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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Molecular dynamics simulation of phase transitions in model lung surfactant monolayers.
TL;DR: The MARTINI coarse-grained model is used to simulate monolayers containing DPPC and additional lipid or peptide components and suggests that the LC phase forms from the LE phase via a nucleation and growth mechanism, while the LC-LE transition occurs by melting that originates from defects in the monolayer.
Journal ArticleDOI
Molecular organization of the tear fluid lipid layer.
Pipsa Kulovesi,Jelena Telenius,Artturi Koivuniemi,Gerald Brezesinski,Antti H. Rantamäki,Tapani Viitala,Esa Puukilainen,Mikko Ritala,Susanne K. Wiedmer,Ilpo Vattulainen,Ilpo Vattulainen,Ilpo Vattulainen,Juha M. Holopainen +12 more
TL;DR: The molecular organization of the anterior lipid layer of the tear film, composed of egg yolk phosphatidylcholine, free fatty acids, cholesteryl oleate, and triglycerides, is described.
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Replica Exchange Molecular Dynamics Simulations of Coarse-grained Proteins in Implicit Solvent
TL;DR: The light computational burden of REMD-OPEP, which enables it to generate many hundred nanoseconds at each temperature and fully assess convergence to equilibrium ensemble, opens the door to the determination of the free energy surface of larger proteins and assemblies.
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Structure of saposin A lipoprotein discs
TL;DR: The crystal structure of saposin A in the presence of detergent is determined and it is revealed that these discs may be the smallest possible lipoprotein structures that are stabilized by lipid self-assembly.
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Molecular mechanism of cardiolipin-mediated assembly of respiratory chain supercomplexes
TL;DR: The molecular mechanism by which cardiolipin glues respiratory complexes into supercomplexes is revealed, which defines a new biophysico-chemical pathway of protein–lipid interplay, with broad general implications for the dynamic organization of crowded cell membranes.
References
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GROMACS: Fast, flexible, and free
David van der Spoel,Erik Lindahl,Berk Hess,Gerrit Groenhof,Alan E. Mark,Herman J. C. Berendsen +5 more
TL;DR: The software suite GROMACS (Groningen MAchine for Chemical Simulation) that was developed at the University of Groningen, The Netherlands, in the early 1990s is described, which is a very fast program for molecular dynamics simulation.
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