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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Journal ArticleDOI
Molecular dynamics simulation of a polysorbate 80 micelle in water
TL;DR: In this paper, the structure and dynamics of a single polysorbate 80 (POE (20) sorbitan monooleate; Tween 80®) as well as a micelle comprising sixty molecules of POE in water have been investigated by molecular dynamics simulation.
Journal ArticleDOI
Expanding the Nanoarchitectural Diversity Through Aromatic Di- and Tri-Peptide Coassembly: Nanostructures and Molecular Mechanisms
Cong Guo,Zohar A. Arnon,Ruxi Qi,Qingwen Zhang,Lihi Adler-Abramovich,Ehud Gazit,Guanghong Wei +6 more
TL;DR: This study provides both structural and mechanistic insights into the coassembly of FF and FFF peptides, thus offering a molecular basis for the rational design of bionanomaterials utilizing peptide coassembly.
Book ChapterDOI
Systematic Methods for Structurally Consistent Coarse-Grained Models
TL;DR: This chapter provides a primer on theories for coarse-grained (CG) modeling and, in particular, reviews several systematic methods for determining effective potentials for CG models.
Journal ArticleDOI
The Role of the Membrane in the Structure and Biophysical Robustness of the Dengue Virion Envelope
Tyler Reddy,Mark S.P. Sansom +1 more
TL;DR: A near-atomic resolution computational model of the envelope of the dengue virion is obtained that exhibits biophysical robustness that matches the cholesterol-rich membrane of influenza A, with similarly anomalous diffusion of lipids.
ComponentDOI
Structure of the mechanosensitive OSCA channels.
Mingfeng Zhang,Dali Wang,Yunlu Kang,Jing-Xiang Wu,Fuqiang Yao,Chengfang Pan,Zhiqiang Yan,Chen Song,Lei Chen +8 more
TL;DR: The structural analysis accompanied with electrophysiological studies identifies the ion permeation pathway within each subunit and suggests a conformational change model for activation.
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