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 New Coarse-Grained Force Field for Membrane-Peptide Simulations.
Zhe Wu,Qiang Cui,Arun Yethiraj +2 more
TL;DR: The model follows the same topology and parametrization strategy as the MARTINI force field but is based on the recently developed big multipole water model for water, which is particularly suitable for describing interactions between highly charged peptides with lipid membranes.
Journal ArticleDOI
On the Calculation of Acyl Chain Order Parameters from Lipid Simulations
TL;DR: This work demonstrates that the majority of the tested tools that calculate the order parameters for unsaturated united-atom lipid tails do so incorrectly, and identifies tools that do perform accurate calculations and includes one such program with this work, enabling rapid and accurate calculation of united- atom lipid order parameters.
Journal ArticleDOI
Paclitaxel-PHBV nanoparticles and their toxicity to endometrial and primary ovarian cancer cells
Cristian Vilos,Francisco Morales,Paula Solar,Natalia Herrera,Fernando D. González-Nilo,Daniel Aguayo,Hegaly Mendoza,Jeffrey Comer,María Loreto Bravo,Pamela Gonzalez,Sumie Kato,Mauricio Cuello,Catalina Alonso,Erasmo Bravo,Eva Bustamante,Gareth I. Owen,Luis A. Velásquez +16 more
TL;DR: It is demonstrated that a paclitaxel-loaded PHBV nanoparticle that demonstrates uptake, release and cytotoxicity in cancer cell lines causes significant cell death in primary cultures of stage IIIc serous ovarian cancer cells isolated from six patients.
Journal ArticleDOI
Molecular view on protein sorting into liquid-ordered membrane domains mediated by gangliosides and lipid anchors
TL;DR: Results from coarse grain molecular dynamics simulations of mixed model membranes consisting of saturated and unsaturated lipids together with cholesterol, in which lipid-anchored membrane proteins are embedded are presented, showing formation of GM1-protein nano-domains that act as shuttles between the differently ordered membrane regions.
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Stability and Comparative Analysis of AOT/Water/Isooctane Reverse Micelle System Using Dynamic Light Scattering and Molecular Dynamics
TL;DR: Good qualitative agreement is found for the size and morphology behavior of the reverse micelle structures between molecular dynamics calculations and DLS measurements; however, the average values for the reverse micellar size distributions are systematically larger for the D LS measurements.
References
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Book
CRC Handbook of Chemistry and Physics
TL;DR: CRC handbook of chemistry and physics, CRC Handbook of Chemistry and Physics, CRC handbook as discussed by the authors, CRC Handbook for Chemistry and Physiology, CRC Handbook for Physics,
Journal ArticleDOI
VMD: Visual molecular dynamics
TL;DR: VMD is a molecular graphics program designed for the display and analysis of molecular assemblies, in particular biopolymers such as proteins and nucleic acids, which can simultaneously display any number of structures using a wide variety of rendering styles and coloring methods.
Book
Intermolecular and surface forces
TL;DR: The forces between atoms and molecules are discussed in detail in this article, including the van der Waals forces between surfaces, and the forces between particles and surfaces, as well as their interactions with other forces.
Journal ArticleDOI
GROMACS: Fast, flexible, and free
David van der Spoel,Erik Lindahl,Berk Hess,Gerrit Groenhof,Alan E. Mark,Herman J. C. Berendsen +5 more
TL;DR: The software suite GROMACS (Groningen MAchine for Chemical Simulation) that was developed at the University of Groningen, The Netherlands, in the early 1990s is described, which is a very fast program for molecular dynamics simulation.
Journal ArticleDOI
GROMACS 3.0: a package for molecular simulation and trajectory analysis
TL;DR: The design includes an extraction of virial and periodic boundary conditions from the loops over pairwise interactions, and special software routines to enable rapid calculation of x–1/2.