Pancreatic phospholipase A(2): new views on old issues

Insight into the Functional Diversification of Lipases in the Endoparasitoid Pteromalus puparum (Hymenoptera: Pteromalidae) by Genome-scale Annotation and Expression Analysis

Lipases play essential roles in digestion, transport, and processing of dietary lipids in insects. For parasitoid wasps with a unique life cycle, lipase functions could be multitudinous in particular. Pteromalus puparum is a pupal endoparasitoid of butterflies. The female adult deposits eggs into its host, along with multifunctional venom, and the developing larvae consume host as its main nutrition source. Parasitoid lipases are known to participate in the food digestion process, but the mechanism remains unclear. P. puparum genome and transcriptome data were interrogated. Multiple alignments and phylogenetic trees were constructed. We annotated a total of 64 predicted lipase genes belonging to five lipase families and suggested that eight venom and four salivary lipases could determine host nutrition environment post-parasitization. Many putative venom lipases were found with incomplete catalytic triads, relatively long β9 loops, and short lids. Data analysis reveals the loss of catalytic activities and weak triacylglycerol (TAG) hydrolytic activities of lipases in venom. Phylogenetic trees indicate various predicted functions of lipases in P. puparum. Our information enriches the database of parasitoid lipases and the knowledge of their functional diversification, providing novel insight into how parasitoid wasps manipulate host lipid storage by using venom lipases.

Tailoring the pH dependence of human non-pancreatic secretory phospholipase A2 by engineering surface charges

Human non-pancreatic secretory phospholipase A2 (hnpsPLA2) catalyzes the sn-2 acyl hydrolysis of phospholipids. It was reported that hnpsPLA2 is involved in various diseases like inflammation, cancer, and so on. This enzyme also exhibits anti-bacterial and anti-virus activities. It is active over a broad pH range, with higher activity at alkaline conditions. In order to make it suitable as a potential bactericide, high activity at neutral pH is preferable. We have tried to tailor the pH dependence of hnpsPLA2 activity by replacing its surface charged residues. Three surface charge replacements, Arg42Glu, Arg100Glu, and Glu89Lys, showed increased activities at neutral pH, which are 2.3, 2.8, and 2.3 times that of the wild-type enzyme at pH 7. Both the positive-to-negative and negative-to-positive mutations lowered the optimum enzymatic reaction pH of hnpsPLA2, indicating that the enzyme pH profile depends on a delicate balance of charged residues. The activity changes are in good agreement with the recently proposed calcium-coordinated catalytic triad mechanism. This study also provides a general means of enhancing hnpsPLA2 activity at low pH.

Secretory phospholipase A2 activity toward diverse substrates

We have studied secretory phospholipase A(2)-IIA (sPLA(2)) activity toward different phospholipid analogues by performing biophysical characterizations and molecular dynamics simulations. The phospholipids were natural substrates, triple alkyl phospholipids, a prodrug anticancer etherlipid, and an inverted ester. The latter were included to study head group-enzyme interactions. Our simulation results show that the lipids are optimally placed into the binding cleft and that water molecules can freely reach the active site through a well-defined pathway; both are indicative that these substrates are efficiently hydrolyzed, which is in good agreement with our experimental data. The phospholipid analogue with three alkyl side chains forms aggregates of different shapes with no well-defined sizes due to its cone-shape structure. Phosphatidylglycerol and phosphatidylcholine head groups interact with specific charged residues, but relatively large fluctuations are observed, suggesting that these interactions are not necessarily important for stabilizing substrate binding to the enzyme.

