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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Journal ArticleDOI
How cardiolipin modulates the dynamics of respiratory complex I
TL;DR: This work suggests that cardiolipin binds to proton-pumping subunits of complex I and induces global conformational changes that modulate the accessibility of the quinone substrate to the enzyme.
Journal ArticleDOI
S-acylation controls SARS-CoV-2 membrane lipid organization and enhances infectivity.
Francisco Mesquita,Laurence Abrami,Oksana A. Sergeeva,Priscilla Turelli,Enya Qing,Béatrice Kunz,Charlène Raclot,Jonathan Paz Montoya,Luciano A. Abriata,Tom Gallagher,Matteo Dal Peraro,Didier Trono,Giovanni D'Angelo,F. Gisou van der Goot +13 more
TL;DR: In this article, a combination of computational, lipidomics, and biochemical approaches was used to find that spike becomes lipid modified during SARS-CoV-2 infection, through the sequential action of the S-acyltransferases ZDHHC20 and 9.
Journal ArticleDOI
Self-assembly and interactions of short antimicrobial cationic lipopeptides with membrane lipids: ITC, FTIR and molecular dynamics studies.
Emilia Sikorska,Małgorzata Dawgul,Katarzyna E. Greber,Emilia Iłowska,Aneta Pogorzelska,Wojciech Kamysz +5 more
TL;DR: The self-organization and the behavior of the surfactant-like peptides in the presence of biological membrane models were studied and a unique interplay between the initial electrostatic and the subsequent hydrophobic interactions enabling the lipopeptides to interact with the lipid bilayer.
Book ChapterDOI
Recent advances in transferable coarse-grained modeling of proteins.
Parimal Kar,Michael Feig +1 more
TL;DR: This review discusses those CG protein models that are transferable and that retain chemical specificity and briefly review recent progress made in the multiscale hybrid all-atom/CG simulations of proteins.
Journal ArticleDOI
Modeling Protein-Protein Recognition in Solution Using the Coarse-Grained Force Field SCORPION.
TL;DR: SCORPION appears as a useful tool to study protein-protein recognition in a solvated environment and a new Polarizable Coarse-Grained Solvent (PCGS) model, which is computationally efficient, consistent with the protein CG representation, and yields accurate electrostatic free energies of proteins.
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