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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Orientation and Dynamics of Peptides in Membranes Calculated from 2H-NMR Data
TL;DR: Solid-state (2)H-NMR is routinely used to determine the alignment of membrane-bound peptides and can also provide a quantitative measure of the fluctuations around the distinct molecular axes, demonstrating that when peptide rigid-body angular fluctuations should be included when data are fitted to extract peptide orientation angles.
Journal ArticleDOI
On the representability problem and the physical meaning of coarse-grained models.
TL;DR: Though these representability challenges are investigated in the framework of systematic coarse-graining, the lessons apply to top-down CG modeling also, with crucial implications for simulation at constant pressure and surface tension and for the interpretations of structural and thermodynamic correlations for comparison to experiment.
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Molecular origins of internal friction effects on protein-folding rates
TL;DR: All-atom simulations of peptide and protein folding in explicit solvent find that an important contribution to this effect, explaining the viscosity dependence of helix formation and the folding of a helix-containing protein, is the insensitivity of torsion angle isomerization to solvent friction.
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Water in Nanopores and Biological Channels: A Molecular Simulation Perspective.
TL;DR: Current level of understanding allows for the design of a nanopore which promotes wetting over dewetting or vice versa, but to design a novel nanopore, which enables fast, selective, and gated flow of water de novo would remain challenging, suggesting a need for further detailed simulations alongside experimental evaluation of more complex nanopore systems.
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BIN1/M-Amphiphysin2 induces clustering of phosphoinositides to recruit its downstream partner dynamin
Laura Picas,Julien Viaud,Kristine Schauer,Stefano Vanni,Karim Hnia,Vincent Fraisier,Aurélien Roux,Patricia Bassereau,Frédérique Gaits-Iacovoni,Bernard Payrastre,Jocelyn Laporte,Jean-Baptiste Manneville,Bruno Goud +12 more
TL;DR: BIN1/M-Amphiphysin2, a protein involved in T-tubule biogenesis in muscle cells and frequently mutated in centronuclear myopathies, clusters PtdIns(4,5)P2 to recruit its downstream partner dynamin and it is proposed that this mechanism plays a key role in the recruitment of downstream phosphoinositide-binding proteins.
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