Phosphatidylcholine as a constituent in the colonic mucosal barrier--physiological and clinical relevance

Phosphatidylcholine (PC) is an important constituent of the gastrointestinal tract. PC molecules are not only important in intestinal cell membranes but also receiving increasing attention as protective agents in the gastrointestinal barrier. They are largely responsible for establishing the hydrophobic surface of the colon. Decreased phospholipids in colonic mucus could be linked to the pathogenesis of ulcerative colitis, a chronic inflammatory bowel disease. Clinical studies revealed that therapeutic addition of PC to the colonic mucus of these patients alleviated the inflammatory activity. This positive role is still elusive, however, we hypothesized that luminal PC has two possible functions: first, it is essential for surface hydrophobicity, and second, it is integrated into the plasma membrane of enterocytes and it modulates the signaling state of the mucosa. The membrane structure and lipid composition of cells is a regulatory component of the inflammatory signaling pathways. In this perspective, we will shortly summarize what is known about the localization and protective properties of PC in the colonic mucosa before turning to its evident medical importance. We will discuss how PC contributes to our understanding of the pathogenesis of ulcerative colitis and how reinforcing the luminal phospholipid monolayer can be used as a therapeutic concept in humans.

Comparative and functional genomics of lipases in holometabolous insects

Lipases have key roles in insect lipid acquisition, storage and mobilisation and are also fundamental to many physiological processes underpinning insect reproduction, development, defence from pathogens and oxidative stress, and pheromone signalling. We have screened the recently sequenced genomes of five species from four orders of holometabolous insects, the dipterans Drosophila melanogaster and Anopheles gambiae, the hymenopteran Apis mellifera, the moth Bombyx mori and the beetle Tribolium castaneum, for the six major lipase families that are also found in other organisms. The two most numerous families in the insects, the neutral and acid lipases, are also the main families in mammals, albeit not in Caenorhabditis elegans, plants or microbes. Total numbers of the lipases vary two-fold across the five insect species, from numbers similar to those in mammals up to numbers comparable to those seen in C. elegans. Whilst there is a high degree of orthology with mammalian lipases in the other four families, the great majority of the insect neutral and acid lipases have arisen since the insect orders themselves diverged. Intriguingly, about 10% of the insect neutral and acid lipases have lost motifs critical for catalytic function. Examination of the length of lid and loop regions of the neutral lipase sequences suggest that most of the insect lipases lack triacylglycerol (TAG) hydrolysis activity, although the acid lipases all have intact cap domains required for TAG hydrolysis. We have also reviewed the sequence databases and scientific literature for insights into the expression profiles and functions of the insect neutral and acid lipases and the orthologues of the mammalian adipose triglyceride lipase which has a pivotal role in lipid mobilisation. These data suggest that some of the acid and neutral lipase diversity may be due to a requirement for rapid accumulation of dietary lipids. The different roles required of lipases at the four discrete life stages of holometabolous insects may also contribute to the diversity of lipases required by insects. In addition, insects use lipases to perform roles for which there are no correlates in mammals, including as yolk and male accessory gland proteins.

Allosteric effect of amphiphile binding to phospholipase A(2)

In the preceding paper, we showed that the formation of the second premicellar complex of pig pancreatic IB phospholipase A2 (PLA2) can be considered a proxy for interface-activated substrate binding. Here we show that this conclusion is supported by results from premicellar E(i)(#) (i = 1, 2, or 3) complexes with a wide range of mutants of PLA2. Results also show a structural basis for the correlated functional changes during the formation of E(2)(#), and this is interpreted as an allosteric T (inactive) to R (active) transition. For example, the dissociation constant K(2)(#) for decylsulfate bound to E(2)(#) is lower at lower pH, at higher calcium concentrations, or with an inhibitor bound to the active site. Also, the lower limits of the K(2)(#) values are comparable under these conditions. The pH-dependent increase in K(2)(#) with a pK(a) of 6.5 is attributed to E71 which participates in the binding of the second calcium which in turn influences the enzyme binding to phosphatidylcholine interface. Most mutants exhibited kinetic and spectroscopic behavior that is comparable to that of native PLA2 and DeltaPLA2 with a deleted 62-66 loop. However, the DeltaY52L substitution mutant cannot undergo the calcium-, pH-, or interface-dependent changes. We suggest that the Y52L substitution impairs the R to T transition and also hinders the approach of the Michaelis complex to the transition state. This allosteric change may be mediated by the structural motifs that connect the D48-D99 catalytic diad, the substrate-binding slot, and the residues of the i-face. Our interpretation is that the 57-72 loop and the H(48)DNCY(52) segment of PLA2 are involved in transmitting the effect of the cooperative amphiphile binding to the i-face as a structural change in the active site.

