ArticleThe journal of physical chemistry. B2013
Quantum and all-atom molecular dynamics simulations of protonation and divalent ion binding to phosphatidylinositol 4,5-bisphosphate (PIP2).
Article in The journal of physical chemistry. B, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 32 papers.
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Who cites it
32 citing papers in PubMed, 39 citations in OpenAlex.
- The Influence of Phosphoinositide Lipids in the Molecular Biology of Membrane Proteins: Recent Insights from Simulations.Journal of molecular biology · 2025Review
- Asymmetric crowders and membrane morphology at the nexus of intracellular trafficking and oncology.Mechanobiology in medicine · 2024Article
- Ion-Induced PIP2 Clustering with Martini3: Modification of Phosphate-Ion Interactions and Comparison with CHARMM36.The journal of physical chemistry. B · 2024Article
- Phosphoinositide switches in cell physiology - From molecular mechanisms to disease.The Journal of biological chemistry · 2024Review
- Lipid remodeling in acrosome exocytosis: unraveling key players in the human sperm.Frontiers in cell and developmental biology · 2024Review
- Systematic simulation of the interactions of pleckstrin homology domains with membranes.Science advances · 2022Article
- Characterization of the membrane interactions of phospholipase Cγ reveals key features of the active enzyme.Science advances · 2022Article
- Simulations of Kindlin-2 PIP binding domains reveal protonation-dependent membrane binding modes.Biophysical journal · 2021Article
- Binding of CaStructure (London, England : 1993) · 2021Article
- Polyelectrolyte Gels Formed by Filamentous Biopolymers: Dependence of Crosslinking Efficiency on the Chemical Softness of Divalent Cations.Gels (Basel, Switzerland) · 2021Article
- The degree and position of phosphorylation determine the impact of toxic and trace metals on phosphoinositide containing model membranes.BBA advances · 2021Article
- Review of PIP2 in Cellular Signaling, Functions and Diseases.International journal of molecular sciences · 2020Review
- Structure and Lateral Organization of Phosphatidylinositol 4,5-bisphosphate.Molecules (Basel, Switzerland) · 2020Review
- The Glycosphingolipid GM3 Modulates Conformational Dynamics of the Glucagon Receptor.Biophysical journal · 2020Article
- A multiscale biophysical model for the recruitment of actin nucleating proteins at the membrane interface.Soft matter · 2020Article
- Divalent cations bind to phosphoinositides to induce ion and isomer specific propensities for nano-cluster initiation in bilayer membranes.Royal Society open science · 2020Article
- The energetics of protein-lipid interactions as viewed by molecular simulations.Biochemical Society transactions · 2020Review
- Multivalent Cation-Bridged PI(4,5)PBiophysical journal · 2018Article
- New tricks for old dogs: improving the accuracy of biomolecular force fields by pair-specific corrections to non-bonded interactions.Physical chemistry chemical physics : PCCP · 2018Review
- Graph-Theoretic Analysis of Monomethyl Phosphate Clustering in Ionic Solutions.The journal of physical chemistry. B · 2018Article
Corrections and comments
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Authors and funding
4 authors at 1 institution in 1 country.
Funding
Abstract
Molecular dynamics calculations have been used to determine the structure of phosphatidylinositol 4,5 bisphosphate (PIP2) at the quantum level and to quantify the propensity for PIP2 to bind two physiologically relevant divalent cations, Mg(2+) and Ca(2+). We performed a geometry optimization at the Hartree-Fock 6-31+G(d) level of theory in vacuum and with a polarized continuum dielectric to determine the conformation of the phospholipid headgroup in the presence of water and its partial charge distribution. The angle between the headgroup and the acyl chains is nearly perpendicular, suggesting that in the absence of other interactions the inositol ring would lie flat along the cytoplasmic surface of the plasma membrane. Next, we employed hybrid quantum mechanics/molecular mechanics (QM/MM) simulations to investigate the protonation state of PIP2 and its interactions with magnesium or calcium. We test the hypothesis suggested by prior experiments that binding of magnesium to PIP2 is mediated by a water molecule that is absent when calcium binds. These results may explain the selective ability of calcium to induce the formation of PIP2 clusters and phase separation from other lipids.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.