Roles of catalytic domain residues in interfacial binding and activation of group IV cytosolic phospholipase A2

Group IV cytosolic phospholipase A(2) (cPLA(2)) has been shown to play a critical role in eicosanoid biosynthesis. cPLA(2) is composed of the C2 domain that mediates the Ca(2+)-dependent interfacial binding of protein and the catalytic domain. To elucidate the mechanism of interfacial activation of cPLA(2), we measured the effects of mutations of selected ionic and hydrophobic residues in the catalytic domain on the enzyme activity and the membrane binding of cPLA(2). Mutations of anionic residues located on (Glu(419) and Glu(420)) or near (Asp(436), Asp(438), Asp(439), and Asp(440)) the active site lid enhanced the affinity for cPLA(2) for anionic membranes, implying that the electrostatic repulsion between these residues and the anionic membrane surface might trigger the opening of the active site. This notion is further supported by a biphasic dependence of cPLA(2) activity on the anionic lipid composition of the vesicles. Mutations of a cluster of cationic residues (Lys(541), Lys(543), Lys(544), and Arg(488)), while significantly enhancing the activity of enzyme, abrogated the specific activation effect by phosphatidylinositol 4,5-bisphosphate (PtdIns(4,5)P(2)). These data, in conjunction with cell activity of cPLA(2) and mutants transfected into HEK293 cells, suggest that the cationic residues form a specific binding site for PtdIns(4,5)P(2) and that the specific PtdIns(4,5)P(2) binding is involved in cellular activation of cPLA(2). Also, three hydrophobic residues at the rim of the active site (Ile(399), Leu(400), and Leu(552)) were shown to partially penetrate the membrane, thereby promoting membrane binding and activation of cPLA(2). Based on these results, we propose an interfacial activation mechanism for cPLA(2) which involves the removal of the active site lid by nonspecific electrostatic repulsion, the interdomain hinge movement induced by specific PtdIns(4,5)P(2) binding, and the partial membrane penetration by catalytic domain hydrophobic residues.     

A structural determinant of the unique interfacial binding mode of bovine pancreatic phospholipase A2.

The catalytic steps of the phospholipase A2 (PLA2)-catalyzed hydrolysis of phospholipids are preceded by interfacial binding. Among various pancreatic PLA2s, bovine pancreatic PLA2 (bpPLA2) has a unique interfacial binding mode in which Lys-56 plays an important role in its binding to anionic lipid surfaces. To identify the structural determinant of this unique interfacial binding mode of bpPLA2, we systematically mutated bpPLA2 and measured the effects of mutations on its interfacial binding and activity. First, different cationic clusters were generated in the amino-terminal alpha-helix by the N6R, G7K, and N6R/G7K mutations. These mutations enhanced the binding of bpPLA2 to anionic liposomes up to 15-fold. For these mutants, however, the K56E mutation still caused a large drop in interfacial affinity for and activity toward anionic liposomes, indicating that the generation of a cationic patch in the amino-terminal alpha-helix of bpPLA2 did not change its interfacial binding mode. Second, residues 62-66 that form a part of the pancreatic loop were deleted. For this deletion mutant (Delta62-66), which was as active as wild-type toward anionic liposomes, the K56E and K116E mutations (Delta62-66/K56E and Delta62-66/K116E) did not have significant effects on interfacial affinity. In contrast, the K10E mutation showed a much larger decrease in interfacial affinity (10-fold), indicating the deletion of residues 62-66 caused a major change in the interfacial binding mode. Finally, hydrophobic residues in positions 63 and 65 were replaced by bulkier ones (V63F and V63F/V65L) to pinpoint the structural determinant of the interfacial binding mode of bpPLA2. The effects of K10E and K56E mutations on the interfacial affinity and activity of these mutants showed that Val-63 and Val-65 of bpPLA2 are the structural determinant of its unique interfacial binding mode and that relatively conservative substitutions at these positions result in large changes in the interfacial binding mode among mammalian pancreatic PLA2s. Taken together, this study reveals how minor structural differences among homologous PLA2s can lead to distinct interfacial binding behaviors.     

