ArticlePLoS computational biology2013
Insertion of the Ca²⁺-independent phospholipase A₂ into a phospholipid bilayer via coarse-grained and atomistic molecular dynamics simulations.
Article in PLoS computational biology, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers.
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Who cites it
28 citing papers in PubMed.
- Unraveling the Molecular Mechanisms of ABHD5 Membrane Targeting.bioRxiv : the preprint server for biology · 2025Article
- The mechanism of allosteric regulation of calcium-independent phospholipase AProceedings of the National Academy of Sciences of the United States of America · 2024Article
- Molecular basis of unique specificity and regulation of group VIA calcium-independent phospholipase APharmacology & therapeutics · 2023Review
- Membrane Association Allosterically Regulates Phospholipase AAccounts of chemical research · 2022Article
- Lipoprotein-associated phospholipase AProceedings of the National Academy of Sciences of the United States of America · 2022Article
- Antioxidant Synergy of Mitochondrial Phospholipase PNPLA8/iPLA2γ with Fatty Acid-Conducting SLC25 Gene Family Transporters.Antioxidants (Basel, Switzerland) · 2021Review
- Characterization of the ExoU activation mechanism using EPR and integrative modeling.Scientific reports · 2020Article
- Hypothesis: Chemical activity regulates and coordinates the processes maintaining glycerophospholipid homeostasis in mammalian cells.FASEB bioAdvances · 2020Article
- Phospholipase ABiochimica et biophysica acta. Molecular and cell biology of lipids · 2019Review
- Characterization of Lipid-Protein Interactions and Lipid-Mediated Modulation of Membrane Protein Function through Molecular Simulation.Chemical reviews · 2019Review
- β-Lactones: A Novel Class of CaJournal of medicinal chemistry · 2019Article
- Membrane Allostery and Unique Hydrophobic Sites Promote Enzyme Substrate Specificity.Journal of the American Chemical Society · 2018Article
- Review of four major distinct types of human phospholipase AAdvances in biological regulation · 2018Review
- Extension of the Highly Mobile Membrane Mimetic to Transmembrane Systems through Customized in Silico Solvents.The journal of physical chemistry. B · 2017Article
- Cooperative Substrate-Cofactor Interactions and Membrane Localization of the Bacterial Phospholipase AThe Journal of biological chemistry · 2017Article
- Analyses of Calcium-Independent Phospholipase AMethods in enzymology · 2017Article
- Liberating Chiral Lipid Mediators, Inflammatory Enzymes, and LIPID MAPS from Biological Grease.The Journal of biological chemistry · 2016Review
- Computer-aided drug design guided by hydrogen/deuterium exchange mass spectrometry: A powerful combination for the development of potent and selective inhibitors of Group VIA calcium-independent phospholipase ABioorganic & medicinal chemistry · 2016Article
- Effects of Concentrations on the Transdermal Permeation Enhancing Mechanisms of Borneol: A Coarse-Grained Molecular Dynamics Simulation on Mixed-Bilayer Membranes.International journal of molecular sciences · 2016Article
- Atomic-level description of protein-lipid interactions using an accelerated membrane model.Biochimica et biophysica acta · 2016Review
Corrections and comments
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Authors and funding
5 authors.
Funding
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.
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