GAFFlipid: a General Amber Force Field for the accurate molecular dynamics simulation of phospholipid

Dickson, Callum J.; Rosso, Lula; Betz, Robin M.; Walker, Ross C.; Gould, Ian R.

doi:10.1039/c2sm26007g

Cited by 199 publications

(251 citation statements)

References 65 publications

(74 reference statements)

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“…However, the APL for POPE lipids is lower than expected and thickness value was overestimated by 10% [11]. The force field has also been shown to be able to reproduce the data on large lipid bilayers containing 288 lipids, with little changes in the APL, V L , and bilayer thickness [11]. The comparison with CHARMM27 and Berger force field also displayed GAFF's ability to reproduce the order asymmetry found at the beginning of lipid acyl chains [13].…”

Section: Bioinformatics -Updated Features and Applications 86mentioning

confidence: 73%

Section: Bioinformatics -Updated Features and Applications 86mentioning

confidence: 98%

“…This strategy has allowed a tensionless simulation of the lipids in the isothermal-isobaric (NPT) ensemble, achieving high level of agreement with experiment data for volume per lipid (V L ) and thickness value within 5% of experiment [11]. However, the APL for POPE lipids is lower than expected and thickness value was overestimated by 10% [11]. The force field has also been shown to be able to reproduce the data on large lipid bilayers containing 288 lipids, with little changes in the APL, V L , and bilayer thickness [11].…”

Section: Bioinformatics -Updated Features and Applications 86mentioning

confidence: 99%

“…The use of surface tension is necessary to achieve the correct APL for POPC [10], DOPC [13], and DMPC [12]. In order to better fit GAFF for lipid molecules, Dickson and colleagues set to re-parameterize the LJ terms for acyl chain carbons and hydrogens as the initial GAFF LJ terms were developed for proteins, nucleic acids, and small organic molecules [11].…”

Section: Bioinformatics -Updated Features and Applications 86mentioning

confidence: 99%

“…However, the general AMBER force field (GAFF) which was originally parameterized for the simulation of arbitrary organic molecules with preexisting AMBER force fields have been shown to reproduce lipid bilayer parameters satisfactorily [10]. GAFF has been tested on a range of lipids, including 1,2-dimyristoyl-d54-snglycero-3-phosphocholine (DMPC), 2-dioleoyl-sn-glycero-3-phosphocholine (DOPC), 1,2-dilauroyl-sn-glycero-3-phosphocholine (DLPC), DPPC, POPC, and 1-palmitoyl-2-oleoyl-snglycero-3-phosphoethanolamine (POPE) [11,12]. The use of surface tension is necessary to achieve the correct APL for POPC [10], DOPC [13], and DMPC [12].…”

Section: Bioinformatics -Updated Features and Applications 86mentioning

confidence: 99%

See 4 more Smart Citations

Bioinformatics for Membrane Lipid Simulations: Models, Computational Methods, and Web Server Tools

Leong¹,

Lim²,

Choong³

2016

Bioinformatics - Updated Features and Applications

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Biological membranes are complex environments consisting of different types of lipids and membrane proteins. The structure of a lipid bilayer is typically difficult to study because the membrane liquid crystalline state is made up of multiple disordered lipid molecules. This complicates the description of the lipid membrane properties by the conformation of any single lipid molecule. Molecular dynamics (MD) simulations have been used extensively to investigate properties of membrane lipids, lipid vesicles, and membrane protein systems. All-atom membrane models can elucidate detailed contacts between membrane proteins and its surrounding lipids, while united-atom and coarsegrained description have allowed larger models and longer timescales up to microsecond mark to be probed. Additionally, membrane models with mixed phospholipids and lipopolysaccharide content have made it possible to model improved views of biological membranes. Here, we present an overview of commonly used lipid force fields by the biosimulation community, useful tools for membrane MD simulations, and recent advances in membrane simulations.

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Section: Bioinformatics -Updated Features and Applications 86mentioning

confidence: 73%

Section: Bioinformatics -Updated Features and Applications 86mentioning

confidence: 98%

Section: Bioinformatics -Updated Features and Applications 86mentioning

confidence: 99%

Section: Bioinformatics -Updated Features and Applications 86mentioning

confidence: 99%

Section: Bioinformatics -Updated Features and Applications 86mentioning

confidence: 99%

See 3 more Smart Citations

Bioinformatics for Membrane Lipid Simulations: Models, Computational Methods, and Web Server Tools

Leong¹,

Lim²,

Choong³

2016

Bioinformatics - Updated Features and Applications

View full text Add to dashboard Cite

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Prediction of EPR Spectra of Lyotropic Liquid Crystals using a Combination of Molecular Dynamics Simulations and the Model‐Free Approach

Prior

Oganesyan

2017

Chemistry A European J

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We report the first application of fully atomistic molecular dynamics (MD) simulations to the prediction of the motional electron paramagnetic resonance (EPR) spectra of lyotropic liquid crystals in different aggregation states doped with a paramagnetic spin probe. The purpose of this study is twofold. First, given that EPR spectra are highly sensitive to the motions and order of the spin probes doped within lyotropic aggregates, simulation of EPR line shapes from the results of MD modelling provides an ultimate test bed for the force fields currently employed to model such systems. Second, the EPR line shapes are simulated using the motional parameters extracted from MD trajectories using the Model-Free (MF) approach. Thus a combined MD-EPR methodology allowed us to test directly the validity of the application of the MF approach to systems with multi-component molecular motions. All-atom MD simulations using the General AMBER Force Field (GAFF) have been performed on sodium dodecyl sulfate (SDS) and dodecyltrimethylammonium chloride (DTAC) liquid crystals. The resulting MD trajectories were used to predict and interpret the EPR spectra of pre-micellar, micellar, rod and lamellar aggregates. The predicted EPR spectra demonstrate good agreement with most of experimental line shapes thus confirming the validity of both the force fields employed and the MF approach for the studied systems. At the same time simulation results confirm that GAFF tends to overestimate the packing and the order of the carbonyl chains of the surfactant molecules.

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The Permeation Mechanism of Cisplatin Through a Dioleoylphosphocholine Bilayer**

2021

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The investigation of the intermolecular interactions between platinum-based anticancer drugs and lipid bilayers is of special relevance to unveil the mechanisms involved in different steps of the anticancer mode of action of these drugs. We have simulated the permeation of cisplatin through a model membrane composed of 1,2-dioleoyl-sn-glycero-3-phosphocholine lipids by means of umbrella sampling classical molecular dynamics simulations. The initial physisorption of cisplatin into the polar region of the lipid membrane is controlled, in a first moment, by long-range electrostatic interactions with the choline groups and, in a second step, by long-range electrostatic and hydrogen bond interactions with the phosphate groups. The second half of the permeation pathway, in which cisplatin diffuses through the nonpolar region of the bilayer, is characterized by the drop of the interactions with the polar heads and the rise of attractive interactions with the non-polar tails, which are dominated by van der Waals contributions.

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GAFFlipid: a General Amber Force Field for the accurate molecular dynamics simulation of phospholipid

Cited by 199 publications

References 65 publications

Bioinformatics for Membrane Lipid Simulations: Models, Computational Methods, and Web Server Tools

Bioinformatics for Membrane Lipid Simulations: Models, Computational Methods, and Web Server Tools

Prediction of EPR Spectra of Lyotropic Liquid Crystals using a Combination of Molecular Dynamics Simulations and the Model‐Free Approach

The Permeation Mechanism of Cisplatin Through a Dioleoylphosphocholine Bilayer**

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