ArticleThe journal of physical chemistry. B2015
A Parameterization of Cholesterol for Mixed Lipid Bilayer Simulation within the Amber Lipid14 Force Field.
Article in The journal of physical chemistry. B, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers.
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Who cites it
25 citing papers in PubMed.
- Conductance of a potassium channel in the limit of zero membrane potential.Biophysical journal · 2026Article
- Force field sensitivity of ion occupancy in potassium channels.Biophysical journal · 2026Article
- Integrating Cryo-Electron Microscopy and Molecular Dynamics Simulations to Investigate Membrane Binding of Influenza Virus Fusion Peptides.Journal of the American Chemical Society · 2025Article
- Quantitative Comparison against Experiments Reveals Imperfections in Force Fields' Descriptions of POPC-Cholesterol Interactions.Journal of chemical theory and computation · 2023Article
- Ionizable Amino Lipids Distribution and Effects on DSPC/Cholesterol Membranes: Implications for Lipid Nanoparticle Structure.The journal of physical chemistry. B · 2023Article
- Modeling of Transmembrane Domain and Full-Length TLRs in Membrane Models.Methods in molecular biology (Clifton, N.J.) · 2023Article
- Inhibition of VMAT2 by β2-adrenergic agonists, antagonists, and the atypical antipsychotic ziprasidone.Communications biology · 2022Article
- Synthetic Heparan Sulfate Mimetic Pixatimod (PG545) Potently Inhibits SARS-CoV-2 by Disrupting the Spike-ACE2 Interaction.ACS central science · 2022Article
- Lipid21: Complex Lipid Membrane Simulations with AMBER.Journal of chemical theory and computation · 2022Article
- Unraveling membrane properties at the organelle-level with LipidDyn.Computational and structural biotechnology journal · 2022Article
- Atomistic simulations modify interpretation of spin-label oximetry data. Part 1: intensified water-lipid interfacial resistances.Applied magnetic resonance · 2021Article
- The structure and flexibility analysis of theLife science alliance · 2021Article
- Double Arylation of the Indole Side Chain of Tri- and Tetrapodal Tryptophan Derivatives Renders Highly Potent HIV-1 and EV-A71 Entry Inhibitors†.Journal of medicinal chemistry · 2021Article
- Coarse-Grained Force Fields from the Perspective of Statistical Mechanics: Better Understanding of the Origins of a MARTINI Hangover.Journal of chemical theory and computation · 2021Article
- Molecular dynamics simulations and experimental studies reveal differential permeability of withaferin-A and withanone across the model cell membrane.Scientific reports · 2021Article
- Simulation Study of Breast Cancer Lipid Changes Affecting Membrane Oxygen Permeability: Effects of Chain Length and Cholesterol.Advances in experimental medicine and biology · 2021Article
- Computer simulations of protein-membrane systems.Progress in molecular biology and translational science · 2020Article
- Characterization of Lipid-Protein Interactions and Lipid-Mediated Modulation of Membrane Protein Function through Molecular Simulation.Chemical reviews · 2019Review
- Computational Modeling of Realistic Cell Membranes.Chemical reviews · 2019Review
- Emerging Diversity in Lipid-Protein Interactions.Chemical reviews · 2019Review
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Authors and funding
3 authors.
Funding
Abstract
The Amber Lipid14 force field is expanded to include cholesterol parameters for all-atom cholesterol and lipid bilayer molecular dynamics simulations. The General Amber and Lipid14 force fields are used as a basis for assigning atom types and basic parameters. A new RESP charge derivation for cholesterol is presented, and tail parameters are adapted from Lipid14 alkane tails. 1,2-Dimyristoyl-sn-glycero-3-phosphocholine (DMPC), 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC), and 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) bilayers are simulated at a range of cholesterol contents. Experimental bilayer structural properties are compared with bilayer simulations and are found to be in good agreement. With this parameterization, another component of complex membranes is available for molecular dynamics with the Amber Lipid14 force field.
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