skip to main content
DOE PAGES title logo U.S. Department of Energy
Office of Scientific and Technical Information

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

Authors:
ORCiD logo [1]; ORCiD logo [2];  [2];  [3];  [1];  [4];  [1];  [2]
  1. Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States). Biosciences and Biotechnology Division. Physical and Life Sciences Directorate
  2. Los Alamos National Lab. (LANL), Los Alamos, NM (United States)
  3. Georgetown Univ., Washington, DC (United States). Biochemistry and Molecular Biology Dept.
  4. Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States). Applications, Simulations, and Quality Division. Computation Directorate
Publication Date:
Research Org.:
Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States); Los Alamos National Lab. (LANL), Los Alamos, NM (United States)
Sponsoring Org.:
USDOE Office of Science (SC). Advanced Scientific Computing Research (ASCR) (SC-21); LANL Laboratory Directed Research and Development (LDRD) Program; National Inst. of Health (NIH) (United States)
OSTI Identifier:
1512613
Alternate Identifier(s):
OSTI ID: 1526950
Report Number(s):
LLNL-JRNL-750994; LA-UR-18-23792
Journal ID: ISSN 1549-9618; 936287
Grant/Contract Number:  
AC52-07NA27344; AC52-06NA25396; AC05-00OR22725; HHSN261200800001E; 89233218CNA000001
Resource Type:
Accepted Manuscript
Journal Name:
Journal of Chemical Theory and Computation
Additional Journal Information:
Journal Volume: 14; Journal Issue: 11; Journal ID: ISSN 1549-9618
Publisher:
American Chemical Society
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; Biological Science

Citation Formats

Carpenter, Timothy S., López, Cesar A., Neale, Chris, Montour, Cameron, Ingólfsson, Helgi I., Di Natale, Francesco, Lightstone, Felice C., and Gnanakaran, S. Capturing Phase Behavior of Ternary Lipid Mixtures with a Refined Martini Coarse-Grained Force Field. United States: N. p., 2018. Web. https://doi.org/10.1021/acs.jctc.8b00496.
Carpenter, Timothy S., López, Cesar A., Neale, Chris, Montour, Cameron, Ingólfsson, Helgi I., Di Natale, Francesco, Lightstone, Felice C., & Gnanakaran, S. Capturing Phase Behavior of Ternary Lipid Mixtures with a Refined Martini Coarse-Grained Force Field. United States. https://doi.org/10.1021/acs.jctc.8b00496
Carpenter, Timothy S., López, Cesar A., Neale, Chris, Montour, Cameron, Ingólfsson, Helgi I., Di Natale, Francesco, Lightstone, Felice C., and Gnanakaran, S. Tue . "Capturing Phase Behavior of Ternary Lipid Mixtures with a Refined Martini Coarse-Grained Force Field". United States. https://doi.org/10.1021/acs.jctc.8b00496. https://www.osti.gov/servlets/purl/1512613.
@article{osti_1512613,
title = {Capturing Phase Behavior of Ternary Lipid Mixtures with a Refined Martini Coarse-Grained Force Field},
author = {Carpenter, Timothy S. and López, Cesar A. and Neale, Chris and Montour, Cameron and Ingólfsson, Helgi I. and Di Natale, Francesco and Lightstone, Felice C. and Gnanakaran, S.},
abstractNote = {},
doi = {10.1021/acs.jctc.8b00496},
journal = {Journal of Chemical Theory and Computation},
number = 11,
volume = 14,
place = {United States},
year = {2018},
month = {9}
}

Journal Article:
Free Publicly Available Full Text
Publisher's Version of Record

Citation Metrics:
Cited by: 11 works
Citation information provided by
Web of Science

Figures / Tables:

Figure. 1 Figure. 1: CG mapping and featured bonded distributions for DPPC and DOPC. CG bead mapping for DOPC (A) and DPPC (B) lipids. Bead colors represent the different chemical groups as in the original Martini parameters set and mapped on all-atom backbone shown as a stick diagram. Hydrogens in the atomisticmore » representations are not depicted for clarity. The unsaturation in the aliphatic tails is highlighted. Color code: blue beads: choline groups, orange beads: phosphates, pink beads: glycerols, gray beads: acyl chains, tan beads: double bond in DOPC. Representative intramolecular geometrical distributions are provided for DOPC (C) and DPPC (D) standard Martini along with all-atom distributions that were used for reparamterization. Also, shown are the resulting reparameterized distributions for Extensible and Optimal parameter sets. The full sets of distributions as well as the numbering reference are provided in Supportive Figs. S6 and S7. The CG bead types associated with these bond and angle distributions are schematically shown for DOPC (E) and DPPC (F).« less

