Lipid Simulations: A Perspective on Lipids in Action

Interactions between lipids and membrane proteins play a key role in determining the nanoscale dynamic and structural properties of biological membranes. Molecular dynamics (MD) simulations provide a valuable tool for studying membrane models, complementing experimental approaches. It is now possible to simulate large membrane systems, such as simplified models of bacterial and viral envelope membranes. Consequently, there is a pressing need to develop tools to visualize and quantify the dynamics of these immense systems, which typically are comprised of millions of particles. To tackle this issue, we have developed visual and quantitative analyses of molecular positions and their velocity field using path line, vector field and streamline techniques. This allows us to highlight large, transient flow-like movements of lipids and to better understand crowding within the lipid bilayer. The current study focuses on visualization and analysis of lipid dynamics. However, the methods are flexible and can be readily applied to e.g. proteins and nanoparticles within large complex membranes. The protocols developed here are readily accessible both as a plugin for the molecular visualization program VMD and as a module for the MDAnalysis library.

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“…vortices. This behaviour has been reported in previous computational 56,57 and experimental 58 studies. Furthermore, Sup.…”

Section: Resultssupporting

confidence: 88%

Methodologies for the analysis of instantaneous lipid diffusion in md simulations of large membrane systems

et al. 2014

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“…MD simulations provide access to short-lived phenomena at atomistic resolution allowing for a direct quantification of molecular packing densities, acyl chain order, lateral pressure profiles and lipid diffusion (Van Der Ploeg and Berendsen, 1982;Van Der Ploeg et al, 1983;Bennett and Tieleman, 2013). Because MD simulations at atomistic resolution are demanding with respect to computational time, it is currently not possible to characterize phenomena on a time scale much longer than ~ 1 μs (Vattulainen and Rog, 2011;Marrink and Tieleman, 2013). Coarse grained models such as the Martini model reduce the complexity at the cost of molecular detail and provide access to longer time scales and larger membrane systems (Marrink and Tieleman, 2013).…”

Section: What Is Membrane Fluidity and How To Measure It?mentioning

confidence: 99%

“…An exciting development is the increased use of molecular dynamics (MD) simulations to study the structure and properties of biological membranes (Smit et al, 1990;Marrink et al, 2007;Vattulainen and Rog, 2011). MD simulations provide access to short-lived phenomena at atomistic resolution allowing for a direct quantification of molecular packing densities, acyl chain order, lateral pressure profiles and lipid diffusion (Van Der Ploeg and Berendsen, 1982;Van Der Ploeg et al, 1983;Bennett and Tieleman, 2013).…”

Section: What Is Membrane Fluidity and How To Measure It?mentioning

confidence: 99%

Control of membrane fluidity: the OLE pathway in focus

Ballweg

Ernst

2016

Biological Chemistry

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Abstract:The maintenance of a fluid lipid bilayer is key for membrane integrity and cell viability. We are only beginning to understand how eukaryotic cells sense and maintain the characteristic lipid compositions and bulk membrane properties of their organelles. One of the key factors determining membrane fluidity and phase behavior is the proportion of saturated and unsaturated acyl chains in membrane lipids. Saccharomyces cerevisiae is an ideal model organism to study the regulation of the lipid acyl chain composition via the OLE pathway. The OLE pathway comprises all steps involved in the regulated mobilization of the transcription factors Mga2 and Spt23 from the endoplasmic reticulum (ER), which then drive the expression of OLE1 in the nucleus. OLE1 encodes for the essential Δ9-fatty acid desaturase Ole1 and is crucial for de novo biosynthesis of unsaturated fatty acids (UFAs) that are used as lipid building blocks. This review summarizes our current knowledge of the OLE pathway, the best-characterized, eukaryotic senseand-control system regulating membrane lipid saturation, and identifies open questions to indicate future directions.

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“…Hydrocarbons May Induce Membrane Flexibility by Accumulating within the Lipid Bilayer Molecular dynamics simulations have become an invaluable technique used to investigate the nanoscale organization of lipid membranes (Marrink et al, 2009;Vattulainen and Rog, 2011), particularly in complex membrane systems (Ingólfsson et al, 2014;Manna et al, 2014). In order to understand how hydrocarbons could affect membrane properties, a novel symmetrical membrane model system was simulated based on the pseudoatomistic Martini force field, with an approximately 4:1 mapping of heavy atoms to coarse-grained particles (Supplemental Fig.…”

Section: The Absence Of Hydrocarbons Has Minor Effects On Photosynthementioning

confidence: 99%

Hydrocarbons Are Essential for Optimal Cell Size, Division, and Growth of Cyanobacteria

et al. 2016

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Cyanobacteria are intricately organized, incorporating an array of internal thylakoid membranes, the site of photosynthesis, into cells no larger than other bacteria. They also synthesize C15-C19 alkanes and alkenes, which results in substantial production of hydrocarbons in the environment. All sequenced cyanobacteria encode hydrocarbon biosynthesis pathways, suggesting an important, undefined physiological role for these compounds. Here, we demonstrate that hydrocarbon-deficient mutants of Synechococcus sp. PCC 7002 and Synechocystis sp. PCC 6803 exhibit significant phenotypic differences from wild type, including enlarged cell size, reduced growth, and increased division defects. Photosynthetic rates were similar between strains, although a minor reduction in energy transfer between the soluble light harvesting phycobilisome complex and membrane-bound photosystems was observed. Hydrocarbons were shown to accumulate in thylakoid and cytoplasmic membranes. Modeling of membranes suggests these compounds aggregate in the center of the lipid bilayer, potentially promoting membrane flexibility and facilitating curvature. In vivo measurements confirmed that Synechococcus sp. PCC 7002 mutants lacking hydrocarbons exhibit reduced thylakoid membrane curvature compared to wild type. We propose that hydrocarbons may have a role in inducing the flexibility in membranes required for optimal cell division, size, and growth, and efficient association of soluble and membrane bound proteins. The recent identification of C15-C17 alkanes and alkenes in microalgal species suggests hydrocarbons may serve a similar function in a broad range of photosynthetic organisms.

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Lipid Simulations: A Perspective on Lipids in Action

Cited by 37 publications

References 86 publications

Methodologies for the analysis of instantaneous lipid diffusion in md simulations of large membrane systems

Methodologies for the analysis of instantaneous lipid diffusion in md simulations of large membrane systems

Control of membrane fluidity: the OLE pathway in focus

Hydrocarbons Are Essential for Optimal Cell Size, Division, and Growth of Cyanobacteria

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