Metal ions and phosphatidylinositol 4,5-bisphosphate as interacting effectors of α-type plant phospholipase D.

Plant phospholipases D (PLD) are typically characterized by a C2 domain with at least two Ca2+ binding sites. In vitro, the predominantly expressed α-type PLDs need 20-100 mM CaCl2 for optimum activity, whereas the essential activator of ß- or γ-type PLDs, phosphatidylinositol 4,5-bisphosphate (PIP2), plays a secondary role. In the present paper, we have studied the interplay between PIP2 and metal ion activation of the well-known α-type PLD from cabbage (PLDα). With mixed micelles containing phosphatidyl-p-nitrophenol as substrate, PIP2-concentrations in the nanomolar range are able to activate the enzyme in addition to the essential Ca2+ activation. Mg2+ ions are able to replace Ca2+ ions but they do not activate PLDα. Rather, they abolish the activation of the enzyme by Ca2+ ions in the absence, but not in the presence, of PIP2. The presence of PIP2 causes a shift in the pH optimum of PLDα activity to the acidic range. Employing fluorescence measurements and replacing Ca2+ by Tb3+ ions, confirmed the presence of two metal ion-binding sites, in which the one of lower affinity proved crucial for PLD activation. Moreover, we have generated a homology model of the C2 domain of this enzyme, which was used for Molecular Dynamics (MD) simulations and docking studies. As is common for C2 domains, it shows two antiparallel ß-sheets consisting of four ß-strands each and loop regions that harbor two Ca2+ binding sites. Based on the findings of the MD simulation, one of the bound Ca2+ ions is coordinated by five amino acid residues. The second Ca2+ ion induces a loop movement upon its binding to three amino acid residues. Docking studies with PIP2 reveal, in addition to the previously postulated PIP2-binding site in the middle of the ß-sheet structure, another PIP2-binding site near the two Ca2+ ions, which is in accordance with the experimental interplay of PIP2, Ca2+ and Mg2+ ions.

Native state dynamics affects the folding transition of porcine pancreatic phospholipase A2.

Porcine pancreatic phospholipase A2, a small and disulfide rich protein, is extremely resistant against chemically or thermally induced unfolding. Despite this marked resistance, the protein displays broad unfolding transitions resulting in comparatively low apparent thermodynamic stability. Broad unfolding transitions may result from undetected folding intermediates, residual structures in the unfolded state or an inhomogeneity of the native state. Using circular dichroism, fluorescence, and NMR spectroscopy, we ruled out the existence of stably populated folding intermediates, whereas UV absorbance measurements hinted at stable residual structures in the unfolded state. These residual structures proved, however, to have no impact on the folding parameters. Studies by limited proteolysis, CD, and NMR spectroscopy under non-denaturing conditions suggested pronounced dynamics of the protein in the native state, which as long as unrestrained by acidic pH or bound Ca(2+) ions exert considerable influence on the unfolding transition.

Purification, sequencing and characterization of phospholipase D from Indian mustard seeds.

Phospholipase D (PLD; E.C. 3.1.4.4) is widespread in plants where it fulfills diverse functions in growth and in the response to stresses. The enzyme occurs in multiple forms that differ in their biochemical properties. In the present paper PLD from medicinally relevant Indian mustard seeds was purified by Ca(2+)-mediated hydrophobic interaction and anion exchange chromatography to electrophoretic homogeneity. Based on mass-spectrometric sequence analysis of tryptic protein fragments, oligonucleotide primers for cloning genomic DNA fragments that encoded the enzyme were designed and used to derive the complete amino acid sequence of this PLD. The sequence data, as well as the molecular properties (molecular mass of 92.0 kDa, pI 5.39, maximum activity at pH 5.5-6.0 and Ca(2+) ion concentrations ⩾60 mM), allowed the assignment of this enzyme to the class of α-type PLDs. The apparent kinetic parameters Vmax and Km, determined for the hydrolysis of phosphatidylcholine (PC) in an aqueous mixed-micellar system were 356±15 µmol min(-1) mg(-1) and 1.84±0.17 mM, respectively. Phosphate analogs such as NaAlF4 and Na3VO4 displayed strong inhibition of the enzyme. Phosphatidylinositol 4,5-bisphosphate had a strong activating effect at 2-10 mM CaCl2. PLD was inactivated at temperatures >45 °C. The enzyme exhibited the highest activity toward PC followed by phosphatidylethanolamine and phosphatidylglycerol. PCs with short-chain fatty acids were better substrates than PCs with long fatty acid chains. Lyso-PC was not accepted as substrate.

