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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Role of lipids in spheroidal high density lipoproteins.
Timo Vuorela,Andrea Catte,Andrea Catte,Perttu S. Niemelä,Anette Hall,Marja T. Hyvönen,Siewert-Jan Marrink,Mikko Karttunen,Ilpo Vattulainen,Ilpo Vattulainen,Ilpo Vattulainen +10 more
TL;DR: The results provide the first detailed structural model for HDL and its dynamics with and without apoA-I, and indicate how the interplay and competition between entropy and detailed interactions may be used in nanoparticle and drug design through self-assembly.
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Nanomaterials in biological environment: a review of computer modelling studies
TL;DR: Current computational techniques have revealed how some nanoparticles interact with biological systems, however, further research is required to determine both useful applications and possible cytotoxic effects that nanoparticles may have on DNA, protein and membrane structure and function within biosystems.
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Biomolecular simulations: From dynamics and mechanisms to computational assays of biological activity
David J. Huggins,David J. Huggins,Philip C. Biggin,Marc A. Dämgen,Jonathan W. Essex,Sarah A. Harris,Richard H. Henchman,Syma Khalid,Antonija Kuzmanic,Charles A. Laughton,Julien Michel,Adrian J. Mulholland,Edina Rosta,Mark S.P. Sansom,Marc W. van der Kamp +14 more
TL;DR: In this review, biomolecular simulation methods are outlined and examples of its application to investigate questions in biology are highlighted, aiming to connect chemical and molecular changes to macroscopic observables.
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Spontaneous curvature, differential stress, and bending modulus of asymmetric lipid membranes
Amirali Hossein,Markus Deserno +1 more
TL;DR: The findings suggest that biomembranes are elastically more complex than previously thought: besides a spontaneous curvature, they might also exhibit significant differential stress, which could strongly affect their curvature energetics.
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Membrane-Protein Interactions in a Generic Coarse-Grained Model for Lipid Bilayers
TL;DR: The simulations show that the lipid-mediated interactions are governed by five competing factors: direct interactions; cholesterol-induced depletion interactions; lipid bridging; lipid packing; and a smooth long-range contribution.
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