Literature DB >> 30253091

Capturing Phase Behavior of Ternary Lipid Mixtures with a Refined Martini Coarse-Grained Force Field.

Timothy S Carpenter1, Cesar A López, Chris Neale, Cameron Montour2, Helgi I Ingólfsson1, Francesco Di Natale3, Felice C Lightstone1, S Gnanakaran.   

Abstract

Whether lipid rafts are present in the membranes of living cells remains hotly disputed despite their incontrovertible existence in liposomes at 298 K. In attempts to resolve this debate, molecular dynamics (MD) simulations have been extensively used to study lipid phase separation at high resolution. However, computation has been of limited utility in this respect because the experimental distributions of phases in lamellar lipid mixtures are poorly reproduced by simulations. In particular, all-atom (AA) approaches suffer from restrictions on accessible time scales and system sizes whereas the more efficient coarse-grained (CG) force fields remain insufficiently accurate to achieve correspondence with experiment. In this work, we refine the CG Martini parameters for the high- and low-melting temperature ( Tm) lipids 1,2-dipalmitoyl- sn-glycero-3-phosphatidylcholine (DPPC) and 1,2-dioleoyl- sn-glycero-3-phosphatidylcholine (DOPC). Our approach involves the modification of bonded Martini parameters based on fitting to atomistic simulations conducted with the CHARMM36 lipid force field. The resulting CG parameters reproduce experimental structural and thermodynamic properties of homogeneous lipid membranes while concurrently improving simulation fidelity to experimental phase diagrams of DPPC, DOPC, and cholesterol lipid mixtures. Importantly, the refined parameters provide much better phase accuracy for regions near the critical point that mimic the lipid concentrations under physiological conditions.

Entities:  

Year:  2018        PMID: 30253091     DOI: 10.1021/acs.jctc.8b00496

Source DB:  PubMed          Journal:  J Chem Theory Comput        ISSN: 1549-9618            Impact factor:   6.006


  13 in total

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Review 8.  Computational Modeling of Realistic Cell Membranes.

Authors:  Siewert J Marrink; Valentina Corradi; Paulo C T Souza; Helgi I Ingólfsson; D Peter Tieleman; Mark S P Sansom
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10.  Martini Coarse-Grained Model of Hyaluronic Acid for the Structural Change of Its Gel in the Presence of Monovalent and Divalent Salts.

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Journal:  Int J Mol Sci       Date:  2020-06-29       Impact factor: 5.923

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