Phospholipase A(2)-catalyzed acylation of lysophospholipids analyzed by experimental design.

The catalytic potential of phospholipase A2 (PLA2) for the synthesis of phospholipids with defined fatty acid structure in the sn-2 position has been underestimated hitherto because of very low conversion in most organic solvents. One of the most suitable solvents for PLA2-catalyzed phospholipid synthesis is glycerol. With the aim to analyze the effect of several interacting reaction parameters on the product yield, we studied the conversion of 1-palmitoyl-2-lyso-sn-glycero-3-phosphocholine (lyso-PC) with oleic acid as model reaction in mixtures of glycerol and methanol or ethanol by methods of experimental design. PLA2 from porcine pancreas (ppPLA2) and from bee venom (bvPLA2) were compared as catalysts. For each of the four systems, nine variables were evaluated using Plackett-Burman designs. The most significant four variables were used for subsequent modified D-optimal designs with 30 runs, yielding regression equations for describing the formation of 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine as a function of the variables. In both solvent systems ppPLA2 was more appropriate for the acylation reaction than bvPLA2. Methanol proved to be more convenient as co-solvent than ethanol. The catalysis by ppPLA2 was more sensitive toward the variables temperature and concentration of Tris-HCl, whereas the reaction time and enzyme activity were more important in the acylation by bvPLA2. Conversion up to 87 (ppPLA2) and 50% (bvPLA2) can be anticipated.

Lanthanides as substitutes for calcium ions in the activation of plant α-type phospholipase D.

Most types of phospholipase D (PLD) from plants contain a C2 domain and are activated by Ca(2+) ions. In this study, other metal ions such as Mg(2+), La(3+), Ce(3+), Tb(3+) and Y(3+) were examined as effectors of recombinantly produced α-type PLD from white cabbage. All the rare earth ions were able to substitute for Ca(2+). The activation curves and displacement experiments reflect a 10- to 50-fold higher affinity of PLD for these ions than for Ca(2+); however, the maximum activity attained only 36% of that in the presence of Ca(2+). Mg(2+) displaced Ca(2+) without being able to activate PLD. All ions were bound to the substrate micelles consisting of phosphatidyl-p-nitrophenol, Triton X-100 and SDS (1:8:1, by mole). The affinity of rare earth ions to the micelles was 100-fold higher than that of Ca(2+) and Mg(2+). A conformational change of the enzyme induced by the low affinity but specific binding of Ca(2+) ions is concluded to be essential for maximal PLD activity. As demonstrated by the measurement of Tb(3+) fluorescence, the substitution of Ca(2+) by rare earth ions provides a new avenue for studying the enigmatic role of Ca(2+) ions in the modulation of PLD activity in plants.

Probing selected structural regions in the secreted phospholipase A2 from Arabidopsis thaliana for their impact on stability and activity.

In contrast to the well characterized secreted phospholipases A2 (sPLA2) from animals, their homologues from plants have been less explored. Their production in purified form is more difficult, and no data on their stability are known. In the present paper, different variants of the sPLA2 isoform α from Arabidopsis thaliana (AtPLA2α) were designed using a new homology model with the aim to probe the impact of regions that are assumed to be important for stability and catalysis. Moreover tryptophan residues were introduced in critical regions to enable stability studies by fluorescence spectroscopy. The variants were expressed in Escherichia coli and the purified enzymes were analyzed to get first insights into the peculiarities of structure stability and structure activity relationships in plant sPLA2s in comparison with the well-characterized homologous enzymes from bee venom and porcine pancreas. Stability data of the AtPLA2 variants obtained by fluorescence or CD measurements of the reversible unfolding by guanidine hydrochloride and urea showed that all enzyme variants are less stable than the enzymes from animal sources although a similar tertiary core structure can be assumed based on molecular modeling. More extended loop structures at the N-terminus in AtPLA2α are suggested to be the main reasons for the much lower thermodynamic stabilities and cooperativities of the transition curves. Modifications in the N-terminal region (insertion, deletion, substitution by a Trp residue) exhibited a strong positive effect on activity whereas amino acid exchanges in other regions of the protein such as the Ca(2+)-binding loop and the loop connecting the two central helices were deleterious with respect to activity.

