Han, Kyungreem Pastor, Richard W. Fenollar-Ferrer, Cristina 2024-01-19T17:03:04Z 2024-01-19T17:03:04Z 2021-09-05 2020-07-20 1932-6203 https://pubs.kist.re.kr/handle/201004/118375 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 andab initiomodeling techniques and use microsecond all-atom molecular dynamics (MD) simulations of the protein in contact with a complex membrane to determine hPLD2-PIP(2)interactions. MD simulations reveal that the intermolecular interactions preferentially occur between specific PIP(2)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. English PUBLIC LIBRARY SCIENCE MAMMALIAN PHOSPHOLIPASE-D K-2P CHANNEL TREK-1 PROTEIN-STRUCTURE FORCE-FIELD GENERAL-ANESTHETICS SOFTWARE NEWS PIP2 BINDING PHOSPHOINOSITIDES VALIDATION PLD2-PI(4,5)P2 interactions in fluid phase membranes: Structural modeling and molecular dynamics simulations Article 10.1371/journal.pone.0236201 1 PLOS ONE, v.15, no.7 PLOS ONE 15 7 scie scopus 000553978400046 Multidisciplinary Sciences Science & Technology - Other Topics Article MAMMALIAN PHOSPHOLIPASE-D K-2P CHANNEL TREK-1 PROTEIN-STRUCTURE FORCE-FIELD GENERAL-ANESTHETICS SOFTWARE NEWS PIP2 BINDING PHOSPHOINOSITIDES VALIDATION