The Molecular Structure of the Liquid-Ordered Phase of Lipid Bilayers

Sodt, Alexander J.; Sandar, Michael Logan; Gawrisch, Klaus; Pastor, Richard W.; Lyman, Edward

doi:10.1021/ja4105667

Cited by 224 publications

(326 citation statements)

References 55 publications

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“…Recently, ten μs-long AAMD simulations of a ternary mixture of DOPC, dipalmitoylphosphatidylcholine (DPPC), and cholesterol obtained on the Anton special purpose computer revealed remarkable heterogeneity in biomembranes 144 . Substructures were identified within the Lo phase of lipid bilayers composed of saturated hydrocarbon chains packed with local hexagonal order and separated by interstitial regions enriched in cholesterol and unsaturated chains.…”

Section: Computational Studies Of Cross-layer Couplingmentioning

confidence: 99%

Lateral organization, bilayer asymmetry, and inter-leaflet coupling of biological membranes

Nickels

Smith

Cheng

2015

Chemistry and Physics of Lipids

108

115

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Understanding of cell membrane organization has evolved significantly from the classic fluid mosaic model. It is now recognized that biological membranes are highly organized structures, with differences in lipid compositions between inner and outer leaflets and in lateral structures within the bilayer plane, known as lipid rafts. These organizing principles are important for protein localization and function as well as cellular signaling. However, the mechanisms and biophysical basis of lipid raft formation, structure, dynamics and function are not clearly understood. One key question, which we focus on in this review, is how lateral organization and leaflet compositional asymmetry are coupled. Detailed information elucidating this question has been sparse because of the small size and transient nature of rafts and the experimental challenges in constructing asymmetric bilayers. Resolving this mystery will require advances in both experimentation and modeling. We discuss here the preparation of model systems along with experimental and computational approaches that have been applied in efforts to address this key question in membrane biology. We seek to place recent and future advances in experimental and computational techniques in context, providing insight into in-plane and transverse organization of biological membranes.

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Section: Computational Studies Of Cross-layer Couplingmentioning

confidence: 99%

Lateral organization, bilayer asymmetry, and inter-leaflet coupling of biological membranes

Nickels

Smith

Cheng

2015

Chemistry and Physics of Lipids

108

115

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“…In a ternary mixture that supports liquid-ordered/liquiddisordered (L o /L d ) coexistence nanoscale heterogeneities in composition and dynamics are observed by stimulated emission depletion fluorescence correlation spectroscopy (8), provided the mixture is deposited on a glass support, which pins a fraction of lipids facing the support. In similar mixtures of a uniform L o phase, heterogeneities are observed on yet smaller lengthscales and timescales by molecular dynamics (MD) simulations (9,10) and interferometric scattering-based single-particle tracking (11).…”

Section: Introductionmentioning

confidence: 99%

Toward Hydrodynamics with Solvent Free Lipid Models: STRD Martini

Zgorski

Lyman

2016

Biophysical Journal

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Solvent hydrodynamics are incorporated into simulations of the solvent-free Dry Martini model. The solvent hydrodynamics are modeled with the stochastic rotation dynamics (SRD) algorithm, a particle-based method for resolving fluid hydrodynamics. SRD does not require calculation of particle-particle distances in the solvent, and so is scalable to arbitrary volumes of solvent with minimal additional computational overhead. The viscosity of the solvent is easily tuned via parameters of the algorithm to span an order of magnitude in viscosity around the viscosity of water at room temperature. The combination ''Stochastic Thermostatted Rotation Dynamics (STRD) with Martini'' was implemented in Gromacs v.5.01. Simulations of an SRD/palmitoyloleoylphosphatidylcholine membrane demonstrate that the solvent may be included without reparametrizing the lipid model, with minimal perturbation to the thermodynamics. A recent generalization of Saffman-Delbruck theory to periodic geometries by Camley and Brown indicates that lipid dynamics are contaminated by a finite-size effect in typical molecular dynamics (MD) simulations, and that very large systems are required for quantitative simulation of dynamics. Analysis of lipid translational diffusion in this work shows good agreement with the theory, and with explicitly solvated simulations. This indicates that STRD Martini is a viable approach for quantitative simulation of membrane dynamics and does not require massive computational overhead to model the solvent.

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“…1) are selected, because these membranes have a different degree of ordering as is observed in the structure factors [6,7]. This study is therefore a precursor to studying liquid (dis)ordered phases (Lo and Ld) [8], which are models of membrane rafts.…”

Section: Introductionmentioning

confidence: 99%

Oxygen Transport to Tissue XL

2018

Advances in Experimental Medicine and Biology

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Rafts are nanoscale ordered domains in biological membranes that are rich in saturated phospholipids. In this study, the influence of chain unsaturation and temperature on oxygen diffusion through lipid membranes is examined using advanced computational modeling. The studied phospholipids with increasing unsaturation are: 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC), 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC), and 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC). The unsaturation correlates with the area per lipid and the order parameter. Oxygen diffusion is found to be faster at higher temperature, and the solubility of oxygen in the membrane with respect to water decreases. Diffusion varies over a larger range across the membrane at 323 K in DPPC than in DOPC, whereas POPC has intermediate diffusivity. Oxygen diffusion in saturated lipids is faster at the membrane center and slower near the head group region than in unsaturated lipids. Oxygen solubility in DPPC is higher than in unsaturated lipids.

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The Molecular Structure of the Liquid-Ordered Phase of Lipid Bilayers

Cited by 224 publications

References 55 publications

Lateral organization, bilayer asymmetry, and inter-leaflet coupling of biological membranes

Lateral organization, bilayer asymmetry, and inter-leaflet coupling of biological membranes

Toward Hydrodynamics with Solvent Free Lipid Models: STRD Martini

Oxygen Transport to Tissue XL

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