Paper Citing NAMD - Abstract
Bucher, Denis; Hsu, Yuan-Hao; Mouchlis, Varnavas D.; Dennis, Edward A.; McCammon, J. Andrew
Insertion of the Ca2+-Independent Phospholipase A(2) into a Phospholipid Bilayer via Coarse-Grained and Atomistic Molecular Dynamics Simulations
PLOS COMPUTATIONAL BIOLOGY, 9 Art. No. e1003156, JUL 2013
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.
