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
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Carsten Kutzner,Szilárd Páll,Martin Fechner,Ansgar Esztermann,Bert L. de Groot,Helmut Grubmüller +5 more
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Joseph H. Lorent,Blanca B. Diaz-Rohrer,Xubo Lin,Kevin J. Spring,Alemayehu A. Gorfe,Kandice R. Levental,Ilya Levental +6 more
TL;DR: It is shown that the surface area, length and palmitoylation of single-pass transmembrane domains are crucial for raft partitioning and a general model to predict protein association with rafts is proposed.
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Protein Crowding in Lipid Bilayers Gives Rise to Non-Gaussian Anomalous Lateral Diffusion of Phospholipids and Proteins
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The materials science of collagen.
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Theoretical and Computational Investigations of Nanoparticle–Biomembrane Interactions in Cellular Delivery
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