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Title: Computational Modeling of Realistic Cell Membranes

Authors:
ORCiD logo [1];  [2];  [1];  [3];  [2]; ORCiD logo [4]
+ Show Author Affiliations
  1. Univ. of Groningen, Groningen (Netherlands)
  2. Univ. of Calgary, AB (Canada)
  3. Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States)
  4. Univ. of Oxford, Oxford (United Kingdom)
Publication Date:
Research Org.:
Univ. of Groningen (Netherlands); Lawrence Livermore National Laboratory (LLNL), Livermore, CA (United States)
Sponsoring Org.:
USDOE National Nuclear Security Administration (NNSA)
OSTI Identifier:
1511596
Alternate Identifier(s):
OSTI ID: 1508816; OSTI ID: 1581493
Report Number(s):
LLNL-JRNL-755168
Journal ID: ISSN 0009-2665
Grant/Contract Number:  
AC52-07NA27344; COMP-MICR-CROW-MEM
Resource Type:
Accepted Manuscript
Journal Name:
Chemical Reviews
Additional Journal Information:
Journal Volume: 119; Journal Issue: 9; Journal ID: ISSN 0009-2665
Publisher:
American Chemical Society
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; Biological and medical sciences

Citation Formats

Marrink, Siewert J., Corradi, Valentina, Souza, Paulo C. T., Ingólfsson, Helgi I., Tieleman, D. Peter, and Sansom, Mark S. P. Computational Modeling of Realistic Cell Membranes. United States: N. p., 2019. Web. doi:10.1021/acs.chemrev.8b00460.
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Marrink, Siewert J., Corradi, Valentina, Souza, Paulo C. T., Ingólfsson, Helgi I., Tieleman, D. Peter, & Sansom, Mark S. P. Computational Modeling of Realistic Cell Membranes. United States. https://doi.org/10.1021/acs.chemrev.8b00460
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Marrink, Siewert J., Corradi, Valentina, Souza, Paulo C. T., Ingólfsson, Helgi I., Tieleman, D. Peter, and Sansom, Mark S. P. Wed . "Computational Modeling of Realistic Cell Membranes". United States. https://doi.org/10.1021/acs.chemrev.8b00460. https://www.osti.gov/servlets/purl/1511596.
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@article{osti_1511596,
title = {Computational Modeling of Realistic Cell Membranes},
author = {Marrink, Siewert J. and Corradi, Valentina and Souza, Paulo C. T. and Ingólfsson, Helgi I. and Tieleman, D. Peter and Sansom, Mark S. P.},
abstractNote = {},
doi = {10.1021/acs.chemrev.8b00460},
journal = {Chemical Reviews},
number = 9,
volume = 119,
place = {United States},
year = {Wed Jan 09 00:00:00 EST 2019},
month = {Wed Jan 09 00:00:00 EST 2019}
}
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Domain Stability in Biomimetic Membranes Driven by Lipid Polyunsaturation
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Update of the CHARMM All-Atom Additive Force Field for Lipids: Validation on Six Lipid Types
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Membrane Compartmentalization Reducing the Mobility of Lipids and Proteins within a Model Plasma Membrane
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Roles of PIP 2 in the membrane binding of MIM I‐ BAR : insights from molecular dynamics simulations
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Localization and Ordering of Lipids Around Aquaporin-0: Protein and Lipid Mobility Effects
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Simulating Gram-Negative Bacterial Outer Membrane: A Coarse Grain Model
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Critical Comparison of Biomembrane Force Fields: Protein–Lipid Interactions at the Membrane Interface
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Self-Assembly Simulations of Classic Claudins—Insights into the Pore Structure, Selectivity, and Higher Order Complexes
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Modeling Diversity in Structures of Bacterial Outer Membrane Lipids
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Coarse-Grained MD Simulations of Membrane Protein-Bilayer Self-Assembly
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Molecular Mechanism of Uptake of Cationic Photoantimicrobial Phthalocyanine across Bacterial Membranes Revealed by Molecular Dynamics Simulations
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Molecular Simulations of Lipid-Mediated Protein-Protein Interactions
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α-Synuclein Has a High Affinity for Packing Defects in a Bilayer Membrane
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A Coarse-Grained Model for Polyethylene Oxide and Polyethylene Glycol: Conformation and Hydrodynamics
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Molecular Dynamics Simulations of the Bacterial UraA H+-Uracil Symporter in Lipid Bilayers Reveal a Closed State and a Selective Interaction with Cardiolipin
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Probing the importance of lipid diversity in cell membranes via molecular simulation
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The Role of Atomic Polarization in the Thermodynamics of Chloroform Partitioning to Lipid Bilayers
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Dual Action of BPC194: A Membrane Active Peptide Killing Bacterial Cells
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Multiscale Modeling of Four-Component Lipid Mixtures: Domain Composition, Size, Alignment, and Properties of the Phase Interface
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More than the sum of its parts: Coarse-grained peptide-lipid interactions from a simple cross-parametrization
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Molecular Dynamics Simulation Analysis of Membrane Defects and Pore Propensity of Hemifusion Diaphragms
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Effects of Transmembrane α-Helix Length and Concentration on Phase Behavior in Four-Component Lipid Mixtures: A Molecular Dynamics Study
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The Integrin Receptor in Biologically Relevant Bilayers: Insights from Molecular Dynamics Simulations
