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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PEBP1 Wardens Ferroptosis by Enabling Lipoxygenase Generation of Lipid Death Signals
Sally E. Wenzel,Yulia Y. Tyurina,Jinming Zhao,Claudette M. St. Croix,Haider H. Dar,Gaowei Mao,Vladimir A. Tyurin,Tamil S. Anthonymuthu,Alexandr A. Kapralov,Andrew A. Amoscato,Karolina Mikulska-Ruminska,Karolina Mikulska-Ruminska,Indira H. Shrivastava,Elizabeth M. Kenny,Qin Yang,Joel C. Rosenbaum,Louis J. Sparvero,David R. Emlet,Xiaoyan Wen,Yoshinori Minami,Feng Qu,Simon C. Watkins,Theodore R. Holman,Andrew P. VanDemark,John A. Kellum,Ivet Bahar,Hülya Bayır,Hülya Bayır,Valerian E. Kagan +28 more
TL;DR: It is discovered that PEBP1, a scaffold protein inhibitor of protein kinase cascades, complexes with two 15LO isoforms, 15LO1 and 15LO2, and changes their substrate competence to generate hydroperoxy-PE, a new target for drug discovery.
Journal ArticleDOI
The power of coarse graining in biomolecular simulations
Helgi I. Ingólfsson,Cesar A. Lopez,Jaakko J. Uusitalo,Djurre H. de Jong,Srinivasa M. Gopal,Xavier Periole,Siewert J. Marrink +6 more
TL;DR: An overview of some of the more popular CG models used in biomolecular applications to date, focusing on models that retain chemical specificity, are provided.
Journal ArticleDOI
Lipids on the move: simulations of membrane pores, domains, stalks and curves.
TL;DR: This review describes the state-of-the-art of computer simulation studies of lipid membranes, showing that many important biological processes including self-aggregation of membrane components into domains, the formation of non-lamellar phases, and membrane poration and curving, are now amenable to detailed simulation studies.
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Optimization of the OPLS-AA Force Field for Long Hydrocarbons.
TL;DR: It is shown that the optimized parameter set (L-OPLS) yields improved hydrocarbon diffusion coefficients, viscosities, and gauche-trans ratios, and its applicability for lipid bilayer simulations is shown for a GMO bilayer in its liquid-crystalline phase.
Journal ArticleDOI
Structure of the yeast F1Fo-ATP synthase dimer and its role in shaping the mitochondrial cristae.
TL;DR: It is proposed that the assembly of ATP synthase dimer rows is driven by the reduction in the membrane elastic energy, rather than by direct protein contacts, and that the dimerrows enable the formation of highly curved ridges in mitochondrial cristae.
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