A micelle nucleation model for the interaction of dodecyl sulphate with Lys49–phospholipases A2

Bothropstoxin-I (BthTx-I) is a Lys49-PLA(2) from the venom of Bothrops jararacussu that lacks detectable catalytic activity, yet causes rapid Ca(2+)-independent membrane damage. With the aim of understanding the interaction between BthTx-I and amphiphilic molecules, we have studied the interaction of sodium dodecyl sulphate (SDS) with the protein. Circular dichroism and attenuated total reflection Fourier-transform infrared spectra of BthTx-I reveal changes in the alpha-helical organization of the protein at an SDS/BthTx-I molar ratio of 20-25. At SDS/BthTx-I ratios of 40-45 the alpha-helices return to a native-like conformation, although fluorescence emission anisotropy measurements of 2-amino-N-hexadecyl-benzamide (AHBA) demonstrate that the total SDS is below the critical micelle concentration when this transition occurs. These results may be interpreted as the result of SDS accumulation by the BthTx-I homodimer and the formation of a pre-micelle SDS/BthTx-I complex, which may subsequently be released from the protein surface as a free micelle. Similar changes in the alpha-helical organization of BthTx-I were observed in the presence of dipalmitoylphosphatidylcholine liposomes, suggesting that protein structure transitions coupled to organization changes of bound amphiphiles may play a role in the Ca(2+)-independent membrane damage by Lys49-PLA(2)s.

Desolvation map of the i-face of phospholipase A2

The changes in the microenvironment of the Trp-3 on the i-face of pig pancreatic IB phospholipase A2 (PLA2) provide a measure of the tight contact (Ramirez and Jain, Protein Sci. 9, 229-239, 1991) with the substrate interface during the processive interfacial turnover. Spectral changes from the single Trp-substituent at position 1, 2, 6, 10, 19, 20, 31, 53, 56 or 87 on the surface of W3F PLA2 are used to probe the Trp-environment. Based on our current understanding only the residue 87 is away from i-face, therefore all other mutants are well suited to report modest differences along the i-face. All Trp-mutants bind tightly to anionic vesicles. Only those with Trp at 1, 2 or 3 near the rim of the active site on the i-face cause significant perturbation of the catalytic functions. Most other Trp-mutants showed < 3-fold change in the interfacial processive turnover rate and the competitive inhibition by MJ33. Binding of calcium to the enzyme in the aqueous phase had modest effect on the Trp-emission intensity. However, on the binding of the enzyme to the interface the fluorescence change is large, and the rate of oxidation of the Trp-substituent with N-bromosuccinimide depends on the location of the Trp-substituent. These results show that the solvation environment of the Trp-substituents on the i-face is shielded in the enzyme bound to the interface. Additional changes are noticeable if the active site of the bound enzyme is also occupied, however, the catalytically inert zymogen of PLA2 (proPLA2) does not show such changes. Significance of these results in relation to the changes in the solvent accessibility and desolvation of the i-face of PLA2 at the interface is discussed.

Investigating porcine pancreatic phospholipase A2 action on vesicles and supported planar bilayers using a quartz crystal microbalance with dissipation

We present an investigation of the activity of porcine pancreatic phospholipase A2 towards phospholipids. The phospholipids are presented in three different ways, namely as tethered vesicles, intact surface-bound vesicles, and supported planar bilayers (SPBs). The process is followed using a quartz crystal microbalance which measures both the frequency shift and the energy dissipation factor. This technique is very sensitive not only to the mass of the material deposited on the crystal, but also to its viscoelasticity. The breakdown of the phospholipid vesicles and bilayers consequently gives rise to very large signal changes. Enzyme binding is separated from vesicle hydrolysis using nonhydrolyzable ether lipids. Intact and tethered vesicles give rise to the same profile, indicating that direct immobilization of the vesicles does not affect hydrolysis significantly. The data fit well to a Voight-based model describing the change in film structure with time. Initial enzyme binding to intact vesicles is accompanied by a significant increase in layer thickness as well as a decrease in viscosity and shear modulus. This effect, which is less pronounced in SPBs, is probably mainly due to the accumulation of hydrolysis products in the vesicle prior to rupture of the vesicles and release of bound water, since it disappears when lysolipid is included in the vesicles prior to hydrolysis.