Save / Share:

Works referenced in this record:

Phase Separation in Biological Membranes: Integration of Theory and Experiment
journal, April 2010


Rafting trips into the cell: Membrane domains in MHC internalization
journal, September 2009

  • Lindner, Robert; Knorr, Ruth
  • Communicative & Integrative Biology, Vol. 2, Issue 5
  • DOI: 10.4161/cib.2.5.8945

Lipid Rafts As a Membrane-Organizing Principle
journal, December 2009


The mystery of membrane organization: composition, regulation and roles of lipid rafts
journal, March 2017

  • Sezgin, Erdinc; Levental, Ilya; Mayor, Satyajit
  • Nature Reviews Molecular Cell Biology, Vol. 18, Issue 6
  • DOI: 10.1038/nrm.2017.16

Lipid-protein interplay and lateral organization in biomembranes
journal, July 2015


The Continuing Mystery of Lipid Rafts
journal, December 2016


Lipid Raft Formation: Key Role of Polyunsaturated Phospholipids
journal, January 2017

  • Wang, Chang; Yu, Yuming; Regen, Steven L.
  • Angewandte Chemie International Edition, Vol. 56, Issue 6
  • DOI: 10.1002/anie.201611367

Liquid-ordered phases induced by cholesterol: A compendium of binary phase diagrams
journal, March 2010


An index of lipid phase diagrams
journal, May 2002


Analysis of lipid raft molecules in the living brain slices
journal, October 2018


New insight into the interaction of TRAF2 C-terminal domain with lipid raft microdomains
journal, September 2017

  • Ceccarelli, Arianna; Di Venere, Almerinda; Nicolai, Eleonora
  • Biochimica et Biophysica Acta (BBA) - Molecular and Cell Biology of Lipids, Vol. 1862, Issue 9
  • DOI: 10.1016/j.bbalip.2017.05.003

Lipid rafts in T cell receptor signalling (Review)
journal, January 2006


Structural determinants and functional consequences of protein affinity for membrane rafts
journal, October 2017


Lateral pressure-mediated protein partitioning into liquid-ordered/liquid-disordered domains
journal, January 2016

  • Frewein, Moritz; Kollmitzer, Benjamin; Heftberger, Peter
  • Soft Matter, Vol. 12, Issue 13
  • DOI: 10.1039/C6SM00042H

Lipid rafts enhance the binding constant of membrane-anchored receptors and ligands
journal, January 2017

  • Li, Long; Hu, Jinglei; Shi, Xinghua
  • Soft Matter, Vol. 13, Issue 23
  • DOI: 10.1039/C7SM00572E

Direct observation of the nanoscale dynamics of membrane lipids in a living cell
journal, December 2008

  • Eggeling, Christian; Ringemann, Christian; Medda, Rebecca
  • Nature, Vol. 457, Issue 7233
  • DOI: 10.1038/nature07596

Rafts: Scale-Dependent, Active Lipid Organization at the Cell Surface: Raft Hypothesis
journal, March 2004


Hallmarks of Reversible Separation of Living, Unperturbed Cell Membranes into Two Liquid Phases
journal, December 2017

  • Rayermann, Scott P.; Rayermann, Glennis E.; Cornell, Caitlin E.
  • Biophysical Journal, Vol. 113, Issue 11
  • DOI: 10.1016/j.bpj.2017.09.029

Correction: Cooling induces phase separation in membranes derived from isolated CNS myelin
journal, November 2017


Signalling of the BCR is regulated by a lipid rafts-localised transcription factor, Bright
journal, February 2009

  • Schmidt, Christian; Kim, Dongkyoon; Ippolito, Gregory C.
  • The EMBO Journal, Vol. 28, Issue 6
  • DOI: 10.1038/emboj.2009.20

Lipid Rafts Associate with Intracellular B Cell Receptors and Exhibit a B Cell Stage-Specific Protein Composition
journal, March 2005


Unraveling the role of membrane microdomains during microbial infections
journal, March 2017

  • Bagam, Prathyusha; Singh, Dhirendra P.; Inda, Maria Eugenia
  • Cell Biology and Toxicology, Vol. 33, Issue 5
  • DOI: 10.1007/s10565-017-9386-9

Shiga Toxin—A Model for Glycolipid-Dependent and Lectin-Driven Endocytosis
journal, October 2017


A Pore-Forming Toxin Requires a Specific Residue for Its Activity in Membranes with Particular Physicochemical Properties
journal, April 2015

