Insertion of the Ca2+-Independent Phospholipase A2 into a Phospholipid Bilayer via Coarse-Grained and Atomistic Molecular Dynamics Simulations

Abstract

Group VI Ca2+-independent phospholipase A2 (iPLA2) is a water-soluble enzyme that is active when associated with phospholipid membranes. Despite its clear pharmaceutical relevance, no X-ray or NMR structural information is currently available for the iPLA2 or its membrane complex. In this paper, we combine homology modeling with coarse-grained (CG) and all-atom (AA) molecular dynamics (MD) simulations to build structural models of iPLA2 in association with a phospholipid bilayer. CG-MD simulations of the membrane insertion process were employed to provide a starting point for an atomistic description. Six AA-MD simulations were then conducted for 60 ns, starting from different initial CG structures, to refine the membrane complex. The resulting structures are shown to be consistent with each other and with deuterium exchange mass spectrometry (DXMS) experiments, suggesting that our approach is suitable for the modeling of iPLA2 at the membrane surface. The models show that an anchoring region (residues 710–724) forms an amphipathic helix that is stabilized by the membrane. In future studies, the proposed iPLA2 models should provide a structural basis for understanding the mechanisms of lipid extraction and drug-inhibition. In addition, the dual-resolution approach discussed here should provide the means for the future exploration of the impact of lipid diversity and sequence mutations on the activity of iPLA2 and related enzymes.

Membranes serve as allosteric activators of phospholipase A 2 , enabling it to extract, bind, and hydrolyze phospholipid substrates

“…The rmsf values for region A (residues 700-719) were higher than 4 Å (Fig. S5B), and it was previously reported to play an important role in the association of the enzyme with the membrane (38). Region B (residues 720-730) exhibited rmsf values between 1.5 Å and 4 Å (Fig.…”

“…3A). The insertion of GVIA iPLA 2 in a POPC membrane patch was also previously studied by our group using coarse-grained and atomistic simulations, as well as DXMS data (38). The proposed model assumes no interactions of the ankyrin repeats with the membrane.…”

“…3B) interacting with the head groups, and its hydrophobic residues (Pro711, Pro714, Trp715, Leu717, Val721, Phe722; Fig. 3B) interacting with the fatty acid tails of the membrane phospholipid (38). GVIA iPLA 2 was also placed in the POPC membrane containing one PAPC molecule according to the published data (Fig.…”

Substrate Efflux Propensity Is the Key Determinant of Ca2+-independent Phospholipase A-β (iPLAβ)-mediated Glycerophospholipid Hydrolysis

“…It was proposed that the substrate has to be extracted (i.e. efflux) from the membrane to be hydrolyzed by iPLA␤, but this could not be proven due to limitations of the methodology used (46).…”

Bioinformatics for Membrane Lipid Simulations: Models, Computational Methods, and Web Server Tools

“…MARTINI achieved 5-to 10-fold faster sampling of the configurational space of liquid hydrocarbons and the lipid tails inside a bilayer compared to AT force fields [44]. Among others, MARTINI has allowed applications in simulations of vesicle formation and fusion [50,51], phase transition of lipid bilayers [52], and the structure and dynamics of membrane-protein assemblies [53,54]. Currently, MARTINI has also been supplemented with an implicit solvent force field, named Dry MARTINI, which provided 1-2 order speed up and is expected to find application in simulations of large membranes containing millions of lipids [55].…”