ArticleBiochemistry2009
PIP(2)-binding site in Kir channels: definition by multiscale biomolecular simulations.
Article in Biochemistry, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 79 papers.
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Who cites it
79 citing papers in PubMed, 137 citations in OpenAlex.
- The SIMDA framework maps PIP2-binding sites regulating the KCNQ1 channel.Nature communications · 2026Article
- The Influence of Phosphoinositide Lipids in the Molecular Biology of Membrane Proteins: Recent Insights from Simulations.Journal of molecular biology · 2025Review
- Cellular lipids regulate the conformational ensembles of the disordered intracellular loop 3 in β2-adrenergic receptor.iScience · 2024Article
- Article
- Cellular Lipids Regulate the Conformational Ensembles of the Disordered Intracellular Loop 3 in β2 Adrenergic Receptor.bioRxiv : the preprint server for biology · 2023Article
- LipIDens: simulation assisted interpretation of lipid densities in cryo-EM structures of membrane proteins.Nature communications · 2023Article
- Molecular Biophysics of Class A G Protein Coupled Receptors-Lipids Interactome at a Glance-Highlights from the ABiomolecules · 2023Review
- Specificities of Protein Homology Modeling for Allosteric Drug Design.Methods in molecular biology (Clifton, N.J.) · 2023Article
- From Crosstalk to Synergism: The Combined Effect of Cholesterol and PI(4,5)PAdvances in experimental medicine and biology · 2023Review
- Bionics design of affinity peptide inhibitors for SARS-CoV-2 RBD to block SARS-CoV-2 RBD-ACE2 interactions.Heliyon · 2023Article
- The dynamic interplay of PIPThe Journal of physiology · 2022Article
- Transition between conformational states of the TREK-1 K2P channel promoted by interaction with PIPBiophysical journal · 2022Article
- Initiating Coarse-Grained MD Simulations for Membrane-Bound Proteins.Methods in molecular biology (Clifton, N.J.) · 2022Article
- From Bench to Biomolecular Simulation: Phospholipid Modulation of Potassium Channels.Journal of molecular biology · 2021Review
- Kir Channel Molecular Physiology, Pharmacology, and Therapeutic Implications.Handbook of experimental pharmacology · 2021Review
- Identification and Characterization of Specific Protein-Lipid Interactions Using Molecular Simulation.Methods in molecular biology (Clifton, N.J.) · 2021Article
- Piezo1 Forms Specific, Functionally Important Interactions with Phosphoinositides and Cholesterol.Biophysical journal · 2020Article
- New insights into KNature reviews. Endocrinology · 2020Review
- Defining how multiple lipid species interact with inward rectifier potassium (Kir2) channels.Proceedings of the National Academy of Sciences of the United States of America · 2020Article
- Codon Harmonization of a Kir3.1-KirBac1.3 Chimera for Structural Study Optimization.Biomolecules · 2020Article
19 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
4 authors at 1 institution in 1 country.
Funding
Abstract
Phosphatidylinositol bisphosphate (PIP(2)) is an activator of mammalian inwardly rectifying potassium (Kir) channels. Multiscale simulations, via a sequential combination of coarse-grained and atomistic molecular dynamics, enabled exploration of the interactions of PIP(2) molecules within the inner leaflet of a lipid bilayer membrane with possible binding sites on Kir channels. Three Kir channel structures were investigated: X-ray structures of KirBac1.1 and of a Kir3.1-KirBac1.3 chimera and a homology model of Kir6.2. Coarse-grained simulations of the Kir channels in PIP(2)-containing lipid bilayers identified the PIP(2)-binding site on each channel. These models of the PIP(2)-channel complexes were refined by conversion to an atomistic representation followed by molecular dynamics simulation in a lipid bilayer. All three channels were revealed to contain a conserved binding site at the N-terminal end of the slide (M0) helix, at the interface between adjacent subunits of the channel. This binding site agrees with mutagenesis data and is in the proximity of the site occupied by a detergent molecule in the Kir chimera channel crystal. Polar contacts in the coarse-grained simulations corresponded to long-lived electrostatic and H-bonding interactions between the channel and PIP(2) in the atomistic simulations, enabling identification of key side chains.
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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.