Computational Modeling of Realistic Cell Membranes

被引:487
作者
Marrink, Siewert J. [1 ,2 ]
Corradi, Valentina [3 ,4 ]
Souza, Paulo C. T. [1 ,2 ]
Ingolfsson, Helgi I. [5 ]
Tieleman, D. Peter [3 ,4 ]
Sansom, Mark S. P. [6 ]
机构
[1] Univ Groningen, Groningen Biomol Sci & Biotechnol Inst, Nijenborgh 7, NL-9747 AG Groningen, Netherlands
[2] Univ Groningen, Zernike Inst Adv Mat, Nijenborgh 7, NL-9747 AG Groningen, Netherlands
[3] Univ Calgary, Ctr Mol Simulat, 2500 Univ Dr NW, Calgary, AB T2N 1N4, Canada
[4] Univ Calgary, Dept Biol Sci, 2500 Univ Dr NW, Calgary, AB T2N 1N4, Canada
[5] Lawrence Livermore Natl Lab, Phys & Life Sci Directorate, Biosci & Biotechnol Div, 7000 East Ave, Livermore, CA 94550 USA
[6] Univ Oxford, Dept Biochem, South Parks Rd, Oxford OX1 3QU, England
基金
英国生物技术与生命科学研究理事会; 加拿大自然科学与工程研究理事会; 加拿大健康研究院; 英国惠康基金; 英国工程与自然科学研究理事会;
关键词
MOLECULAR-DYNAMICS SIMULATIONS; GRAINED FORCE-FIELD; BACTERIAL OUTER-MEMBRANE; PROTEIN-COUPLED RECEPTORS; CHOLESTEROL INTERACTION SITES; ADENINE-NUCLEOTIDE TRANSLOCASE; HELIX-HELIX INTERACTIONS; LIPID-BINDING SITES; SMALL-ANGLE NEUTRON; PHASE-SEPARATION;
D O I
10.1021/acs.chemrev.8b00460
中图分类号
O6 [化学];
学科分类号
0703 ;
摘要
Cell membranes contain a large variety of lipid types and are crowded with proteins, endowing them with the plasticity needed to fulfill their key roles in cell functioning. The compositional complexity of cellular membranes gives rise to a heterogeneous lateral organization, which is still poorly understood. Computational models, in particular molecular dynamics simulations and related techniques, have provided important insight into the organizational principles of cell membranes over the past decades. Now, we are witnessing a transition from simulations of simpler membrane models to multicomponent systems, culminating in realistic models of an increasing variety of cell types and organelles. Here, we review the state of the art in the field of realistic membrane simulations and discuss the current limitations and challenges ahead.
引用
收藏
页码:6184 / 6226
页数:43
相关论文
共 703 条
  • [1] Structural basis for maintenance of bacterial outer membrane lipid asymmetry
    Abellon-Ruiz, Javier
    Kaptan, Shreyas S.
    Basle, Arnaud
    Claudi, Beatrice
    Bumann, Dirk
    Kleinekathoefer, Ulrich
    van den Berg, Bert
    [J]. NATURE MICROBIOLOGY, 2017, 2 (12): : 1616 - 1623
  • [2] Gromacs: High performance molecular simulations through multi-level parallelism from laptops to supercomputers
    Abraham, Mark James
    Murtola, Teemu
    Schulz, Roland
    Páll, Szilárd
    Smith, Jeremy C.
    Hess, Berk
    Lindah, Erik
    [J]. SoftwareX, 2015, 1-2 : 19 - 25
  • [3] Transmembrane Recognition of the Semaphorin Co-Receptors Neuropilin 1 and Plexin A1: Coarse-Grained Simulations
    Aci-Seche, Samia
    Sawma, Paul
    Hubert, Pierre
    Sturgis, James N.
    Bagnard, Dominique
    Jacob, Laurent
    Genest, Monique
    Garnier, Norbert
    [J]. PLOS ONE, 2014, 9 (05):
  • [4] Effects of Transmembrane α-Helix Length and Concentration on Phase Behavior in Four-Component Lipid Mixtures: A Molecular Dynamics Study
    Ackerman, David G.
    Feigenson, Gerald W.
    [J]. JOURNAL OF PHYSICAL CHEMISTRY B, 2016, 120 (17) : 4064 - 4077
  • [5] Multiscale Modeling of Four-Component Lipid Mixtures: Domain Composition, Size, Alignment, and Properties of the Phase Interface
    Ackerman, David G.
    Feigenson, Gerald W.
    [J]. JOURNAL OF PHYSICAL CHEMISTRY B, 2015, 119 (11) : 4240 - 4250
  • [6] Insight into the Properties of Cardiolipin Containing Bilayers from Molecular Dynamics Simulations, Using a Hybrid All-Atom/United-Atom Force Field
    Aguayo, Daniel
    Gonzalez-Nilo, Fernando D.
    Chipot, Christophe
    [J]. JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 2012, 8 (05) : 1765 - 1773
  • [7] Arginine-rich cell-penetrating peptides induce membrane multilamellarity and subsequently enter via formation of a fusion pore
    Allolio, Christoph
    Magarkar, Aniket
    Jurkiewicz, Piotr
    Baxova, Katarina
    Javanainen, Matti
    Mason, Philip E.
    Sachl, Radek
    Cebecauer, Marek
    Hof, Martin
    Horinek, Dominik
    Heinz, Veronika
    Rachel, Reinhard
    Ziegler, Christine M.
    Schrofel, Adam
    Jungwirth, Pavel
    [J]. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2018, 115 (47) : 11923 - 11928
  • [8] Membrane proteins structures: A review on computational modeling tools
    Almeida, Jose G.
    Preto, Antonio J.
    Koukos, Panagiotis I.
    Bonvin, Alexandre M. J. J.
    Moreira, Irina S.
    [J]. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES, 2017, 1859 (10): : 2021 - 2039
  • [9] An Ensemble-Based Protocol for the Computational Prediction of Helix-Helix Interactions in G Protein-Coupled Receptors using Coarse-Grained Molecular Dynamics
    Altwaijry, Nojood A.
    Baron, Michael
    Wright, David W.
    Coveney, Peter V.
    Townsend-Nicholson, Andrea
    [J]. JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 2017, 13 (05) : 2254 - 2270
  • [10] Molecular dynamics study of lipid bilayers modeling the plasma membranes of normal murine thymocytes and leukemic GRSL cells
    Andoh, Yoshimichi
    Okazaki, Susumu
    Ueoka, Ryuichi
    [J]. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES, 2013, 1828 (04): : 1259 - 1270