ArticleThe journal of physical chemistry. B2006
Coarse grained protein-lipid model with application to lipoprotein particles.
Article in The journal of physical chemistry. B, 2006. 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, 263 citations in OpenAlex.
- Molecular Mechanisms Governing Peptide Nanodisc Assembly and Stability.bioRxiv : the preprint server for biology · 2026Article
- Critical Role of MgThe journal of physical chemistry. B · 2025Article
- Partitioning Indicator Displacement Assay.ACS omega · 2025Article
- Computational Design and In Vitro and In Vivo Characterization of an ApoE-Based Synthetic High-Density Lipoprotein for Sepsis Therapy.Biomolecules · 2025Article
- Thermodynamic Transferability in Coarse-Grained Force Fields Using Graph Neural Networks.Journal of chemical theory and computation · 2024Article
- An atomistic characterization of high-density lipoproteins and the conserved "LN" region of apoA-I.Biophysical journal · 2024Article
- Applications of Molecular Dynamics Simulation in Protein Study.Membranes · 2022Review
- Replenishing HDL with synthetic HDL has multiple protective effects against sepsis in mice.Science signaling · 2022Article
- Deep geometric representations for modeling effects of mutations on protein-protein binding affinity.PLoS computational biology · 2021Article
- Formation and Properties of a Self-Assembled Nanoparticle-Supported Lipid Bilayer Probed through Molecular Dynamics Simulations.Langmuir : the ACS journal of surfaces and colloids · 2020Article
- Computational Nanoscopy of Tight Junctions at the Blood-Brain Barrier Interface.International journal of molecular sciences · 2019Review
- Characterization of Lipid-Protein Interactions and Lipid-Mediated Modulation of Membrane Protein Function through Molecular Simulation.Chemical reviews · 2019Review
- An Overview of Molecular Modeling for Drug Discovery with Specific Illustrative Examples of Applications.Molecules (Basel, Switzerland) · 2019Review
- mol2sphere: spherical decomposition of multi-domain molecules for visualization and coarse grained spatial modeling.Bioinformatics (Oxford, England) · 2018Article
- Molecular dynamics simulations of lipid nanodiscs.Biochimica et biophysica acta. Biomembranes · 2018Article
- Polymer Nanodiscs: Discoidal Amphiphilic Block Copolymer Membranes as a New Platform for Membrane Proteins.Scientific reports · 2017Article
- Effects of Coarse Graining and Saturation of Hydrocarbon Chains on Structure and Dynamics of Simulated Lipid Molecules.Scientific reports · 2017Article
- Nanodiscs in Membrane Biochemistry and Biophysics.Chemical reviews · 2017Review
- Fast Photochemical Oxidation of Proteins Maps the Topology of Intrinsic Membrane Proteins: Light-Harvesting Complex 2 in a Nanodisc.Analytical chemistry · 2016Article
- Binding equilibrium and kinetics of membrane-anchored receptors and ligands in cell adhesion: Insights from computational model systems and theory.Cell adhesion & migration · 2016Review
19 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors at 1 institution in 1 country.
Funding
Abstract
A coarse-grained model for molecular dynamics simulations is extended from lipids to proteins. In the framework of such models pioneered by Klein, atoms are described group-wise by beads, with the interactions between beads governed by effective potentials. The extension developed here is based on a coarse-grained lipid model developed previously by Marrink et al., although future versions will reconcile the approach taken with the systematic approach of Klein and other authors. Each amino acid of the protein is represented by two coarse-grained beads, one for the backbone (identical for all residues) and one for the side-chain (which differs depending on the residue type). The coarse-graining reduces the system size about 10-fold and allows integration time steps of 25-50 fs. The model is applied to simulations of discoidal high-density lipoprotein particles involving water, lipids, and two primarily helical proteins. These particles are an ideal test system for the extension of coarse-grained models. Our model proved to be reliable in maintaining the shape of preassembled particles and in reproducing the overall structural features of high-density lipoproteins accurately. Microsecond simulations of lipoprotein assembly revealed the formation of a protein-lipid complex in which two proteins are attached to either side of a discoidal lipid bilayer.
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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.