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A Coarse Grained Model for a Lipid Membrane with Physiological Composition and Leaflet Asymmetry
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A refined polarizable water model for the coarse-grained MARTINI force field with long-range electrostatic interactions
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The Role of the Membrane in the Structure and Biophysical Robustness of the Dengue Virion Envelope
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Characterizing the Membrane-Bound State of Cytochrome P450 3A4: Structure, Depth of Insertion, and Orientation
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Cholesterol in Bilayers with PUFA Chains: Doping with DMPC or POPC Results in Sterol Reorientation and Membrane-Domain Formation
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Atomistic insights into cardiolipin binding sites of cytochrome c oxidase
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A Role for a Specific Cholesterol Interaction in Stabilizing the Apo Configuration of the Human A 2A Adenosine Receptor
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The nanoscale organization of the B lymphocyte membrane
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Pore Formation Coupled to Ion Transport through Lipid Membranes as Induced by Transmembrane Ionic Charge Imbalance:  Atomistic Molecular Dynamics Study
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α-Synuclein Induces Both Positive Mean Curvature and Negative Gaussian Curvature in Membranes
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A Comparison of Coarse-Grained and Continuum Models for Membrane Bending in Lipid Bilayer Fusion Pores
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Binding and Aggregation Mechanism of Amyloid β-Peptides onto the GM1 Ganglioside-Containing Lipid Membrane
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Multiple interactions between an Arf/GEF complex and charged lipids determine activation kinetics on the membrane
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Conical Lipids in Flat Bilayers Induce Packing Defects Similar to that Induced by Positive Curvature
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Molecular View of Cholesterol Flip-Flop and Chemical Potential in Different Membrane Environments
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A Role for Weak Electrostatic Interactions in Peripheral Membrane Protein Binding
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Molecular Dynamics of Photosystem II Embedded in the Thylakoid Membrane
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Lipid Properties and the Orientation of Aromatic Residues in OmpF, Influenza M2, and Alamethicin Systems:  Molecular Dynamics Simulations
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Interactions of the EphA2 Kinase Domain with PIPs in Membranes: Implications for Receptor Function
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Structural Basis of Phosphatidic Acid Sensing by APH in Apicomplexan Parasites
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Structural Lipids Enable the Formation of Functional Oligomers of the Eukaryotic Purine Symporter UapA
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Cardiolipin binds selectively but transiently to conserved lysine residues in the rotor of metazoan ATP synthases
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Predictions for Cholesterol Interaction Sites on the A 2A Adenosine Receptor
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Extension of the Slipids Force Field to Polyunsaturated Lipids
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Membrane invagination induced by Shiga toxin B-subunit: from molecular structure to tube formation
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Docosahexaenoic acid regulates the formation of lipid rafts: A unified view from experiment and simulation
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Lipid tempering simulation of model biological membranes on parallel platforms
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Going Backward: A Flexible Geometric Approach to Reverse Transformation from Coarse Grained to Atomistic Models
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Coarse-Grained Model for PEGylated Lipids: Effect of PEGylation on the Size and Shape of Self-Assembled Structures
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Solvent-exposed lipid tail protrusions depend on lipid membrane composition and curvature
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Composition Fluctuations in Lipid Bilayers
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Validating lipid force fields against experimental data: Progress, challenges and perspectives
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Insight into the Properties of Cardiolipin Containing Bilayers from Molecular Dynamics Simulations, Using a Hybrid All-Atom/United-Atom Force Field
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Two distinct anionic phospholipid-dependent events involved in SecA-mediated protein translocation
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Membrane undulation induced by NS4A of Dengue virus: a molecular dynamics simulation study
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A new force field for simulating phosphatidylcholine bilayers
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Model-based approaches for the determination of lipid bilayer structure from small-angle neutron and X-ray scattering data
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Lipid chain branching at the iso- and anteiso-positions in complex chlamydia membranes: A molecular dynamics study
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Complementary biophysical tools to investigate lipid specificity in the interaction between bioactive molecules and the plasma membrane: A review