The interfacial binding surface of phospholipase A2s

For membrane-associated enzymes, which access substrate from either a monolayer or bilayer of the aggregate substrate, the partitioning from the aqueous phase to this phospholipid interface is critical for catalysis. Despite a large and expanding body of knowledge regarding interfacial enzymes, the biophysical steps involved in interfacial recognition and adsorption remain relatively poorly understood. The surface of the enzyme that contacts the phospholipid surface is referred to as its interfacial binding surface, or more simply, its i-face. The interaction of a protein's i-face with the aggregate substrate may simply control access to substrate. However, it can be more complex, and this interaction often serves to allosterically activate the enzyme on this surface. First we briefly review what is currently known about i-face structure and function for a prototypical interfacial enzyme, the secreted Phospholipase A2 (PLA2). Then we develop, characterize, compare, and discuss models of the PLA2 i-face across a subset of five homologous PLA2 family members, groups IA, IB, IIA, V, and X. A homology model of human group-V is included in this comparison, suggesting that a similar approach could be used to explore interfacial function of any of the PLA2 family members. Despite moderate sequence identity, structural homology and sequence similarity are well conserved. We find that the residues predicted to be interfacial, while conserved structurally, are not highly conserved in sequence. Implications for this divergence on interfacial selectivity are discussed.     

Role of tryptophan residues in interfacial binding of phosphatidylinositol-specific phospholipase C

The phosphatidylinositol-specific phospholipase C (PI-PLC) from Bacillus thuringiensis exhibits several types of interfacial activation. In the crystal structure of the closely related Bacillus cereus PI-PLC, the rim of the active site is flanked by a short helix B and a loop that show an unusual clustering of hydrophobic amino acids. Two of the seven tryptophans in PI-PLC are among the exposed residues. To test the importance of these residues in substrate and activator binding, we prepared several mutants of Trp-47 (in helix B) and Trp-242 (in the loop). Two other tryptophans, Trp-178 and Trp-280, which are not near the rim, were mutated as controls. Kinetic (both phosphotransferase and cyclic phosphodiesterase activities), fluorescence, and vesicle binding analyses showed that both Trp-47 and Trp-242 residues are important for the enzyme to bind to interfaces, both activating zwitterionic and substrate anionic surfaces. Partitioning of the enzyme to vesicles is decreased more than 10-fold for either W47A or W242A, and removal of both tryptophans (W47A/W242A) yields enzyme with virtually no affinity for phospholipid surfaces. Replacement of either tryptophan with phenylalanine or isoleucine has moderate effects on enzyme affinity for surfaces but yields a fully active enzyme. These results are used to describe how the enzyme is activated by interfaces.     

Sphingomyelin modulates interfacial binding of Taiwan cobra phospholipase A2

The goal of the present study is to elucidate the effect of sphingomyelin on interfacial binding of Taiwan cobra phospholipase A₂ (PLA₂). Substitution of Asn-1 with Met caused a reduction in enzymatic activity and membrane-damaging activity of PLA₂ toward phospholipid vesicles, while sphingomyelin exerted an inhibitory effect on the biological activities of native and mutated PLA₂. Incorporation of sphingomyelin reduced membrane fluidity of phospholipid vesicles as evidenced by Laurdan fluorescence measurement. The results of self-quenching studies, binding of fluorescent probe, trinitrophenylation of Lys residues and fluorescence energy transfer between protein and lipid revealed that sphingomyelin altered differently membrane-bound mode of native and mutated PLA₂. Moreover, it was found that PLA₂ and N-terminally mutated PLA₂ adopted different conformation and geometrical arrangement on binding with membrane bilayer. Nevertheless, the binding affinity of PLA₂ and N-terminal mutant for phospholipid vesicles was not greatly affected by sphingomyelin. Together with the finding that mutation on N-terminus altered the gross conformation of PLA₂, our data indicate that sphingomyelin modulates the mode of membrane binding of PLA₂ at water/lipid interface, and suggest that the modulated effect of sphingomyelin depends on inherent structural elements of PLA₂.     