  • Morante, Koldo; Caaveiro, Jose M. M.; Tanaka, Koji
  • Journal of Biological Chemistry, Vol. 290, Issue 17
  • DOI: 10.1074/jbc.M114.615211

With or without rafts? Alternative views on cell membranes
journal, December 2015


Sizes of lipid domains: What do we know from artificial lipid membranes? What are the possible shared features with membrane rafts in cells?
journal, May 2017

  • Rosetti, Carla M.; Mangiarotti, Agustín; Wilke, Natalia
  • Biochimica et Biophysica Acta (BBA) - Biomembranes, Vol. 1859, Issue 5
  • DOI: 10.1016/j.bbamem.2017.01.030

The Molecular Structure of the Liquid-Ordered Phase of Lipid Bilayers
journal, January 2014

  • Sodt, Alexander J.; Sandar, Michael Logan; Gawrisch, Klaus
  • Journal of the American Chemical Society, Vol. 136, Issue 2
  • DOI: 10.1021/ja4105667

Hexagonal Substructure and Hydrogen Bonding in Liquid-Ordered Phases Containing Palmitoyl Sphingomyelin
journal, September 2015

  • Sodt, Alexander J.; Pastor, Richard W.; Lyman, Edward
  • Biophysical Journal, Vol. 109, Issue 5
  • DOI: 10.1016/j.bpj.2015.07.036

The MARTINI Force Field:  Coarse Grained Model for Biomolecular Simulations
journal, July 2007

  • Marrink, Siewert J.; Risselada, H. Jelger; Yefimov, Serge
  • The Journal of Physical Chemistry B, Vol. 111, Issue 27
  • DOI: 10.1021/jp071097f

Perspective on the Martini model
journal, January 2013

  • Marrink, Siewert J.; Tieleman, D. Peter
  • Chemical Society Reviews, Vol. 42, Issue 16
  • DOI: 10.1039/c3cs60093a

The molecular face of lipid rafts in model membranes
journal, November 2008

  • Risselada, H. J.; Marrink, S. J.
  • Proceedings of the National Academy of Sciences, Vol. 105, Issue 45
  • DOI: 10.1073/pnas.0807527105

Transmembrane helices can induce domain formation in crowded model membranes
journal, April 2012

  • Domański, Jan; Marrink, Siewert J.; Schäfer, Lars V.
  • Biochimica et Biophysica Acta (BBA) - Biomembranes, Vol. 1818, Issue 4
  • DOI: 10.1016/j.bbamem.2011.08.021

Lipid packing drives the segregation of transmembrane helices into disordered lipid domains in model membranes
journal, January 2011

  • Schafer, L. V.; de Jong, D. H.; Holt, A.
  • Proceedings of the National Academy of Sciences, Vol. 108, Issue 4
  • DOI: 10.1073/pnas.1009362108

Peptide Nanopores and Lipid Bilayers: Interactions by Coarse-Grained Molecular-Dynamics Simulations
journal, May 2009

  • Klingelhoefer, Jochen W.; Carpenter, Timothy; Sansom, Mark S. P.
  • Biophysical Journal, Vol. 96, Issue 9
  • DOI: 10.1016/j.bpj.2009.01.046

Lipid Organization of the Plasma Membrane
journal, October 2014

  • Ingólfsson, Helgi I.; Melo, Manuel N.; van Eerden, Floris J.
  • Journal of the American Chemical Society, Vol. 136, Issue 41
  • DOI: 10.1021/ja507832e

Computational Lipidomics of the Neuronal Plasma Membrane
journal, November 2017

  • Ingólfsson, Helgi I.; Carpenter, Timothy S.; Bhatia, Harsh
  • Biophysical Journal, Vol. 113, Issue 10
  • DOI: 10.1016/j.bpj.2017.10.017

Coarse Grained Model for Semiquantitative Lipid Simulations
journal, January 2004

  • Marrink, Siewert J.; de Vries, Alex H.; Mark, Alan E.
  • The Journal of Physical Chemistry B, Vol. 108, Issue 2
  • DOI: 10.1021/jp036508g

Martini Force Field Parameters for Glycolipids
journal, February 2013

  • López, César A.; Sovova, Zofie; van Eerden, Floris J.
  • Journal of Chemical Theory and Computation, Vol. 9, Issue 3
  • DOI: 10.1021/ct3009655

Computational Lipidomics with insane : A Versatile Tool for Generating Custom Membranes for Molecular Simulations
journal, April 2015

