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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A tethering complex drives the terminal stage of SNARE-dependent membrane fusion
Massimo D'Agostino,Herre Jelger Risselada,Herre Jelger Risselada,Anna Lürick,Christian Ungermann,Andreas Mayer +5 more
TL;DR: It is proposed that SNAREs and tethering proteins should be considered as a single, non-dissociable device that drives fusion, and the core fusion machinery may then be larger and more complex than previously thought.
Journal ArticleDOI
Changes in transmembrane helix alignment by arginine residues revealed by solid-state NMR experiments and coarse-grained MD simulations
TL;DR: Independent experimental and computational approaches show agreement concerning arginine/membrane interactions when a singleArginine is introduced at selected positions within the membrane-spanning region of acetyl-GGALW(5)LALALAL(12)AL(14)ALAlW(19)LAGA-ethanolamide, designated GWALP23.
Journal ArticleDOI
Micellization behavior of coarse grained surfactant models.
TL;DR: The critical micelle concentration (cmc) and equilibrium aggregate size distributions at low surfactant loadings are obtained and the aggregation numbers for both zwitterionic and nonionic surfactants are near those observed experimentally, but the temperature dependence of the cmc is incorrect in both cases.
Journal ArticleDOI
Classical Reactive Molecular Dynamics Implementations: State of the Art
TL;DR: Reactive molecular dynamics implementations equipped with force field approaches to simulate both the time evolution as well as chemical reactions of a broad class of materials are reviewed herein.
Journal ArticleDOI
Multiple C2 domains and transmembrane region proteins (MCTPs) tether membranes at plasmodesmata.
Marie L Brault,Jules D. Petit,Jules D. Petit,Françoise Immel,William J Nicolas,Marie Glavier,Lysiane Brocard,Amèlia Gaston,Mathieu Fouché,Timothy J. Hawkins,Jean-Marc Crowet,Magali S. Grison,Véronique Germain,Marion Rocher,Max E. Kraner,Vikram Alva,Stéphane Claverol,Andrea Paterlini,Yrjö Helariutta,Magali Deleu,Laurence Lins,Jens Tilsner,Jens Tilsner,Emmanuelle Bayer +23 more
TL;DR: It is shown that the multiple C2 domains and transmembrane region protein (MCTP) family, key regulators of cell‐to‐cell signalling in plants, act as ER‐PM tethers specifically at plasmodesmata.
References
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