Substrate specificity for interfacial catalysis by phospholipase A2 in the scooting mode

Action of pig pancreatic phospholipase A2 on vesicles and micelles of homologous anionic phospholipids is examined in the absence of additives. As shown elsewhere (Jain et al. (1986) Biochim. Biophys. Acta 860, 435-447), hydrolysis of anionic vesicles occurs by interfacial catalysis in the scooting mode, i.e., the catalytic turnover is fast relative to the off-rate of the enzyme from the interface. When the rate of intervesicle exchange of the enzyme is negligibly slow, it hydrolyses only the substrate molecules in the outer monolayer of the vesicle to which it is bound. Interfacial catalysis in the scooting mode with a high processivity occurs on vesicles of anionic phospholipids, and under these conditions the dynamics and order of the substrate in the interface influences the catalytic turnover only moderately, i.e., about 2- to 10-fold. Similarly, anomalous kinetic effects of the thermotropic gel-fluid phase transition or of a change in the general disorder of the bilayer organization (fluidity) has a minor effect on the kinetics of hydrolysis in the scooting mode. Similarly, higher unsaturation and shorter acyl chains in the substrate modestly increase the rate of catalytic turnover by the low-calcium form of the enzyme without noticeably influencing the affinity of the enzyme for the interface. On the other hand, perturbation of the charge distribution in the substrate interface can shift the proportion of the bound enzyme by several orders of magnitude. For example, the membrane perturbing amphiphiles (e.g., mepacrine, indomethacin, compound 48/80, aristolochic acid, local anesthetics, and the products of hydrolysis) do not influence the catalytic turnover of the bound enzyme but the proportion of the bound enzyme. Short-chain anionic phospholipids are readily hydrolyzed by phospholipase A2. Now no anomalous increase in the rate of hydrolysis is observed at the critical micelle as is the case with the zwitterionic analogs. This is because with anionic (but not with zwitterionic) substrates the enzyme forms an aggregated complex below the cmc of the monomer. The stability of these micellar complexes does not appear to change noticeably with the acyl chain length of the monomers. These observations show that the factors regulating the quality of interface substantially influence the binding of the enzyme, but not the catalytic turnover in the interface.     

The catalytic site residues and interfacial binding of human pancreatic lipase.

In this study, the essential serine residue and 2 other amino acids in human pancreatic triglyceride lipase (triacylglycerol acylhydrolase, EC 3.1.1.3) were tested for their contribution to the enzyme's catalytic site or interfacial binding site. By site-specific mutagenesis of the cDNA for human pancreatic lipase, amino acid substitutions were made at Ser153, His264, and Asp177. The mutant cDNAs were expressed in transfected COS-1 cells. Both the medium and the cells were examined for the presence of pancreatic lipase by Western blot analysis. The activity of the expressed proteins against triolein and the interfacial binding was measured. Proteins with mutations in Ser153 were secreted by the cells and bound to interfaces but had no detectable activity. Changing His264 to a leucine or Asp177 to an asparagine also produced inactive lipase. Substituting glutamic acid for Asp177 produced an active protein. These results demonstrate that Ser153 is involved in the catalytic site of pancreatic lipase and is not crucial for interfacial binding. Moreover, the essential roles of His264 and Asp177 in catalysis were demonstrated. A Ser-His-Asp catalytic triad similar to that present in serine proteases is present in human pancreatic lipase.     

Thermodynamics of the binding of Ca2+ to porcine pancreatic phospholipase A2

The binding of Ca2+ to porcine pancreatic phospholipase A2 was studied by batch microcalorimetry. Enthalpies of binding at 25 degrees C were determined as a function of Ca2+ concentration in buffered solutions at pH 8.0 using both the Tris-HCl and Hepes-NaOH buffer systems. The calorimetric results indicate that protons are released on calcium binding and that in addition to the binding of the active-site calcium, there appears to be weak binding of a second Ca2+. Results from potentiometric titrations indicate that this proton release on binding Ca2+ arises from a change in pK of a histidine(s) functional group. The thermodynamic functions delta G0, delta H0 and delta S0 for calcium binding to phospholipase A2 have been determined. These results are compared with literature data for Ca2+ complex formation with some small molecules and also the protein troponin-C.     

