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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Membrane Position of Ibuprofen Agrees with Suggested Access Path Entrance to Cytochrome P450 2C9 Active Site
TL;DR: An atomistic model of complete CYP2C9 in a dioleoylphosphatidylcholine membrane is constructed and evolved by molecular dynamics simulations in explicit water on a 100+ ns time-scale and agrees well with known experimental data about membrane positioning of cytochromes P450.
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Membrane Protein Structure, Function, and Dynamics: a Perspective from Experiments and Theory
Zoe Cournia,Toby W. Allen,Toby W. Allen,Ioan Andricioaei,Bruno Antonny,Daniel Baum,Grace Brannigan,Nicolae-Viorel Buchete,Jason Deckman,Lucie Delemotte,Coral del Val,Ran Friedman,Paraskevi Gkeka,Hans-Christian Hege,Jérôme Hénin,Marina A. Kasimova,Marina A. Kasimova,Antonios Kolocouris,Michael L. Klein,Syma Khalid,M. Joanne Lemieux,Norbert Lindow,Mahua Roy,Jana Selent,Mounir Tarek,Mounir Tarek,Florentina Tofoleanu,Stefano Vanni,Sinisa Urban,David J. Wales,Jeremy C. Smith,Ana-Nicoleta Bondar +31 more
TL;DR: Current studies in computational and experimental membrane protein biophysics are presented, and how they address outstanding challenges in understanding the complex environmental effects on the structure, function, and dynamics of membrane proteins are shown.
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From residue coevolution to protein conformational ensembles and functional dynamics
TL;DR: This paper adapts the Boltzmann-learning algorithm to the analysis of homologous protein sequences and develops a coarse-grained protein model specifically tailored to convert the resulting contact predictions to a protein structural ensemble, and analyzes the set of conformations consistent with the observed residue correlations.
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Water models for biomolecular simulations
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TL;DR: It is argued that verifying robustness of simulation results to the choice of water model can be of immediate benefit even in the absence of a clear replacement for older models; a specific strategy is proposed.
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Sphere-to-rod transitions of nonionic surfactant micelles in aqueous solution modeled by molecular dynamics simulations.
TL;DR: In this paper, coarse-grained molecular dynamics simulations were used to describe micellar assemblies of pentaethylene glycol monododecyl ether (C12E5) in aqueous solution at different concentrations.
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