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Effects of protein crowding on membrane systems
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Exploring DNA dynamics within oligonucleosomes with coarse-grained simulations: SIRAH force field extension for protein-DNA complexes
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Mechanism of Membrane Curvature Sensing by Amphipathic Helix Containing Proteins
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Molecular Dynamics Simulation Analysis of Membrane Defects and Pore Propensity of Hemifusion Diaphragms
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Molecular Dynamics and NMR Spectroscopy Studies of E. coli Lipopolysaccharide Structure and Dynamics
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Interactions between Fengycin and Model Bilayers Quantified by Coarse-Grained Molecular Dynamics
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Macroscopic Phase Separation, Modulated Phases, and Microemulsions: A Unified Picture of Rafts
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Not Just an Oil Slick: How the Energetics of Protein-Membrane Interactions Impacts the Function and Organization of Transmembrane Proteins
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Bilayer Properties of Lipid A from Various Gram-Negative Bacteria
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Toward Hydrodynamics with Solvent Free Lipid Models: STRD Martini
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Lipid Perturbation by Membrane Proteins and the Lipophobic Effect
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Effect of Ceramide Tail Length on the Structure of Model Stratum Corneum Lipid Bilayers
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Lipids Alter Rhodopsin Function via Ligand-like and Solvent-like Interactions
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Lipids and Ions Traverse the Membrane by the Same Physical Pathway in the nhTMEM16 Scramblase
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Molecular Dynamics of the Association of L-Selectin and FERM Regulated by PIP2
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Interplay between Membrane Curvature and Cholesterol: Role of Palmitoylated Caveolin-1
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Biomembranes research using thermal and cold neutrons
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Generation and sensing of membrane curvature: Where materials science and biophysics meet
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CellSim3D: GPU accelerated software for simulations of cellular growth and division in three dimensions
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Multiscale molecular dynamics simulations of lipid interactions with P-glycoprotein in a complex membrane
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Shedding light on the puzzle of drug-membrane interactions: Experimental techniques and molecular dynamics simulations
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MemProtMD: Automated Insertion of Membrane Protein Structures into Explicit Lipid Membranes
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A Thermodynamic Funnel Drives Bacterial Lipopolysaccharide Transfer in the TLR4 Pathway
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Lipid-Mediated Interactions between Intrinsic Membrane Proteins: Dependence on Protein Size and Lipid Composition
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Computer Simulation of the Rough Lipopolysaccharide Membrane of Pseudomonas aeruginosa
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Modeling Diversity in Structures of Bacterial Outer Membrane Lipids
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Hybrid Particle-Field Model for Conformational Dynamics of Peptide Chains
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Simulating Gram-Negative Bacterial Outer Membrane: A Coarse Grain Model
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Cholesterol in Bilayers with PUFA Chains: Doping with DMPC or POPC Results in Sterol Reorientation and Membrane-Domain Formation
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From Coarse Grained to Atomistic: A Serial Multiscale Approach to Membrane Protein Simulations
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Improved Parameters for the Martini Coarse-Grained Protein Force Field
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Going Backward: A Flexible Geometric Approach to Reverse Transformation from Coarse Grained to Atomistic Models
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Dry Martini, a Coarse-Grained Force Field for Lipid Membrane Simulations with Implicit Solvent
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Simulation of the Spontaneous Aggregation of Phospholipids into Bilayers
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Lipids Out of Equilibrium:  Energetics of Desorption and Pore Mediated Flip-Flop
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Molecular View of the Role of Fusion Peptides in Promoting Positive Membrane Curvature
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Predictions for Cholesterol Interaction Sites on the A 2A Adenosine Receptor
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Transmembrane Fragment Structures of Amyloid Precursor Protein Depend on Membrane Surface Curvature
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α-Synuclein-Induced Membrane Remodeling Is Driven by Binding Affinity, Partition Depth, and Interleaflet Order Asymmetry
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Lateral Diffusion in Lipid Membranes through Collective Flows
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Calcium Directly Regulates Phosphatidylinositol 4,5-Bisphosphate Headgroup Conformation and Recognition
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