Activation of Ca2+-independent membrane-damaging activity in Lys49–phospholipase A2 promoted by amphiphilic molecules

Association of class-II phospholipase A(2) (PLA(2)) with aggregated phospholipid substrate results in elevated levels of the Ca(2+)-dependent hydrolytic activity. The Asp49 residue participates in coordination of the Ca(2+) ion cofactor, however, in Lys49-PLA(2) homologues (Lys49-PLA(2)s), substitution of the Asp49 by Lys results in loss of Ca(2+) binding and lack of detectable phospholipid hydrolysis. Nevertheless, Lys49-PLA(2)s cause Ca(2+)-independent damage of liposome membranes. Bothropstoxin-I is a homodimeric Lys49-PLA(2) from the venom of Bothrops jararacussu, and in fluorescent marker release and dynamic light scattering experiments with DPPC liposomes we demonstrate activation of the Ca(2+)-independent membrane damaging activity by approximately 4 molecules of sodium dodecyl sulphate (SDS) per protein monomer. Activation is accompanied by significant changes in the intrinsic tryptophan fluorescence emission (ITFE) and near UV circular dichroism (UVCD) spectra of the protein. Subsequent binding of 7-10 SDS molecules results in further alterations in the ITFE and far UVCD spectra. Reduction in the rate of N-bromosuccinimide modification of Trp77 at the dimer interface suggests that initial binding of SDS to this region accompanies the activation of the membrane damaging activity. 1-anilinonaphthalene-8-sulphonic acid binding studies indicate that subsequent SDS binding to the active site is concomitant with the second structural transition. These results provide insights in the structural basis of amphiphile/protein coupling in class-II PLA(2)s.

Mapping structural determinants of biological activities in snake venom phospholipases A2 by sequence analysis and site directed mutagenesis

In addition to their catalytic activity, snake venom phospholipases A2 (vPLA2) present remarkable diversity in their biological effects. Sequence alignment analyses of functionally related PLA2 are frequently used to predict the structural determinants of these effects, and the predictions are subsequently evaluated by site directed mutagenesis experiments and functional assays. In order to improve the predictive potential of computer-based analysis, a simple method for scanning amino acid variation analysis (SAVANA) has been developed and included in the analysis of the lysine 49 PLA2 myotoxins (Lys49-PLA2). The SAVANA analysis identified positions in the C-terminal loop region of the protein, which were not identified using previously available sequence analysis tools. Site directed mutagenesis experiments of bothropstoxin-I, a Lys49-PLA2 isolated from the venom of Bothrops jararacussu, reveals that these residues are exactly those involved in the determination of myotoxic and membrane damaging activities. The SAVANA method has been used to analyse presynaptic neurotoxic and anti-coagulant vPLA2s, and the predicted structural determinants of these activities are in excellent agreement with the available results of site directed mutagenesis experiments. The positions of residues involved in the myotoxic and neurotoxic determinants demonstrate significant overlap, suggesting that the multiple biological effects observed in many snake vPLA2s are a consequence of superposed structural determinants on the protein surface.

Enzymatic catalysis via liquid-liquid interfaces

Enzymes acting in a biphasic liquid of water and organic solvent may show catalytic activity dependent on the amount of phase interface available. Such an effect may be caused by several mechanisms. For example, for hydroxynitrile lyase from Prunus amygdalus, substrate mass transfer limitation has been advocated, but also adsorption of the enzyme on the interface. In this commentary it is shown that often these two mechanisms will have qualitatively similar consequences. The reaction rate will be influenced by the organic substrate concentration, by the initial enzyme concentration, and by the volume-specific interfacial area, and these influences will be linear at low values but reach a saturation level at high values. To rule out any of the models, their quantitative mathematical descriptions should be compared, taking into account that both models may be valid simultaneously.

