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

被引:66
作者
Carpenter, Timothy S. [1 ]
Lopez, Cesar A. [2 ]
Neale, Chris [2 ,3 ]
Montour, Cameron [4 ,6 ]
Ingolfsson, Helgi I. [1 ]
Di Natale, Francesco [5 ]
Lightstone, Felice C. [1 ]
Gnanakaran, S. [2 ]
机构
[1] Lawrence Livermore Natl Lab, Phys & Life Sci Directorate, Biosci & Biotechnol Div, Livermore, CA 94550 USA
[2] Los Alamos Natl Lab, Theoret Biol & Biophys Grp, Los Alamos, NM 87545 USA
[3] Los Alamos Natl Lab, Ctr Nonlinear Studies, Los Alamos, NM 87545 USA
[4] Georgetown Univ, Biochem & Mol Biol Dept, Washington, DC 20057 USA
[5] Lawrence Livermore Natl Lab, Computat Directorate, Applicat Simulat & Qual Div, Livermore, CA 94550 USA
[6] Clin Div, Syneos Hlth, Princeton, NJ USA
基金
美国国家卫生研究院;
关键词
LIQUID-ORDERED PHASES; MOLECULAR-DYNAMICS; COMPUTATIONAL LIPIDOMICS; TRANSMEMBRANE HELICES; RAFTS; MEMBRANES; MODEL; SEPARATION; ORGANIZATION; BILAYERS;
D O I
10.1021/acs.jctc.8b00496
中图分类号
O64 [物理化学(理论化学)、化学物理学];
学科分类号
070304 ; 081704 ;
摘要
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 (T-m) 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.
引用
收藏
页码:6050 / 6062
页数:13
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