The MARTINI force field : Coarse grained model for biomolecular simulations
TLDR
An improved and extended version of the coarse grained lipid model is presented, coined the MARTINI force field, based on the reproduction of partitioning free energies between polar and apolar phases of a large number of chemical compounds to reproduce the free energies of these chemical building blocks.Abstract:
We present an improved and extended version of our coarse grained lipid model. The new version, coined the MARTINI force field, is parametrized in a systematic way, based on the reproduction of partitioning free energies between polar and apolar phases of a large number of chemical compounds. To reproduce the free energies of these chemical building blocks, the number of possible interaction levels of the coarse-grained sites has increased compared to those of the previous model. Application of the new model to lipid bilayers shows an improved behavior in terms of the stress profile across the bilayer and the tendency to form pores. An extension of the force field now also allows the simulation of planar (ring) compounds, including sterols. Application to a bilayer/cholesterol system at various concentrations shows the typical cholesterol condensation effect similar to that observed in all atom representations.read more
Citations
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Dynamic interactions between a membrane binding protein and lipids induce fluctuating diffusivity
TL;DR: This work reveals two diffusive properties of a PH domain bound to the surface of a PIP-containing membrane using molecular dynamics simulations and provides evidence that the complexity of protein-lipid interactions plays a crucial role in the diffusion of proteins on biological membrane surfaces.
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GROMACS—the road ahead
TL;DR: The state of the art in MD simulations is reviewed with a focus on imminent challenges for the GROMACS (GROningen MAchine for Chemical Simulation) software.
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Disaccharides Impact the Lateral Organization of Lipid Membranes
Gemma Moiset,Cesar A. Lopez,Rianne Bartelds,Lukasz Syga,Egon M. A. Rijpkema,Abhishek Cukkemane,Marc Baldus,Bert Poolman,Siewert J. Marrink +8 more
TL;DR: It is found that nonreducing disaccharides, sucrose and trehalose, strongly destabilize the phase separation leading to uniformly mixed membranes as opposed to monosaccharide and reducing disac Charcoal, which might prove to be a more generic way by which surface bound agents could affect membranes.
Journal ArticleDOI
High Density Lipoprotein structural changes and drug response in lipidomic profiles following the long-term fenofibrate therapy in the FIELD substudy
Laxman Yetukuri,Ilkka Huopaniemi,Artturi Koivuniemi,Marianna Maranghi,Marianna Maranghi,Anne Hiukka,Heli Nygren,Samuel Kaski,Marja-Riitta Taskinen,Ilpo Vattulainen,Ilpo Vattulainen,Ilpo Vattulainen,Matti Jauhiainen,Matti Jauhiainen,Matej Orešič,Matej Orešič +15 more
TL;DR: It is found that fenofibrate leads to complex HDL compositional changes including increased apoA-II, diminishment of lysophosphatidylcholines and increase of sphingomyelins and apo-II is more deeply buried in the lipid matrix than apOA-I.
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Molecular Dynamics Simulations of DPPC Bilayers Using “LIME”, a New Coarse-Grained Model
Emily M. Curtis,Carol K. Hall +1 more
TL;DR: A new intermediate resolution model for phospholipids, LIME, designed for use with discontinuous molecular dynamics (DMD) simulations is presented, which quantitatively reproduces the main structural properties that are observed experimentally.
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