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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Structure and phase transformations of DPPC lipid bilayers in the presence of nanoparticles: insights from coarse-grained molecular dynamics simulations.
TL;DR: It is demonstrated that the presence of all types of nanoparticles induces disorder effects in the structure of the lipid bilayer, including a negatively charged hydrophobic nanoparticle located at the surface of the bilayer causes slight shift of the fluid-gel transformation to a lower temperature, compared to the bulk bilayer case.
Journal ArticleDOI
Engineering Antimicrobial Peptides with Improved Antimicrobial and Hemolytic Activities
TL;DR: The most active mutants with the balanced substitutions of positively charged Arg and hydrophobic Trp residues at specific positions were discovered to achieve the improved antimicrobial activity while minimizing red blood cell lysis.
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SAFT-γ force field for the simulation of molecular fluids: 4. A single-site coarse-grained model of water applicable over a wide temperature range
TL;DR: In this paper, the statistical associating fluid theory for Mie (generalised Lennard-Jones) potentials of variable range (SAFT-VR Mie) is used to parameterise spherically symmetrical (isotropic) force fields for water.
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Coarse-grain modelling of DMPC and DOPC lipid bilayers
TL;DR: The recently developed coarse-grain model for dimyristoylphosphatidylcholine (DMPC) has been improved and extended to DOPC, a more typical constituent of real biological membranes, and the dipole potential is studied, a basic physical feature of paramount biological importance that cannot be currently modelled by other coarse- grain approaches.
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The structural basis for peptide selection by the transport receptor OppA
Ronnie P.-A. Berntsson,Mark K. Doeven,Fabrizia Fusetti,Ria H. Duurkens,Durba Sengupta,Siewert-Jan Marrink,Andy-Mark W. H. Thunnissen,Bert Poolman,Dirk Jan Slotboom +8 more
TL;DR: The crystal structures of OppA in the open‐ and closed‐liganded conformations are presented, and a new mechanism for peptide selection based on amino‐acid composition rather than sequence is proposed.
References
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