ArticleBiophysical journal2009
Molecular dynamics simulations of PIP2 and PIP3 in lipid bilayers: determination of ring orientation, and the effects of surface roughness on a Poisson-Boltzmann description.
Article in Biophysical journal, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 30 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
30 citing papers in PubMed, 71 citations in OpenAlex.
- Cholesterol-dependent dimerization and conformational dynamics of EphA2 receptors from coarse-grained and all-atom simulations.Structure (London, England : 1993) · 2025Article
- Inositol and PIP2/PIP3 Ratio: At the Crossroad of the Biodynamic Interface Between Cells and Their Microenvironment.Biomolecules · 2025Review
- Nanoscopy reveals integrin clustering reliant on kindlin-3 but not talin-1.Cell communication and signaling : CCS · 2025Article
- Atomistic Simulations and Analysis of Peripheral Membrane Proteins with Model Lipid Bilayers.Methods in molecular biology (Clifton, N.J.) · 2025Article
- Modeling the membrane binding mechanism of a lipid transport protein Osh4 to single membranes.Biophysical journal · 2022Article
- Simulations of Kindlin-2 PIP binding domains reveal protonation-dependent membrane binding modes.Biophysical journal · 2021Article
- The degree and position of phosphorylation determine the impact of toxic and trace metals on phosphoinositide containing model membranes.BBA advances · 2021Article
- Neuroligin-2 dependent conformational activation of collybistin reconstituted in supported hybrid membranes.The Journal of biological chemistry · 2020Article
- Review of PIP2 in Cellular Signaling, Functions and Diseases.International journal of molecular sciences · 2020Review
- Divalent cations bind to phosphoinositides to induce ion and isomer specific propensities for nano-cluster initiation in bilayer membranes.Royal Society open science · 2020Article
- Insight into Phosphatidylinositol-Dependent Membrane Localization of the Innate Immune Adaptor Protein Toll/Interleukin 1 Receptor Domain-Containing Adaptor Protein.Frontiers in immunology · 2018Article
- Computational Modeling Reveals that Signaling Lipids Modulate the Orientation of K-Ras4A at the Membrane Reflecting Protein Topology.Structure (London, England : 1993) · 2017Article
- Calcium Directly Regulates Phosphatidylinositol 4,5-Bisphosphate Headgroup Conformation and Recognition.Journal of the American Chemical Society · 2017Article
- Lipid interaction sites on channels, transporters and receptors: Recent insights from molecular dynamics simulations.Biochimica et biophysica acta · 2016Review
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- Solvent-Free, Highly Coarse-Grained Models for Charged Lipid Systems.Journal of chemical theory and computation · 2014Article
- Counterion-mediated cluster formation by polyphosphoinositides.Chemistry and physics of lipids · 2014Review
- Article
- Article
- Molecular mechanism of membrane binding of the GRP1 PH domain.Journal of molecular biology · 2013Article
Corrections and comments
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Authors and funding
5 authors at 3 institutions in 1 country.
Funding
Abstract
Molecular dynamics (MD) simulations of phosphatidylinositol (4,5)-bisphosphate (PIP2) and phosphatidylinositol (3,4,5)-trisphosphate (PIP3) in 1-palmitoyl 2-oleoyl phosphatidylcholine (POPC) bilayers indicate that the inositol rings are tilted approximately 40 degrees with respect to the bilayer surface, as compared with 17 degrees for the P-N vector of POPC. Multiple minima were obtained for the ring twist (analogous to roll for an airplane). The phosphates at position 1 of PIP2 and PIP3 are within an Angström of the plane formed by the phosphates of POPC; lipids in the surrounding shell are depressed by 0.5-0.8 A, but otherwise the phosphoinositides do not substantially perturb the bilayer. Finite size artifacts for ion distributions are apparent for systems of approximately 26 waters/lipid, but, based on simulations with a fourfold increase of the aqueous phase, the phosphoinositide positions and orientations do not show significant size effects. Electrostatic potentials evaluated from Poisson-Boltzmann (PB) calculations show a strong dependence of potential height and ring orientation, with the maxima on the -25 mV surfaces (17.1 +/- 0.1 A for PIP2 and 19.4 +/- 0.3 A for PIP3) occurring near the most populated orientations from MD. These surfaces are well above the background height of 10 A estimated for negatively charged cell membranes, as would be expected for lipids involved in cellular signaling. PB calculations on microscopically flat bilayers yield similar maxima as the MD-based (microscopically rough) systems, but show less fine structure and do not clearly indicate the most probable regions. Electrostatic free energies of interaction with pentalysine are also similar for the rough and flat systems. These results support the utility of a rigid/flat bilayer model for PB-based studies of PIP2 and PIP3 as long as the orientations are judiciously chosen.
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Registered trials
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