Fe(III)-resorcylate as a spectrophotometric probe for phospholipid-cation interactions.

A simple spectrophotometric microplate assay that allows quantification of the interaction between phospholipids and metal ions or other small cationic compounds has been developed. The assay is based on the competition of the phospholipids for the Fe(3+) ion in the purple-colored Fe(III)-γ-resorcylate complex and for other cations. To compare the binding affinities of several cation-phospholipid interactions, K0.5 values were derived from binding curves constructed by determination of the absorbance of the Fe(III)-γ-resorcylate at 490 nm as a function of the cation concentration. The assay was used to analyze the binding of lanthanide ions, calcium ions, and amines (hydrochlorides of ethanolamine, spermidine, and hexyltrimethylammonium chloride) to small unilamellar vesicles (SUVs) and mixed micelles containing anionic lipids such as phosphatidic acid and phosphatidyl-p-nitrophenol. The method was evaluated by fluorescence measurements with Eu(3+) ions as tracer. Lanthanide ions such as La(3+) and Ce(3+) ions showed K0.5 values smaller by one to two orders of magnitude compared with Ca(2+) ions. In the presence of increasing amounts of detergents such as Triton X-100, the method also reflected transitions from SUVs to micelles. The binding capacity for metal ions was higher for phospholipid-containing micelles than for the corresponding SUVs.

Differences in the effect of phosphatidylinositol 4,5-bisphosphate on the hydrolytic and transphosphatidylation activities of membrane-bound phospholipase D from poppy seedlings.

The hydrolytic activity of phospholipase D (PLD) yielding phosphatidic acid from phosphatidylcholine and other glycerophospholipids is known to be involved in many cellular processes. In contrast, it is not clear whether the competitive transphosphatidylation activity of PLD catalyzing the head group exchange of phospholipids has a natural function. In poppy seedlings (Papaver somniferum L.) where lipid metabolism and alkaloid synthesis are closely linked, five isoenzymes with different substrate and hydrolysis/transphosphatidylation selectivities have been detected hitherto. A membrane-bound PLD, found in microsomal fractions of poppy seedlings, is active at micromolar concentrations of Ca(2+) ions and needs phosphatidylinositol 4,5-bisphosphate (PIP2) as effector in the hydrolysis of phosphatidylcholine (PC). The optimum PIP2 concentration at 1.2 mol% of the concentration of the substrate PC indicates a specific activation effect. Transphosphatidylation with glycerol, ethanolamine, l-serine, or myo-inositol as acceptor alcohols is also activated by PIP2, however, with an optimum concentration at 0.6-0.9 mol%. In contrast to hydrolysis, a basic transphosphatidylation activity occurs even in the absence of PIP2, suggesting a different fine-tuning of the two competing reactions.

New cardiolipin analogs synthesized by phospholipase D-catalyzed transphosphatidylation.

Cardiolipin (CL) and related diphosphatidyl lipids are hardly accessible because of the complexity of their chemical synthesis. In the present paper, the transphosphatidylation reaction catalyzed by phospholipase D (PLD) from Streptomyces sp. has been proven as an alternative enzyme-assisted strategy for the synthesis of new CL analogs. The formation of this type of compounds from phosphatidylcholine was compared for a series of N- and C2-substituted ethanolamine derivatives as well as non-charged alcohols such as glycerol and ethylene glycol. The rapid exchange of the choline head group by ethanolamine derivatives having a low molecular volume (diethanolamine and serinol) gave rise to an efficient production of the corresponding CL analogs. In contrast, the yields were comparably low in the reaction with bulky nitrogenous acceptor alcohols (triethanolamine, tris(hydroxymethyl)aminomethane, tetrakis(hydroxyethyl)ammonium) or the non-charged alcohols. Therefore, a strong dependence of the conversion of the monophosphatidyl to the diphosphatidyl compound on steric parameters and the head group charge was concluded. The enzyme-assisted strategy was used for the preparation of purified diphosphatidyldiethanolamine and diphosphatidylserinol.

