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
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Martini Coarse-Grained Force Field: Extension to RNA
TL;DR: The coarse-grain Martini force field is extended to include RNA, and the tertiary structure of RNA is constrained using an elastic network, which opens the way to large-scale explicit-solvent molecular dynamics simulations of complex systems involving RNA.
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Lipid bodies containing oxidatively truncated lipids block antigen cross-presentation by dendritic cells in cancer
Filippo Veglia,Vladimir A. Tyurin,Dariush Mohammadyani,Dariush Mohammadyani,Maria Blasi,Elizabeth K. Duperret,Laxminarasimha Donthireddy,Ayumi Hashimoto,Alexandr A. Kapralov,Andrew A. Amoscato,Roberto Angelini,Sima Patel,Kevin Alicea-Torres,David B. Weiner,Maureen E. Murphy,Judith Klein-Seetharaman,Esteban Celis,Valerian E. Kagan,Dmitry I. Gabrilovich +18 more
TL;DR: It is found that impaired cross-presentation in DCs is largely associated with defect in trafficking of peptide–MHC class I (pMHC) complexes to the cell surface, caused by the interaction of electrophilic lipids with chaperone heat shock protein 70.
Journal ArticleDOI
Pressure−Area Isotherm of a Lipid Monolayer from Molecular Dynamics Simulations
TL;DR: The pressure-area isotherm of a dipalmitoyl-phosphatidylcholine lipid monolayer is calculated from molecular dynamics simulations using a coarse-grained molecular model and the results show liquid-expanded and liquid-condensed phases and their coexistence plateau.
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Polyunsaturated Lipids Regulate Membrane Domain Stability by Tuning Membrane Order.
Kandice R. Levental,Joseph H. Lorent,Xubo Lin,Allison D. Skinkle,Michal A. Surma,Emily A. Stockenbojer,Alemayehu A. Gorfe,Ilya Levental +7 more
TL;DR: It is demonstrated that polyunsaturated fats affect the composition and organization of biological membranes, suggesting a potential mechanism for the extensive effects of dietary fat on health and disease.
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Modeling and simulation of protein–surface interactions: achievements and challenges
TL;DR: This review addresses the challenges posed to theoretical and computational methods in achieving accurate descriptions of the physical, chemical and mechanical properties of protein-surface systems and examines the applicability of different modeling and simulation techniques ranging from quantum mechanics through all-atom molecular mechanics to coarse-grained approaches.
References
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