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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Formation of raft-like assemblies within clusters of influenza hemagglutinin observed by MD simulations.
TL;DR: It is suggested that a local aggregation of HA can be sufficient to drive association of the protein with raft-type lipids within the area of membrane spanned by the protein cluster, which may represent a general mechanism for the targeting of TM proteins to rafts in the plasma membrane, which is of functional importance in a wide range of cellular processes.
Journal ArticleDOI
Temperature dependence of coarse-grained potentials for liquid hexane
TL;DR: The present molecular dynamics study is an investigation of the temperature (T) dependence of liquid hexane coarse-grained potentials optimized with the Iterative Boltzmann Inversion method, and the results are encouraging for the use of potential interpolations as a practical means for devising coarse- Grained Potentials within a wider temperature range.
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Conserved Lipid and Small-Molecule Modulation of COQ8 Reveals Regulation of the Ancient Kinase-like UbiB Family.
Andrew G. Reidenbach,Andrew G. Reidenbach,Zachary A. Kemmerer,Zachary A. Kemmerer,Deniz Aydin,Deniz Aydin,Adam Jochem,Molly T. McDevitt,Molly T. McDevitt,Paul D. Hutchins,Jaime L. Stark,Jonathan A. Stefely,Jonathan A. Stefely,Thiru R. Reddy,Alexander S. Hebert,Emily M. Wilkerson,Isabel E. Johnson,Isabel E. Johnson,Craig A. Bingman,John L. Markley,Joshua J. Coon,Matteo Dal Peraro,Matteo Dal Peraro,David J. Pagliarini,David J. Pagliarini +24 more
TL;DR: It is demonstrated that COQ8 possesses evolutionarily conserved ATPase activity that is activated by binding to membranes containing cardiolipin and by phenolic compounds that resemble CoQ pathway intermediates and is established a chemical genetic system for further exploring the mechanistic role ofCOQ8 in CoQ biosynthesis.
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Stability of peptide (P1 and P2) binding to a graphene sheet via an all-atom to all-residue coarse-grained approach
TL;DR: In this paper, the relative adsorption energy of each residue is normalized to describe its coarse-grained interactions with graphene which is used as an input to a phenomenological interaction in an all-residue coarsegrained (ARCG) representation of the peptide chain.
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Coarse-Grained Models for Protein-Cell Membrane Interactions
Ryan Bradley,Ravi Radhakrishnan +1 more
TL;DR: In this paper, a review of continuum modeling and coarse-grained molecular dynamics methods, which connect atomistic simulations and single-molecule experiments with the observed microscopic or mesoscale properties of soft-matter systems essential to our understanding of cells, particularly those involved in sculpting and remodeling cell membranes.
References
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