A low-barrier hydrogen bond between histidine of secreted phospholipase A2 and a transition state analog inhibitor

This work describes in-depth NMR characterization of a unique low-barrier hydrogen bond (LBHB) between an active site residue from the enzyme and a bound inhibitor: the complex between secreted phospholipase A(2) (sPLA(2), from bee venom and bovine pancreas) and a transition-state analog inhibitor HK32. A downfield proton NMR resonance, at 17-18 ppm, was observed in the complex but not in the free enzyme. On the basis of site-specific mutagenesis and specific 15N-decoupling, this downfield resonance was assigned to the active site H48, which is part of the catalytic dyad D99-H48. These results led to a hypothesis that the downfield resonance represents the proton (H(epsilon 2) of H48) involved in the H-bonding between D99 and H48, in analogy with serine proteases. However, this was shown not to be the case by use of the bovine enzyme labeled with specific [15N(epsilon 2)]His. Instead, the downfield resonance arises from H(delta1) of H48, which forms a hydrogen bond with a non-bridging phosphonate oxygen of the inhibitor. Further studies showed that this proton displays a fractionation factor of 0.62(+/-0.06), and an exchange rate protection factor of >100 at 285 K and >40 at 298 K, which are characteristic of a LBHB. The pK(a) of the imidazole ring of H48 was shown to be shifted from 5.7 for the free enzyme to an apparent value of 9.0 in the presence of the inhibitor. These properties are very similar to those of the Asp em leader His LBHBs in serine proteases. Possible structural bases and functional consequences for the different locations of the LBHB between these two types of enzymes are discussed. The results also underscore the importance of using specific isotope labeling, rather than extrapolation of NMR results from other enzyme systems, to assign the downfield proton resonance to a specific hydrogen bond. Although our studies did not permit the strength of the LBHB to be accurately measured, the data do not provide support for an unusually strong hydrogen bond strength (i.e. >10 kcal/mol).

Different modulation of phospholipase A2 activity by saturated and monounsaturated N-acylethanolamines

The physiological functions of N-acylethanolamines (NAEs) are poorly understood, although many functions were suggested for these naturally occurring membrane components of plants and animals. The binding with cannabinoid receptors CB1 and CB2 was demonstrated for some NAEs, such as anandamide. However, the chemical nature of these molecules suggests that some of their biological effects on biomembranes could be related, at least partially, to physical interactions with the lipid bilayer. The present work studies the effect of saturated and monounsaturated NAEs on phospholipase A2 (PLA2) activity, which is dependent on lipid bilayer features. The present study, performed by 2-dimethylamino-(6-lauroyl)-naphthalene (Laurdan) fluorescence, demonstrates that the acyl chain length and the presence of a single double bond are crucial for the enzymatic activity modulation by NAEs. In fact, saturated NAEs with 10 carbon atoms don't affect the PLA2 activity, while NAEs with 12 and 16 carbon atoms largely activate the enzyme. On the other hand, an acyl chain length of 18 carbon atoms, with or without the presence of a double bond, only slightly affects the enzymatic activity. A structural model for NAE-lipid interactions is proposed in order to explain the differences in PLA2 activity modulation by these fatty acid derivatives.

A novel phospholipase A(2) from the venom glands of Bungarus candidus: cloning and sequence-comparison

The presence of phospholipase A(2) (PLA(2)) in the venom of Malayan krait (Bungarus candidus) and its structure were studied. The PLA(2) cDNAs from the venom gland of B. candidus (Indonesia origin) were amplified by the polymerase chain reactions (PCR) and cloned. The primers used were based on the cDNA sequences of several homologous B. multicinctus venom PLA(2)s. In addition to the A-chains of beta-bungarotoxins, a novel B. candidus PLA(2) was cloned and its full amino acid sequence deduced. Having totally 125 amino acid residues, the PLA(2) contains a pancreatic loop and is 61% identical to the acidic PLA(2) of king cobra venom. However, the enzyme was not detected from the venom sample. Its structural relationships to other elapid venom PLA(2)s were analyzed with a phylogenetic tree and discussed.

