PLD2-PI(4,5)P2 Interactions in Fluid Phase Membranes: Structural Modeling and Molecular Dynamics Simulations
- PLD2-PI(4,5)P2 Interactions in Fluid Phase Membranes: Structural Modeling and Molecular Dynamics Simulations
- 한경림; Richard W. Pastor; Cristina Fenollar-ferrer
- Issue Date
- PLoS ONE
- VOL 15, NO 7, e0236201
- Interaction of phospholipase D2 (PLD2) with phosphatidylinositol (4,5)-bisphosphate (PIP2) is regarded as the critical step of numerous physiological processes. Here we build a full-length model of human PLD2 (hPLD2) combining template-based and ab initio modeling techniques and use microsecond all-atom molecular dynamics (MD) simulations of the protein in contact with a complex membrane to determine hPLD2-PIP2 interactions. MD simulations reveal that the intermolecular interactions preferentially occur between specific PIP2 phosphate groups and hPLD2 residues; the most strongly interacting residues are arginine at the pbox consensus sequence (PX) and pleckstrin homology (PH) domain. Interaction networks indicate formation of clusters at the protein-membrane interface consisting of amino acids, PIP2, and 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphatidic acid (POPA); the largest cluster was in the PH domain.
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