generation of PI-synthesizing variants by saturation mutagenesis targeting positions involved in acceptor accommodation, W187, Y191, and Y385. The isolated variants generated PI as a mixture of positional isomers, among which only 1-PI exists in nature. Thus, the current study has focused to improve positional specificity of W187N/Y191Y/Y385R SaPLD (NYR) which generates PI as a mixture of 1-PI and 3-PI in the ratio of 76/24, by subjecting four residues of its acceptor-binding site to saturation mutagenesis. Subsequent screening pointed at NYR-186T and NYR-186L as the most improved variants producing PI with a ratio of 1-/3-PI = 93/7 and 87/13, respectively, at 37°C. Lowering the reaction temperature further improved the specificity of both variants to 1-/3-PI > 97/3 at 20°C with no change in total PI yield. Structure model analyses imply that G186T and G186L mutations increased rigidity of the acceptor-binding site, thus limiting the possible orientations of myo-inositol. The two newly isolated PLDs are promising for future application in large-scale 1-PI production.

Phospholipase D as a catalyst: application in phospholipid synthesis, molecular structure and protein engineering

Phospholipase D (PLD) is a useful enzyme for its transphosphatidylation activity, which enables the enzymatic synthesis of various phospholipids (PLs). Many reports exist on PLD-mediated synthesis of natural and tailor-made PLs with functional head groups, from easily available lecithin or phosphatidylcholine. Early studies on PLD-mediated synthesis mainly employed enzymes of plant origin, which were later supplanted by ones from microorganisms, especially actinomycetes. Many PLDs are members of the PLD superfamily, having one or two copies of a signature sequence, HxKxxxxD or HKD motif, in the primary structures. PLD superfamily members share a common core structure, and thereby, a common catalytic mechanism. The catalysis proceeds via two-step reaction with the formation of phosphatidyl-enzyme intermediate. Both of the two catalytic His residues are critical in the reaction course, where one acts as a nucleophile, while the other functions as a general acid/base. PLD is being engineered to improve its activity and stability, alter head group specificity and further identify catalytically important residues. Since the knowledge on PLD enzymology is constantly expanding, this review focuses on recent advances in the field, regarding PLD-catalyzed synthesis of bioactive PLs, deeper understanding of substrate recognition and binding mechanism, altering substrate specificity, and improving thermostability. We introduced some of our recent results in combination with existing facts to further deepen the story on the nature of this useful enzyme.