Cooperative binding of monodisperse anionic amphiphiles to the i-face: phospholipase A2-paradigm for interfacial binding

Equilibrium parameters for the binding of monodisperse alkyl sulfate along the i-face (the interface binding surface) of pig pancreatic IB phospholipase A(2) (PLA2) to form the premicellar complexes (E(i)(#)) are characterized to discern the short-range specific interactions. Typically, E(i)(#) complexes are reversible on dilution. The triphasic binding isotherm, monitored as the fluorescence emission from the single tryptophan of PLA2, is interpreted as a cooperative equilibrium for the sequential formation of three premicellar complexes (E(i)(#), i = 1, 2, 3). In the presence of calcium, the dissociation constant K(1) for the E(1)(#) complex of PLA2 with decyl sulfate (CMC = 4500 microM) is 70 microM with a Hill coefficient n(1) = 2.1 +/- 0.2; K(2) for E(2)(#) is 750 microM with n(2) = 8 +/- 1, and K(3) for E(3)(#) is 4000 microM with an n(3) value of about 12. Controls show that (a) self-aggregation of decyl sulfate alone is not significant below the CMC; (b) occupancy of the active site is not necessary for the formation of E(i)(#); (c) K(i) and n(i) do not change significantly due to the absence of calcium, possibly because alkyl sulfate does not bind to the active site of PLA2; (d) the E(i)(#) complexes show a significant propensity for aggregation; and (e) PLA2 is not denatured in E(i)(#). The results are interpreted to elaborate the model for atomic level interactions along the i-face: The chain length dependence of the fit parameters suggests that short-range specific anion binding of the headgroup is accompanied by desolvation of the i-face of E(i)(#). We suggest that allosteric activation of PLA2 results from such specific interactions of the amphiplies and the desolvation of the i-face. The significance of these primary interfacial binding events and the coexistence of the E and E(i)(#) aggregates is discussed.     

Calcium-dependent binding of calmodulin to phospholipase A2 subunits induces enzymatic activation

Calmodulin interacted with phospholipase A₂ from two different sources, as established by affinity chromatography, dimethylsuberimidate protein crosslinking, and phospholipase A₂ assays. Calmodulin was covalently crosslinked to pancreatic and bee venom phospholipases A₂ in a calcium-dependent manner, and enhanced the enzymatic activities of these phospholipases. Pancreatic phospholipase A₂ was separated into two species of identical molecular weight by calmodulin affinity chromatography; the species that bound to immobilized calmodulin in a calcium-dependent manner was stimulated by calmodulin. This presents further evidence that phospholipase A₂ is directly activated by calmodulin.     

Role of helix B residues in interfacial activation of a bacterial phosphatidylinositol-specific phospholipase C

The Bacillus thuringiensis phosphatidylinositol-specific phospholipase C (PI-PLC), an interfacial enzyme associated with prokaryotic infectivity, is activated by binding to zwitterionic surfaces, particularly phosphatidycholine (PC). Two tryptophan residues (Trp47 in the two-turn helix B and Trp242 in a disordered loop) at the rim of the barrel structure are critical for this interaction. The helix B region (Ile43 to Gly48) in wild-type PI-PLC orients the side chains of Ile43 and Trp47 so that they pack together and form a hydrophobic protrusion from the protein surface that likely facilitates initial membrane binding. In previous studies we reported that in the crystal structure of the dimeric W47A/W242A mutant, which is unable to bind to PC, the helix B region has been reorganized by the mutation into an extended loop. Here we report the construction and characterization (catalytic activity, fluorescence, and NMR studies) of a series of PI-PLC mutants targeting helix B residues and surrounding regions to explore what is needed to stabilize the "membrane-active" conformation of the helix B region. Results strongly suggest that, while hydrophobic groups and presumably an intact helix B are critical for the initial binding of PI-PLC to membranes, disruption of helix B to allow enzyme dimerization is what leads to the activated PI-PLC conformation.     

Interfacial catalysis by phospholipase A2: activation by substrate replenishment.

