Insertion of the Ca(2+)-Independent Phospholipase A(2) into a Phospholipid Bilayer via Coarse-Grained and Atomistic Molecular Dynamics Simulations
Group VI Ca(2+)-independent phospholipase A(2) (iPLA(2)) 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 iPLA(2) or its membrane complex. In this pa...
Autores principales: | , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
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Public Library of Science
2013
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Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3723492/ https://www.ncbi.nlm.nih.gov/pubmed/23935474 http://dx.doi.org/10.1371/journal.pcbi.1003156 |
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author | Bucher, Denis Hsu, Yuan-Hao Mouchlis, Varnavas D. Dennis, Edward A. McCammon, J. Andrew |
author_facet | Bucher, Denis Hsu, Yuan-Hao Mouchlis, Varnavas D. Dennis, Edward A. McCammon, J. Andrew |
author_sort | Bucher, Denis |
collection | PubMed |
description | Group VI Ca(2+)-independent phospholipase A(2) (iPLA(2)) 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 iPLA(2) 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 iPLA(2) 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 iPLA(2) 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 iPLA(2) 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 iPLA(2) and related enzymes. |
format | Online Article Text |
id | pubmed-3723492 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2013 |
publisher | Public Library of Science |
record_format | MEDLINE/PubMed |
spelling | pubmed-37234922013-08-09 Insertion of the Ca(2+)-Independent Phospholipase A(2) into a Phospholipid Bilayer via Coarse-Grained and Atomistic Molecular Dynamics Simulations Bucher, Denis Hsu, Yuan-Hao Mouchlis, Varnavas D. Dennis, Edward A. McCammon, J. Andrew PLoS Comput Biol Research Article Group VI Ca(2+)-independent phospholipase A(2) (iPLA(2)) 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 iPLA(2) 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 iPLA(2) 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 iPLA(2) 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 iPLA(2) 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 iPLA(2) and related enzymes. Public Library of Science 2013-07-25 /pmc/articles/PMC3723492/ /pubmed/23935474 http://dx.doi.org/10.1371/journal.pcbi.1003156 Text en © 2013 Bucher et al http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited. |
spellingShingle | Research Article Bucher, Denis Hsu, Yuan-Hao Mouchlis, Varnavas D. Dennis, Edward A. McCammon, J. Andrew Insertion of the Ca(2+)-Independent Phospholipase A(2) into a Phospholipid Bilayer via Coarse-Grained and Atomistic Molecular Dynamics Simulations |
title | Insertion of the Ca(2+)-Independent Phospholipase A(2) into a Phospholipid Bilayer via Coarse-Grained and Atomistic Molecular Dynamics Simulations |
title_full | Insertion of the Ca(2+)-Independent Phospholipase A(2) into a Phospholipid Bilayer via Coarse-Grained and Atomistic Molecular Dynamics Simulations |
title_fullStr | Insertion of the Ca(2+)-Independent Phospholipase A(2) into a Phospholipid Bilayer via Coarse-Grained and Atomistic Molecular Dynamics Simulations |
title_full_unstemmed | Insertion of the Ca(2+)-Independent Phospholipase A(2) into a Phospholipid Bilayer via Coarse-Grained and Atomistic Molecular Dynamics Simulations |
title_short | Insertion of the Ca(2+)-Independent Phospholipase A(2) into a Phospholipid Bilayer via Coarse-Grained and Atomistic Molecular Dynamics Simulations |
title_sort | insertion of the ca(2+)-independent phospholipase a(2) into a phospholipid bilayer via coarse-grained and atomistic molecular dynamics simulations |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3723492/ https://www.ncbi.nlm.nih.gov/pubmed/23935474 http://dx.doi.org/10.1371/journal.pcbi.1003156 |
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