Phospholipid acylhydrolases trigger membrane degradation during fungal sporogenesis.

Armillaria ostoyae is a phytopathogen infecting coniferous trees. Fruiting bodies of this basidiomycete contain high phospholipase A(1) (PLA(1)) activity. In this paper, the role of phospholipid-deacylating activity, which was also detected in fruiting bodies of other basidiomycetes, in the fungal lipid metabolism is elucidated. For A. ostoyae the occurrence of PLA(1) activity is shown to be restricted to the late reproductive phase, correlating with the release of mature spores. Specific expression in the spore-producing tissue provides evidence for the involvement of PLA(1) in spore formation. Based on lipid analysis, the degradation of membrane phospholipids in this tissue can be ascribed mainly to PLA(1) activity because other enzymes such as phospholipases C and D, triglyceride lipase and phosphatidic acid phosphatase had only low activities. A concomitant increase in the concentration of fatty acids and their anabolites (di- and triglycerides), which are used as storage lipids in the developing fungal spore cells, was observed. Therefore, PLA(1) contributes to the formation of spores by providing membrane constituents as a source of fatty acids.

Discrimination between the regioisomeric 1,2- and 1,3-diacylglycerophosphocholines by phospholipases.

The artificial 1,3-diacyl-glycero-2-phosphocholines (1,3-PCs), which form similar aggregate structures as the naturally occurring 1,2-diacyl-sn-glycero-3-phosphocholines (1,2-PCs), were tested as substrates for different classes of phospholipases such as phospholipase A(2) (PLA(2)) from porcine pancreas, bee and snake venom, and Arabidopsis thaliana, phospholipase C (PLC) from Bacillus cereus, and phospholipase D (PLD) from cabbage and Streptomyces species. The regioisomers of the natural phospholipids were shown to bind to all investigated phospholipases with an affinity similar to the corresponding naturally occurring phospholipids, however their hydrolysis was reduced to different degrees (PLA(2)s and PLC) or even abolished (PLDs belonging to the PLD superfamily). The results are in accordance with binding models obtained by docking the substrates to the crystal structures or homology models of the phospholipases.

Disulfide bonds of phospholipase A2 from bee venom yield discrete contributions to its conformational stability.

Disulfide bonds are known to be crucial for protein stability. To probe the contribution of each of the five disulfide bonds (C9-C31, C30-C70, C37-C63, C61-C95, and C105-C113) in bee venom phospholipase A(2) to stability, variants with deleted disulfide bonds were produced by substituting two serine residues for each pair of cysteine residues. The mutations started from the pseudo-wild-type variant (pWT) with the mutation I1A (Markert et al., Biotechnol. Bioeng. 98 (2007) 48-59). All variants were expressed in Escherichia coli, refolded from inclusion bodies and purified as pWT. The activity of the variants ranged from 12 to 82% of pWT. From the transition curves of guanidine hydrochloride-induced unfolding, the contributions of the individual disulfide bonds to conformational stability were estimated. They increased in the sequence C9-C31

The transphosphatidylation potential of a membrane-bound phospholipase D from poppy seedlings.

Plant phospholipases D (PLDs) occur in a large variety of isoenzymes, which differ in Ca(2+) ion requirement, phosphatidylinositol-4,5-bisphosphate (PIP(2)) activation and substrate selectivity. In the present study a membrane-bound PLD has been identified in the microsomal fractions of poppy seedlings (Papaver somniferum). The maximum PLD activity is found after 2 days of germination in endosperms and after 3 days in developing seedlings. In contrast to the four poppy PLD isoenzymes described hitherto, the membrane-bound form is active at lower Ca(2+) ion concentrations (in the micromolar instead of millimolar range) and needs PIP(2) for hydrolytic activity. Remarkable differences are also observed in head group exchange reactions. The reaction rates of the transphosphatidylation of phosphatidylcholine by various acceptor alcohols follow the sequence glycerol>serine>myo-inositol>ethanolamine, whereas ethanolamine is preferred by most other PLDs. Despite the biocatalytic differences, the membrane-bound PLD interacts with polyclonal antibodies raised against α-type PLD, which reveals some structural similarities between these two enzymes.