  • Wassenaar, Tsjerk A.; Ingólfsson, Helgi I.; Böckmann, Rainer A.
  • Journal of Chemical Theory and Computation, Vol. 11, Issue 5
  • DOI: 10.1021/acs.jctc.5b00209

Calculating the Bending Modulus for Multicomponent Lipid Membranes in Different Thermodynamic Phases
journal, August 2013

  • Khelashvili, George; Kollmitzer, Benjamin; Heftberger, Peter
  • Journal of Chemical Theory and Computation, Vol. 9, Issue 9
  • DOI: 10.1021/ct400492e

Phase Separation in a Lipid/Cholesterol System: Comparison of Coarse-Grained and United-Atom Simulations
journal, March 2013

  • Hakobyan, Davit; Heuer, Andreas
  • The Journal of Physical Chemistry B, Vol. 117, Issue 14
  • DOI: 10.1021/jp312245y

Predictions of Phase Separation in Three-Component Lipid Membranes by the MARTINI Force Field
journal, April 2013

  • Davis, Ryan S.; Sunil Kumar, P. B.; Sperotto, Maria Maddalena
  • The Journal of Physical Chemistry B, Vol. 117, Issue 15
  • DOI: 10.1021/jp4000686

Molecular View of Phase Coexistence in Lipid Monolayers
journal, October 2012

  • Baoukina, Svetlana; Mendez-Villuendas, Eduardo; Tieleman, D. Peter
  • Journal of the American Chemical Society, Vol. 134, Issue 42
  • DOI: 10.1021/ja304792p

Composition Fluctuations in Lipid Bilayers
journal, December 2017

  • Baoukina, Svetlana; Rozmanov, Dmitri; Tieleman, D. Peter
  • Biophysical Journal, Vol. 113, Issue 12
  • DOI: 10.1016/j.bpj.2017.10.009

Key Molecular Requirements for Raft Formation in Lipid/Cholesterol Membranes
journal, February 2014


Update of the CHARMM All-Atom Additive Force Field for Lipids: Validation on Six Lipid Types
journal, June 2010

  • Klauda, Jeffery B.; Venable, Richard M.; Freites, J. Alfredo
  • The Journal of Physical Chemistry B, Vol. 114, Issue 23
  • DOI: 10.1021/jp101759q

Implementation of the CHARMM Force Field in GROMACS: Analysis of Protein Stability Effects from Correction Maps, Virtual Interaction Sites, and Water Models
journal, January 2010

  • Bjelkmar, Pär; Larsson, Per; Cuendet, Michel A.
  • Journal of Chemical Theory and Computation, Vol. 6, Issue 2
  • DOI: 10.1021/ct900549r

Going Backward: A Flexible Geometric Approach to Reverse Transformation from Coarse Grained to Atomistic Models
journal, January 2014

  • Wassenaar, Tsjerk A.; Pluhackova, Kristyna; Böckmann, Rainer A.
  • Journal of Chemical Theory and Computation, Vol. 10, Issue 2
  • DOI: 10.1021/ct400617g

GROMACS: High performance molecular simulations through multi-level parallelism from laptops to supercomputers
journal, September 2015


Parameters for Martini sterols and hopanoids based on a virtual-site description
journal, December 2015

  • Melo, M. N.; Ingólfsson, H. I.; Marrink, S. J.
  • The Journal of Chemical Physics, Vol. 143, Issue 24
  • DOI: 10.1063/1.4937783

Martini straight: Boosting performance using a shorter cutoff and GPUs
journal, February 2016

  • de Jong, Djurre H.; Baoukina, Svetlana; Ingólfsson, Helgi I.
  • Computer Physics Communications, Vol. 199
  • DOI: 10.1016/j.cpc.2015.09.014

Canonical sampling through velocity rescaling
journal, January 2007

  • Bussi, Giovanni; Donadio, Davide; Parrinello, Michele
  • The Journal of Chemical Physics, Vol. 126, Issue 1
  • DOI: 10.1063/1.2408420

Molecular dynamics with coupling to an external bath
journal, October 1984

  • Berendsen, H. J. C.; Postma, J. P. M.; van Gunsteren, W. F.
  • The Journal of Chemical Physics, Vol. 81, Issue 8
  • DOI: 10.1063/1.448118

Polymorphic transitions in single crystals: A new molecular dynamics method
journal, December 1981

  • Parrinello, M.; Rahman, A.
  • Journal of Applied Physics, Vol. 52, Issue 12
  • DOI: 10.1063/1.328693

Simulation of gel phase formation and melting in lipid bilayers using a coarse grained model
journal, June 2005


Thermotropic and barotropic phase transitions of N-methylated dipalmitoylphosphatidylethanolamine bilayers
journal, February 2005