Identification of essential acidic residues of outer membrane protease OmpT supports a novel active site

Escherichia coli outer membrane protease OmpT has previously been classified as a serine protease with Ser(99) and His(212) as active site residues. The recently solved X-ray structure of the enzyme was inconsistent with this classification, and the involvement of a nucleophilic water molecule was proposed. Here, we substituted all conserved aspartate and glutamate residues by alanines and measured the residual enzymatic activities of the variants. Our results support the involvement of a nucleophilic water molecule that is activated by the Asp(210)/His(212) catalytic dyad. Activity is also strongly dependent on Asp(83) and Asp(85). Both may function in binding of the water molecule and/or oxyanion stabilization. The proposed mechanism implies a novel proteolytic catalytic site.

On the role of conserved histidine 106 in 10-formyltetrahydrofolate dehydrogenase catalysis: connection between hydrolase and dehydrogenase mechanisms

The enzyme, 10-formyltetrahydrofolate dehydrogenase (FDH), converts 10-formyltetrahydrofolate (10-formyl-THF) to tetrahydrofolate in an NADP(+)-dependent dehydrogenase reaction or an NADP(+)-independent hydrolase reaction. The hydrolase reaction occurs in a 310-amino acid long amino-terminal domain of FDH (N(t)-FDH), whereas the dehydrogenase reaction requires the full-length enzyme. The amino-terminal domain of FDH shares some sequence identity with several other enzymes utilizing 10-formyl-THF as a substrate. These enzymes have two strictly conserved residues, aspartate and histidine, in the putative catalytic center. We have shown recently that the conserved aspartate is involved in FDH catalysis. In the present work we studied the role of the conserved histidine, His(106), in FDH function. Site-directed mutagenesis experiments showed that replacement of the histidine with alanine, asparagine, aspartate, glutamate, glutamine, or arginine in N(t)-FDH resulted in expression of insoluble proteins. Replacement of the histidine with another positively charged residue, lysine, produced a soluble mutant with no hydrolase activity. The insoluble mutants refolded from inclusion bodies adopted a conformation inherent to the wild-type N(t)-FDH, but they did not exhibit any hydrolase activity. Substitution of alanine for three non-conserved histidines located close to the conserved one did not reveal any significant changes in the hydrolase activity of N(t)-FDH. Expressed full-length FDH with the substitution of lysine for the His(106) completely lost both the hydrolase and dehydrogenase activities. Thus, our study showed that His(106), besides being an important structural residue, is also directly involved in both the hydrolase and dehydrogenase mechanisms of FDH. Modeling of the putative hydrolase catalytic center/folate-binding site suggested that the catalytic residues, aspartate and histidine, are unlikely to be adjacent to the catalytic cysteine in the aldehyde dehydrogenase catalytic center. We hypothesize that 10-formyl-THF dehydrogenase reaction is not an independent reaction but is a combination of hydrolase and aldehyde dehydrogenase reactions.

Cloning and recombinant expression of a structurally novel human secreted phospholipase A2

Mammals contain a diverse set of secreted phospholipases A(2) (sPLA(2)s) that liberate arachidonic acid from phospholipids for the production of eicosanoids and exert a variety of physiological and pathological effects. We report the cloning, recombinant expression, and kinetic properties of a novel human sPLA(2) that defines a new structural class of sPLA(2)s called group XII. The human group XII (hGXII) cDNA contains a putative signal peptide of 22 residues followed by a mature protein of 167 amino acids that displays homology to all known sPLA(2)s only over a short stretch of amino acids in the active site region. Northern blot and reverse transcription-polymerase chain reaction analyses show that the tissue distribution of hGXII is distinct from the other human sPLA(2)s with strong expression in heart, skeletal muscle, kidney, and pancreas and weaker expression in brain, liver, small intestine, lung, placenta, ovaries, testis, and prostate. Catalytically active hGXII was produced in Escherichia coli and shown to be Ca(2+)-dependent despite the fact that it is predicted to have an unusual Ca(2+)-binding loop. Similar to the previously characterized mouse group IIE sPLA(2)s, the specific activity of hGXII is low in comparison to that of other mammalian sPLA(2), suggesting that hGXII could have novel functions that are independent of its phospholipase A(2) activity.