Polymyxin B (Px), a cyclic cationic peptide, was shown to act as a potent activator of interfacial catalysis by phospholipase A2 (PLA2) acting on dimyristoylphosphatidylmethanol vesicles in the scooting mode. A 7-fold increase in the initial enzymatic velocity was seen with the pig pancreatic PLA2 in the presence of 1 microM Px. Initial experiments including the dependency of the degree of activation by Px on the source of the PLA2 suggested that Px bound to a cationic binding site on the enzyme. However, numerous additional observations led to the conclusion that activation by Px was due to its effects on the substrate interface. For example, the activation by Px was only seen when the PLA2 acted on small vesicles rather than larger ones, and all of the available substrate was eventually hydrolyzed in the presence of a small mole fraction of Px. Px did not promote the intervesicle exchange of PLA2, and it did not alter the binding of the evidence led to the conclusion that Px activated interfacial catalysis by promoting the replenishment of substrate in the enzyme-containing vesicles. When PLA2 was acting on small vesicles in the scooting mode, the observed initial velocity was lower than that measured with large vesicles because the surface concentration of substrate decreased relatively rapidly in the small vesicles. Px promoted the transfer of phospholipids between the vesicles and functioned as an activator by keeping the mole fraction of substrate in the enzyme-containing vesicles close to 1. This effect of Px was consistent with the ability of polycationic peptides to induce the intervesicle mixing of anionic phospholipids in vesicles [Bondeson, J., & Sundler, R. (1990) Biochim. Biophys. Act 1026, 186-194]. Activation by substrate replenishment was quantitatively predicted by the theory of interfacial catalysis on vesicles in the scooting mode. The role of substrate replenishment in the kinetics of interfacial catalysis in phospholipid micelles was discussed. Finally, the protocols developed in this paper were outlined in view of their utility in the analysis of activators of interfacial catalysis.     

Kinetics of interfacial catalysis by phospholipase A2 in intravesicle scooting mode,and heterofusion of anionic and zwitterionic vesicles

In this and the following three papers we examine the kinetics of action of pig pancreatic phospholipase A₂ on vesicles of anionic phospholipids without any additives. The results provide the first unequivocal demonstration of interfacial catalysis in intravesicle scooting mode. In this paper we describe the conditions in which the action of pig pancreatic phospholipase A₂ on DMPMe (ester) vesicles in the absence of any additive commences without a latency. Under these conditions the free monomer substrate concentration is insignificant; the bilayer enclosed vesicle organization remains intact even when all the substrate in the outer monolayer has been hydrolyzed; the rate of intervesicle exchange and the rate of transbilayer movement (flip-flop) of molecules is negligibly slow; and the rate of fusion of vesicles is insignificant. Thus an enzyme molecule bound to one vesicle hydrolyzes all the DMPMe molecules in the outer monolayer of the vesicle by a first-order process with a rate constant of 0.6 per min at 30°C; or viewed another way, one enzyme molecule in a DMPMe vesicle can hydrolyze all the available substrate molecules at the rate of 3000 per min. At low anion concentrations excess substrate vesicles are not hydrolyzed unless the rate of intervesicle exchange of the bound enzyme is stimulated by anions in the aqueous phase. Higher calcium concentrations promote not only homofusion of DMPMe vesicles but also heterofusion of DMPMe and DMPC vesicles. It is proposed that calcium-induced isothermal lateral phase separation in DMPMe vesicles induces defects in the bilayer organization, and such defects are the sites for phospholipase A₂ binding and for heterofusion with DMPC (ester) vesicles which do not have such sites.     

Roles of aromatic residues in high interfacial activity of Naja naja atra phospholipase A2

Acidic phospholipase A2 (PLA2) from the venom of Chinese cobra (Naja naja atra) has high activity on zwitterionic membranes and contains six aromatic residues, including Tyr-3, Trp-18, Trp-19, Trp-61, Phe-64, and Tyr-110, on its putative interfacial binding surface. To assess the roles of these aromatic residues in the interfacial catalysis of N. n. atra PLA2, we mutated them to Ala and measured the effects on its interfacial catalysis. Enzymatic activities of the mutants toward various vesicle substrates and human neutrophils indicate that all but Trp-18 make significant contributions to interfacial catalysis. Among these aromatic residues, Trp-19, Trp-61, and Phe-64 play the most important roles. Binding affinities of the mutants for phospholipid-coated beads and their monolayer penetration indicate that Trp-19, Trp-61, and Phe-64 are critically involved in interfacial binding of N. n. atra PLA2 and penetrate into the membrane during the interfacial catalysis of N. n. atra PLA2. Further thermodynamic analysis suggests that the side chain of Phe-64 is fully inserted into the hydrophobic core of membrane whereas those of Trp-19 and Trp-61 are located in the membrane-water interface. Together, these results show that all three types of aromatic residues can play important roles in interfacial binding of PLA2 depending on their location and side-chain orientation. They also indicate that these aromatic side chains interact with membranes in distinct modes because of their different intrinsic preference for different parts of membranes.     