Crystal structure of RNase A tandem enzymes and their interaction with the cytosolic ribonuclease inhibitor.

Because of their ability to degrade RNA, RNases are potent cytotoxins. The cytotoxic activity of most members of the RNase A superfamily, however, is abolished by the cytosolic ribonuclease inhibitor (RI). RNase A tandem enzymes, in which two RNase A molecules are artificially connected by a peptide linker, and thus have a pseudodimeric structure, exhibit remarkable cytotoxic activity. In vitro, however, these enzymes are still inhibited by RI. Here, we present the crystal structures of three tandem enzymes with the linker sequences GPPG, SGSGSG, and SGRSGRSG, which allowed us to analyze the mode of binding of RI to the RNase A tandem enzymes. Modeling studies with the crystal structures of the RI-RNase A complex and the SGRSGRSG-RNase A tandem enzyme as templates suggested a 1 : 1 binding stoichiometry for the RI-RNase A tandem enzyme complex, with binding of the RI molecule to the N-terminal RNase A entity. These results were experimentally verified by analytical ultracentrifugation, quantitative electrophoresis, and proteolysis studies with trypsin. As other dimeric RNases, which are comparably cytotoxic, either evade RI binding or potentially even bind two RI molecules, inactivation by RI cannot be the crucial limitation to the cytotoxicity of dimeric RNases.

Impact of the C-terminal disulfide bond on the folding and stability of onconase.

The two homologous proteins ribonuclease A and onconase fold through conserved initial contacts but differ significantly in their thermodynamic stability. A disulfide bond is located in the folding initiation site of onconase (the C-terminal part of the protein molecule) that is missing in ribonuclease A, whereas the other three disulfide bonds of onconase are conserved in ribonuclease A. Consequently, the deletion of this C-terminal disulfide bond (C87-C104) allows the impact of the contacts in this region on the folding of onconase to be studied. We found the C87A/C104A-onconase variant to be less active and less stable than the wild-type protein, whereas the tertiary structure, which was determined by both X-ray crystallography and NMR spectroscopy, was only marginally affected. The folding kinetics of the variant, however, were found to be changed considerably in comparison to wild-type onconase. Proton exchange experiments in combination with two-dimensional NMR spectroscopy revealed differences in the native-state dynamics of the two proteins in the folding initiation site, which are held responsible for the changed folding mechanism. Likewise, the molecular dynamics simulation of the unfolding reaction indicated disparities for both proteins. Our results show that the high stability of onconase is based on the efficient stabilization of the folding initiation site by the C-terminal disulfide bond. The formation of the on-pathway intermediate, which is detectable during the folding of the wild-type protein and promotes the fast and efficient refolding reaction, requires the presence of this covalent bond.

Refolding of the non-specific neutral protease from Bacillus stearothermophilus proceeds via an autoproteolytically sensitive intermediate.

A very thermostable variant of the thermolysin-like protease from Bacillus stearothermophilus (G8C/N60C) was previously created by introduction of a disulfide bond into the cysteine-free pseudo-wild type variant (pWT) and thus fixing the unfolding region 56-69. In the present paper, we show that G8C/N60C and pWT can be reactivated from the completely unfolded states, accessible at >or=7.5M guanidine hydrochloride, and analyze the kinetics of folding, autoproteolytic degradation and aggregation. From changes in the fluorescence spectra with time of renaturation, it can be concluded that a folding intermediate with native-like structure, but which is still inactive and sensitive to autoproteolysis, is rapidly formed after renaturation has initiated. The critical region 56-69 of pWT is involved in the autoproteolytic sensitivity of the intermediate as we conclude from the differences in the chevron plots of the first-order rate constants of reactivation and the fragmentation patterns in SDS-PAGE of pWT and G8C/N60C.