  • Kusube, Masataka; Matsuki, Hitoshi; Kaneshina, Shoji
  • Biochimica et Biophysica Acta (BBA) - Biomembranes, Vol. 1668, Issue 1
  • DOI: 10.1016/j.bbamem.2004.11.002

Maximum solubility of cholesterol in phosphatidylcholine and phosphatidylethanolamine bilayers
journal, February 1999

  • Huang, Juyang; Buboltz, Jeffrey T.; Feigenson, Gerald W.
  • Biochimica et Biophysica Acta (BBA) - Biomembranes, Vol. 1417, Issue 1
  • DOI: 10.1016/S0005-2736(98)00260-0

Phase Equilibria in DOPC/DPPC-d62/Cholesterol Mixtures
journal, January 2009


Separation of Liquid Phases in Giant Vesicles of Ternary Mixtures of Phospholipids and Cholesterol
journal, November 2003


Diffusion of Liquid Domains in Lipid Bilayer Membranes
journal, April 2007

  • Cicuta, Pietro; Keller, Sarah L.; Veatch, Sarah L.
  • The Journal of Physical Chemistry B, Vol. 111, Issue 13
  • DOI: 10.1021/jp0702088

Orientation of Tie-Lines in the Phase Diagram of DOPC/DPPC/Cholesterol Model Biomembranes
journal, November 2010

  • Uppamoochikkal, Pradeep; Tristram-Nagle, Stephanie; Nagle, John F.
  • Langmuir, Vol. 26, Issue 22
  • DOI: 10.1021/la103024f

VMD: Visual molecular dynamics
journal, February 1996


APL@Voro: A Voronoi-Based Membrane Analysis Tool for GROMACS Trajectories
journal, November 2013

  • Lukat, Gunther; Krüger, Jens; Sommer, Björn
  • Journal of Chemical Information and Modeling, Vol. 53, Issue 11
  • DOI: 10.1021/ci400172g

Hysteresis and the Cholesterol Dependent Phase Transition in Binary Lipid Mixtures with the Martini Model
journal, December 2016

  • Arnarez, Clement; Webb, Alexis; Rouvière, Eric
  • The Journal of Physical Chemistry B, Vol. 120, Issue 51
  • DOI: 10.1021/acs.jpcb.6b09728

DPPC-cholesterol phase diagram using coarse-grained Molecular Dynamics simulations
journal, November 2016

  • Wang, Yin; Gkeka, Paraskevi; Fuchs, Julian E.
  • Biochimica et Biophysica Acta (BBA) - Biomembranes, Vol. 1858, Issue 11
  • DOI: 10.1016/j.bbamem.2016.08.005

Phase Behavior of Lipid Bilayers under Tension
journal, February 2012


Understanding the Phase Behavior of Coarse-Grained Model Lipid Bilayers through Computational Calorimetry
journal, January 2012

  • Rodgers, Jocelyn M.; Sørensen, Jesper; de Meyer, Frédérick J. -M.
  • The Journal of Physical Chemistry B, Vol. 116, Issue 5
  • DOI: 10.1021/jp207837v

Phase Behavior of a Lipid Bilayer System Studied by a Replica-Exchange Molecular Dynamics Simulation
journal, February 2012

  • Nagai, Tetsuro; Ueoka, Ryuichi; Okamoto, Yuko
  • Journal of the Physical Society of Japan, Vol. 81, Issue 2
  • DOI: 10.1143/JPSJ.81.024002

In Situ Determination of Structure and Fluctuations of Coexisting Fluid Membrane Domains
journal, February 2015

  • Heftberger, Peter; Kollmitzer, Benjamin; Rieder, Alexander A.
  • Biophysical Journal, Vol. 108, Issue 4
  • DOI: 10.1016/j.bpj.2014.11.3488

Critical fluctuations in domain-forming lipid mixtures
journal, October 2007

  • Veatch, S. L.; Soubias, O.; Keller, S. L.
  • Proceedings of the National Academy of Sciences, Vol. 104, Issue 45
  • DOI: 10.1073/pnas.0703513104

    Works referencing / citing this record:

    Dimerization energetics of the G‐protein coupled bile acid receptor TGR5 from all‐atom simulations
    journal, December 2019

    • Wäschenbach, Lucas; Gertzen, Christoph G. W.; Keitel, Verena
    • Journal of Computational Chemistry, Vol. 41, Issue 9
    • DOI: 10.1002/jcc.26135

      Figures/Tables have been extracted from DOE-funded journal article accepted manuscripts.