Localizing the Membrane Binding Region of Group VIA Ca2+-independent Phospholipase A2 Using Peptide Amide Hydrogen/Deuterium Exchange Mass Spectrometry

The Group VIA-2 Ca²⁺-independent phospholipase A₂ (GVIA-2 iPLA₂) is composed of seven consecutive N-terminal ankyrin repeats, a linker region, and a C-terminal phospholipase catalytic domain. No structural information exists for this enzyme, and no information is known about the membrane binding surface. We carried out deuterium exchange experiments with the GVIA-2 iPLA₂ in the presence of both phospholipid substrate and the covalent inhibitor methyl arachidonoyl fluorophosphonate and located regions in the protein that change upon lipid binding. No changes were seen in the presence of only methyl arachidonoyl fluorophosphonate. The region with the greatest change upon lipid binding was region 708–730, which showed a >70% decrease in deuteration levels at numerous time points. No decreases in exchange due to phospholipid binding were seen in the ankyrin repeat domain of the protein. To locate regions with changes in exchange on the enzyme, we constructed a computational homology model based on homologous structures. This model was validated by comparing the deuterium exchange results with the predicted structure. Our model combined with the deuterium exchange results in the presence of lipid substrate have allowed us to propose the first structural model of GVIA-2 iPLA₂ as well as the interfacial lipid binding region.The Group VIA phospholipase A₂ is a member of the phospholipase A₂ superfamily that cleaves fatty acids from the sn-2 position of phospholipids (1, 2). The human Group VIA PLA₂³ gene yields multiple splice variants, including GVIA-1, GVIA-2, GVIA-3 PLA₂, GVIA Ankyrin-1, and GVIA Ankyrin-2 (3, 4). At least two isoforms, GVIA-1 and GVIA-2 iPLA₂, are active. Our laboratory purified and characterized the first mammalian iPLA₂, the 85-kDa GVIA-2 iPLA₂ (5), which became the first cloned iPLA₂ (6). This enzyme can hydrolyze the sn-2 fatty acyl bond of phospholipids and also has potent lysophospholipase and transacylase activity (7). GVIA iPLA₂ is involved in cell proliferation (8), apoptosis (9–11), bone formation (12), sperm development (13), and glucose-induced insulin secretion (14, 15), so its function may vary by cell and tissue.The human GVIA-2 iPLA₂ (806 amino acids), the form of the enzyme studied here, contains seven ankyrin repeats (residues 152–382), a linker region (residues 383–474) with the eighth repeat disrupted by a 54-amino acid insert (16), and a catalytic domain (residues 475–806). The active site serine of the GVIA iPLA₂ lies within a lipase consensus sequence (Gly-X-Ser⁵¹⁹-X-Gly) (1). The activity of GVIA iPLA₂ has been reported to be regulated through several mechanisms. A caspase-3 cleavage site at the N terminus of the enzyme has been identified that is clipped in vitro (17). This truncated form of the enzyme was hyperactive and reduced cell viability when overexpressed in HEK293 cells (17). Another possible control mechanism is through ATP binding on the ⁴⁸⁵GXGXXG motif (18).The activity of phospholipases depends critically on the interaction of the protein with phospholipid membranes. In vitro, GVIA iPLA₂ does not have any specificity for the fatty acid in the sn-2 position of substrate phospholipids (5). GVIA-2 iPLA₂ was found to be membrane-associated when overexpressed in COS-7 cells, and this was further confirmed in rat vascular smooth muscle cells (4, 19). The other active splice variant, GVIA-1, is cytosolic and not specific in targeting membrane surfaces (4, 19), indicating two different regulatory mechanisms between these two splice variants. The 54-residue insertion in the eighth ankyrin repeat alters the property of GVIA-2 iPLA₂ for membrane association. The ankyrin repeats have been reported to be involved in protein-protein interactions, such as 53BP2-p53, GA-binding protein α-GA-binding protein β, p16^INK4a-CDK6, and IκBα-NFκB (16). The ankyrin repeats of GVIA iPLA₂ may directly or indirectly assist membrane association because the catalytic domain by itself does not have activity (3). Determining the regions of the protein that interact with the membrane surface will allow for a more in-depth analysis of the regulatory mechanisms of the enzyme.There is an increasing interest in GVIA iPLA₂ because of its various newly discovered functions in vivo and in vitro. However, there is no published crystal or NMR structure to facilitate analysis on the molecular level. Amide hydrogen/deuterium exchange coupled with mass spectrometry (DXMS) has been widely used to analyze the interface of protein-protein interactions (20), protein conformational changes (21, 22), and protein dynamics (23), and we have now introduced it to study protein-phospholipid interactions (24, 25). There are also reports of using DXMS with homology modeling to validate enzymes where structural information does not exist (26). We used deuterium exchange along with homology modeling to generate models of the ankyrin repeats based on the Ankyrin-R (Protein Data Bank code 1N11) and of the catalytic domain based on patatin (Protein Data Bank code 1OXW). To study the interfacial activation of GVIA iPLA₂, we generated 1-palmitoyl-2-arachidonoyl-sn-phosphatidylcholine (PAPC) vesicles containing the methyl arachidonyl fluorophosphonate (MAFP) inhibitor, which binds to the active site and irreversibly inhibits GVIA iPLA₂ (7). By applying DXMS to the iPLA₂ and using our structural model, we were now able to monitor how GVIA iPLA₂ associates with phospholipid membranes.