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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The structural dynamics of macromolecular processes
Daniel Russel,Keren Lasker,Keren Lasker,Jeremy Phillips,Dina Schneidman-Duhovny,Javier A. Velázquez-Muriel,Andrej Sali +6 more
TL;DR: The relevant sources of information are reviewed and a framework for integrating the data to produce representations of dynamic processes of macromolecular complexes is introduced.
Journal ArticleDOI
Membrane proteins structures : A review on computational modeling tools
Jose G. Almeida,António J Preto,Panagiotis I. Koukos,Alexandre M. J. J. Bonvin,Irina S. Moreira,Irina S. Moreira +5 more
TL;DR: This review highlights the importance of membrane proteins and how computational methods are capable of overcoming challenges associated with their experimental characterization and focuses on computational techniques to determine the 3D structure of MP and characterize their binding interfaces.
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Strong influence of periodic boundary conditions on lateral diffusion in lipid bilayer membranes
TL;DR: I simulations of LacY membrane protein diffusion and LacY dimer diffusion in DPPC membranes and lipid diffusion in pure DPPC bilayers support the underlying hydrodynamic model.
Journal ArticleDOI
Understanding the Interaction of Block Copolymers with DMPC Lipid Bilayer Using Coarse-Grained Molecular Dynamics Simulations
TL;DR: A computational model of the adsorption and percolation mechanism of poloxamers across a 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) lipid bilayer shows that polymer chains containing a PPO block with a length comparable to the DMPC bilayer thickness, such as P85, tends to percolate across the lipid bilayers.
Journal ArticleDOI
Structural and Molecular Determinants of Membrane Binding by the HIV-1 Matrix Protein.
Peter Y. Mercredi,Nadine Bucca,Burk Loeliger,Christy R. Gaines,Mansi Mehta,Pallavi Bhargava,Philip R. Tedbury,Landry Charlier,Nicolas Floquet,Delphine Muriaux,Cyril Favard,Charles R. Sanders,Eric O. Freed,Jan Marchant,Michael F. Summers +14 more
TL;DR: These findings call to question extended-lipid MA:membrane binding models, and instead support a model put forward from coarse-grained simulations indicating that binding is mediated predominantly by dynamic, electrostatic interactions between conserved basic residues of MA and multiple PI(4,5)P2 and phosphatidylserine molecules.
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