ArticleBiophysical journal2008
The interaction of phospholipase A2 with a phospholipid bilayer: coarse-grained molecular dynamics simulations.
Article in Biophysical journal, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed.
- The Phospholipase A2 Superfamily: Structure, Isozymes, Catalysis, Physiologic and Pathologic Roles.International journal of molecular sciences · 2023Review
- Structural aspects and activation mechanism of human secretory group IIA phospholipase.European biophysics journal : EBJ · 2020Article
- Characterization of Lipid-Protein Interactions and Lipid-Mediated Modulation of Membrane Protein Function through Molecular Simulation.Chemical reviews · 2019Review
- Article
- Interfacial activation of M37 lipase: A multi-scale simulation study.Biochimica et biophysica acta. Biomembranes · 2017Article
- Alchembed: A Computational Method for Incorporating Multiple Proteins into Complex Lipid Geometries.Journal of chemical theory and computation · 2015Article
- Coarse-grained simulations of the HIV-1 matrix protein anchoring: revisiting its assembly on membrane domains.Biophysical journal · 2014Article
- Conformational changes in talin on binding to anionic phospholipid membranes facilitate signaling by integrin transmembrane helices.PLoS computational biology · 2013Article
- Insertion of the Ca²⁺-independent phospholipase A₂ into a phospholipid bilayer via coarse-grained and atomistic molecular dynamics simulations.PLoS computational biology · 2013Article
- Structural insights into the inhibition of actin-capping protein by interactions with phosphatidic acid and phosphatidylinositol (4,5)-bisphosphate.PLoS computational biology · 2012Article
- The structure of the talin/integrin complex at a lipid bilayer: an NMR and MD simulation study.Structure (London, England : 1993) · 2010Article
- Substrate efflux propensity plays a key role in the specificity of secretory A-type phospholipases.The Journal of biological chemistry · 2010Article
- The 3-dimensional structure of a hepatitis C virus p7 ion channel by electron microscopy.Proceedings of the National Academy of Sciences of the United States of America · 2009Article
- Location of inhibitors bound to group IVA phospholipase A2 determined by molecular dynamics and deuterium exchange mass spectrometry.Journal of the American Chemical Society · 2009Article
- Systematic multiscale simulation of membrane protein systems.Current opinion in structural biology · 2009Review
- Multiscale methods for macromolecular simulations.Current opinion in structural biology · 2008Review
- Article
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Authors and funding
4 authors.
Funding
Abstract
A number of membrane-active enzymes act in a complex environment formed by the interface between a lipid bilayer and bulk water. Although x-ray diffraction studies yield structures of isolated enzyme molecules, a detailed characterization of their interactions with the interface requires a measure of how deeply such a membrane-associated protein penetrates into a lipid bilayer. Here, we apply coarse-grained (CG) molecular dynamics (MD) simulations to probe the interaction of porcine pancreatic phospholipase A2 (PLA2) with a lipid bilayer containing palmitoyl-oleoyl-phosphatidyl choline and palmitoyl-oleoyl-phosphatidyl glycerol molecules. We also used a configuration from a CG-MD trajectory to initiate two atomistic (AT) MD simulations. The results of the CG and AT simulations are evaluated by comparison with available experimental data. The membrane-binding surface of PLA2 consists of a patch of hydrophobic residues surrounded by polar and basic residues. We show this proposed footprint interacts preferentially with the anionic headgroups of the palmitoyl-oleoyl-phosphatidyl glycerol molecules. Thus, both electrostatic and hydrophobic interactions determine the location of PLA2 relative to the bilayer. From a general perspective, this study demonstrates that CG-MD simulations may be used to reveal the orientation and location of a membrane-surface-bound protein relative to a lipid bilayer, which may subsequently be refined by AT-MD simulations to probe more detailed interactions.
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