The folding pathway of onconase is directed by a conserved intermediate.

A promising approach to unravel the relationship between sequence information, tertiary structure, and folding mechanism of proteins is the analysis of the folding behavior of proteins with low sequence identity but comparable tertiary structures. Ribonuclease A (RNase A) and its homologues, forming the RNase A superfamily, provide an excellent model system for respective studies. RNase A has been used extensively as a model protein for folding studies. However, little is known about the folding of homologous RNases. Here, we analyze the folding pathway of onconase, a homologous protein from the Northern leopard frog with great potential as a tumor therapeutic, by high-resolution techniques. Although onconase and RNase A significantly differ in the primary structure (28% sequence identity) and in thermodynamic stability (DeltaDeltaG = 20 kJ mol(-1)), both enzymes possess very similar tertiary structures. The present folding studies on onconase by rapid mixing techniques in combination with fluorescence and NMR spectroscopy allow the structural assignment of the three kinetic phases observed in stopped-flow fluorescence spectroscopy. After a slow peptidyl-prolyl cis-to-trans isomerization reaction in the unfolded state, ONC folds via an on-pathway intermediate to the native state. By quenched-flow hydrogen/deuterium exchange experiments coupled with 2D NMR spectroscopy, 31 amino acid residues were identified to be involved in the structure formation of the intermediate. Twelve of these residues are identical in the RNase A sequence, which is a significantly higher percentage (39%) than the overall 28% sequence identity. Moreover, the structure of this intermediate closely resembles two of the intermediates that occur early during the refolding of RNase A. Obviously, in spite of considerable differences in their amino acid sequence the initial folding events of both proteins are comparable, guided by a limited number of conserved residues.

Spectrophotometric determination of phosphatidic acid via iron(III) complexation for assaying phospholipase D activity.

The ability of negatively charged phosphatidates to form complexes with Fe(3+) ions was used to design a simple spectrophotometric assay for the quantitative determination of phosphatidic acid (PA). In the reaction with the purple iron(III)-salicylate, PA extracts Fe(3+) ions and decreases the absorbance at 490 nm. Lower competition with salicylate for Fe(3+) ions was observed with single negatively charged phosphatidates such as phosphatidylglycerol (PG), whereas neutral phosphatidates such as phosphatidylcholine (PC) and phosphatidylethanolamine (PE) showed no influence on the absorbance of the iron(III) complex. The detection limit of the method on a microplate scale was 10 microM PA. Based on these results, an assay for determining the activity of phospholipase D (PLD) toward natural phospholipids such as PC, PE, and PG was developed. In contrast to other spectroscopic PLD assays, this method is able to determine PLD activity toward different lipids or even lipid mixtures.

Modulation of phospholipase D activity in vitro.

Most phospholipases D (PLDs) occurring in microorganisms, plants and animals belong to a superfamily which is characterized by several conserved regions of amino acid sequence including the two HKD motifs necessary for catalytic activity. Most eukaryotic PLDs possess additional regulatory structures such as the Phox and Pleckstrin homology domains in mammalian PLDs and the C2 domain in most plant PLDs. Owing to recombinant expression techniques, an increasing number of PLDs from different organisms has been obtained in purified form, allowing the investigation of specific and unspecific interactions of the enzymes with regulatory components in vitro. The present paper gives an overview on different factors which can modulate PLD activity and compares their influence on the enzymes from different sources. While no biological regulator can be recognized for extracellular bacterial PLDs, the most prominent specific activator of eukaryotic PLDs is phosphatidylinositol-4,5-bisphosphate (PIP(2)). In a sophisticated interplay PIP(2) seems to cooperate with several regulatory proteins in mammalian PLDs, whereas in plant PLDs it mainly acts in concert with Ca(2+) ions. Moreover, curvature, charges and heterogeneities of membrane surfaces are assessed as unspecific modulators. A possible physiological role of the transphosphatidylation reaction catalyzed by PLDs in competition with phospholipid hydrolysis is discussed.