A Coarse Grain Model for Phospholipid Simulations

Shelley, John C.; Shelley, Mee; Reeder, Robert C.; Bandyopadhyay, Sanjoy; Klein, Michael L.

doi:10.1021/jp010238p

Cited by 499 publications

(609 citation statements)

References 25 publications

(37 reference statements)

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“…All MD simulations were performed in the constant NVT ensemble using the GROMACS 3.3.0 software package, 33 with V 0 =(1.8602 nm) 3 and T = 298K maintained with the Nose-Hoover thermostat. 34,35 All quantities computed from MD simulation were tabulated on a grid with Δr = 0.001nm according to the discrete delta function basis defined in eq (9). Because the grid is so fine, the systems were simulated for 30ns in order to adequately converge all relevant quantities and accurately evaluate necessary numerical derivatives.…”

Section: Resultsmentioning

confidence: 99%

“…The force field, f(r ), minimizing the residual under these constraints is uniquely determined and may be conveniently described by a discrete delta function basis for which δ D (r) =1 when −Δr / 2 ≤r < Δr / 2 and is 0 otherwise. In this basis the force field may be represented as: (9) This definition corresponds to tabulating the force field at a discrete set of points, r d , about which ( r d − Δr / 2 < r < r d + Δr / 2 ) the force field is assumed to be constant. Previous applications of the MS-CG method 16,17,24-27 have typically employed a spline basis for representing the FM force field.…”

Section: Force-matching To a Central Pair Potentialmentioning

confidence: 99%

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Multiscale Coarse-Graining and Structural Correlations: Connections to Liquid-State Theory

et al. 2007

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(2005)]. If no approximations are made, the MS-CG method yields a many-body multi-dimensional potential of mean force describing the interactions between CG sites. However, numerical applications of the MS-CG method typically employ a set of pair potentials to describe non-bonded interactions. The analogy between coarse-graining and the inverse problem of liquid state theory clarifies the general significance of three-particle correlations for the development of such CG pair potentials. It is demonstrated that the MS-CG methodology incorporates critical three-body correlation effects and that, for isotropic homogeneous systems evolving under a central pair potential, the MS-CG equations are a discretized representation of the well-known Yvon-Born-Green equation. Numerical calculations validate the theory and illustrate the role of these structural correlations in the MS-CG method.

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Section: Resultsmentioning

confidence: 99%

Section: Force-matching To a Central Pair Potentialmentioning

confidence: 99%

Multiscale Coarse-Graining and Structural Correlations: Connections to Liquid-State Theory

et al. 2007

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“…In order to understand the larger scale effects, simulations with simpler models have to be applied [58,59,60,61].…”

Section: Discussionmentioning

confidence: 99%

Structural effects of small molecules on phospholipid bilayers investigated by molecular simulations

Lee

Faller

Sum

et al. 2004

Fluid Phase Equilibria

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We summarize and compare recent Molecular Dynamics simulations on the interactions of dipalmitoylphosphatidylcholine (DPPC) bilayers in the liquid crystalline phase with a number of small molecules including trehalose, a disaccharide of glucose, alcohols, and dimethylsulfoxide (DMSO). The sugar molecules tend to stabilize the structure of the bilayer as they bridge adjacent lipid headgroups. They do not strongly change the structure of the bilayer. Alcohols and DMSO destabilize the bilayer as they increase its area per molecule in the bilayer plane and decrease the order parameter. Alcohols have a stronger detrimental effect than DMSO. The observables which we compare are the area per molecule in the plane of the bilayer, the membrane thickness, and the NMR order parameter of DPPC hydrocarbon tails. The area per molecule and the order parameter are very well correlated whereas the bilayer thickness is not necessarily correlated with them.

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“…29,30,31 One of the first CG MD lipid models to successfully show assembly of lipids was developed by Klein and coworkers. 29,32 The developed DMPC CG model was parameterized to mimic structural features resulting from all-atom simulations. Successful assembly of lamellar and inverted hexagonal phases from a random distribution demonstrated the ability of the model to investigate the dynamics of lipid assembly.…”

Section: Introductionmentioning

confidence: 99%

Coarse Grained Protein−Lipid Model with Application to Lipoprotein Particles

et al. 2006

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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 previously developed by Marrink et al., though further 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 coarsegraining reduces system size about ten-fold and allows integration time steps of 25 to 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 coarsegrained models. Our model proved reliable in maintaining the shape of pre-assembled particles and in accurately reproducing overall structural features of high-density lipoproteins. Microsecond simulations of lipoprotein assembly revealed formation of a protein-lipid complex in which two proteins are attached to either side of a discoidal lipid bilayer.

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A Coarse Grain Model for Phospholipid Simulations

Cited by 499 publications

References 25 publications

Multiscale Coarse-Graining and Structural Correlations: Connections to Liquid-State Theory

Multiscale Coarse-Graining and Structural Correlations: Connections to Liquid-State Theory

Structural effects of small molecules on phospholipid bilayers investigated by molecular simulations

Coarse Grained Protein−Lipid Model with Application to Lipoprotein Particles

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