Phospholipid binding and the activation of group IA secreted phospholipase A2

Equilibrium dialysis was used to study the binding of two nonhydrolyzable, short chain phospholipid analogues to the secreted group IA phospholipase A(2) (PLA(2)), which has been shown to contain several phospholipid binding sites that dramatically affect activity. This study provides new insight into how these activations occur. One analogue contained a phosphorylethanolamine (DiC(6)SNPE) headgroup, while the other contained a phosphorylcholine (DiC(6)SNPC) headgroup. Using phospholipase D, we incorporated tritium into each analogue. No binding of DiC(6)SNPE to PLA(2) was observed under submicellar conditions. Addition of submicellar amounts of Triton X-100 resulted in a linear nonsaturating response to lipid concentration, suggestive of premicellar aggregation of the DiC(6)SNPE with Triton X-100 and PLA(2). Binding of DiC(6)SNPE when presented as Triton X-100 mixed micelles saturated at 0.93 binding sites per PLA(2) with a K(D) of 38 microM. Addition of sphingomyelin, a potent activator of PLA(2) hydrolysis of phosphorylethanolamine containing compounds, resulted in a 13-fold decrease in the K(D), to 2.8 microM. This suggests that changes in the catalytic site binding affinity contribute to "phosphatidylcholine activation". Binding of DiC(6)SNPC with 2.0 mM Triton X-100 showed positive cooperativity (Hill coefficient of 1.7), which saturated at 2.0 binding sites per PLA(2). No binding of either analogue was observed when the catalytic site was alkylated with p-bromophenacyl bromide. Since p-bromophenacyl bromide does not physically block the phosphatidylcholine activator site, this indicates that the two phosphatidylcholine binding sites interact. The binding studies show that DiC(6)SNPC binds cooperatively to two sites on group IA PLA(2), while DiC(6)SNPE binds to only one site.     

Coupling of the i-face and the active site of phospholipase A2 for interfacial activation

Interfacial enzymes bind to organized interfaces where they access their substrates. As an example of interfacial activation, phospholipase A2 has an observed rate of hydrolysis of the sn-2-acyl chain of phospholipids at bilayer and micellar interfaces that is more than 1,000 times larger than with monodisperse phospholipids. The major challenge for the study of interfacial enzymes is to correlate the elementary steps of the interfacial function of the enzyme with the structure of the enzyme at the interface. Having kinetically resolved the steps of the interfacial turnover cycle, here we outline our recent (mostly since 2000) approaches to address remaining issues of interfacial activation and also the protocols that are likely to provide insights into the distinguishing structural features of the interface-activated enzyme.     

Contributions of conserved serine and tyrosine residues to catalysis, ligand binding, and cofactor processing in the active site of tyrosine ammonia lyase

Tyrosine ammonia lyase (TAL) catalyzes the conversion of L-tyrosine to p-coumaric acid using a 3,5-dihydro-5-methylidene-4H-imidazole-4-one (MIO) prosthetic group. In bacteria, TAL is used for production of the photoactive yellow protein chromophore and for caffeic acid biosynthesis in certain actinomycetes. Here we biochemically examine wild-type and mutant forms of TAL from Rhodobacter sphaeroides (RsTAL). Kinetic analysis of RsTAL shows that the enzyme displays a 90-fold preference for L-tyrosine versus L-phenylalanine as a substrate. The pH-dependence of TAL activity with L-tyrosine and L-phenylalanine demonstrates a common protonation state for catalysis, but indicates a difference in charge-state for binding of either amino acid. Site-directed mutagenesis demonstrates that Ser150, Tyr60, and Tyr300 are essential for catalysis. Mutation of Ser150 to an alanine abrogates formation of the MIO prosthetic group, as shown by mass spectrometry, and prevents catalysis. The Y60F and Y300F mutants were inactive with both amino acid substrates, but bound p-coumaric and cinnamic acids with less than 12-fold changes in affinity compared the wild-type enzyme. Analysis of MIO-dithiothreitol adduct formation shows that the reactivity of the prosthetic group is not significantly altered by mutation of either Tyr60 or Tyr300. The mechanistic roles of Ser150, Tyr60, and Tyr300 are discussed in relation to the three-dimensional structure of RsTAL and related MIO-containing enzymes.