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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Molecular dynamics of wetting layer formation and forced water invasion in angular nanopores with mixed wettability
TL;DR: This study investigates the threshold capillary pressure of oil and water displacements in a capillary dominated regime inside nanoscale pores using nonequilibrium molecular dynamics (NEMD) simulations and shows that the oil layer formed between water in the corner and in the center of the pore is not stable and collapses as the simulation continues.
Journal ArticleDOI
Interactions of phosphatase and tensin homologue (PTEN) proteins with phosphatidylinositol phosphates: insights from molecular dynamics simulations of PTEN and voltage sensitive phosphatase.
TL;DR: Although a PIP3 molecule binds close to the active site of PTEN, the simulations suggest a further conformational change of the protein may be required for catalytically productive binding to occur, and a novel mechanism of association of the PTEN with such bilayers is suggested.
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Multiscale simulation of protein mediated membrane remodeling.
Gary S. Ayton,Gregory A. Voth +1 more
TL;DR: Current multiscale simulation methodologies that have been employed to examine protein mediated membrane remodeling are surveyed.
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Modes of Interaction of Pleckstrin Homology Domains with Membranes: Toward a Computational Biochemistry of Membrane Recognition
TL;DR: These simulations demonstrate that simultaneous binding of multiple PIP molecules by PH domains contributes to high-affinity membrane interactions, informing the understanding of membrane recognition byPH domains in vivo.
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Structure of Human Acid Sphingomyelinase Reveals the Role of the Saposin Domain in Activating Substrate Hydrolysis
TL;DR: The crystal structure of human ASM is reported and the organization of the three main regions of the enzyme are described: the N-terminal saposin domain, the proline-rich connector, and the catalytic domain.
References
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