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PLD2-PI(4,5)P2 interactions in fluid phase membranes: Structural modeling and molecular dynamics simulations.
- Source :
-
PloS one [PLoS One] 2020 Jul 20; Vol. 15 (7), pp. e0236201. Date of Electronic Publication: 2020 Jul 20 (Print Publication: 2020). - Publication Year :
- 2020
-
Abstract
- 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.<br />Competing Interests: The authors have declared that no competing interests exist.
- Subjects :
- Amino Acid Sequence
Arabidopsis Proteins chemistry
Arabidopsis Proteins ultrastructure
Bacterial Proteins chemistry
Bacterial Proteins ultrastructure
Binding Sites
Cell Membrane chemistry
Consensus Sequence
Crystallography, X-Ray
Molecular Docking Simulation
Molecular Dynamics Simulation
Phosphatidic Acids metabolism
Phosphatidylinositol 4,5-Diphosphate chemistry
Phospholipase D chemistry
Phospholipase D ultrastructure
Protein Binding
Protein Domains
Sequence Homology, Amino Acid
Cell Membrane metabolism
Phosphatidylinositol 4,5-Diphosphate metabolism
Phospholipase D metabolism
Subjects
Details
- Language :
- English
- ISSN :
- 1932-6203
- Volume :
- 15
- Issue :
- 7
- Database :
- MEDLINE
- Journal :
- PloS one
- Publication Type :
- Academic Journal
- Accession number :
- 32687545
- Full Text :
- https://doi.org/10.1371/journal.pone.0236201