A brief history of visualizing membrane systems in molecular dynamics simulations

被引:6
作者
Corey, R. A. [1 ]
Baaden, M. [2 ]
Chavent, M. [3 ]
机构
[1] Univ Oxford, Dept Biochem, Oxford, England
[2] Univ Paris Cite, CNRS, Lab Biochim Theor, Paris, France
[3] Univ Toulouse, CNRS, Inst Pharmacol & Biol Struct, Toulouse, France
来源
FRONTIERS IN BIOINFORMATICS | 2023年 / 3卷
基金
英国惠康基金;
关键词
molecular dynamics simulation; multiscale modelling and simulation; membrane system; molecular graphics; membrane protein; COARSE-GRAINED MODEL; FORCE-FIELD; COMPUTATIONAL LIPIDOMICS; STRUCTURAL DETERMINANTS; COMPUTER-SIMULATION; ION-CHANNEL; DIFFUSION; PROTEINS; PHOSPHOLIPIDS; ORGANIZATION;
D O I
10.3389/fbinf.2023.1149744
中图分类号
Q [生物科学];
学科分类号
07 ; 0710 ; 09 ;
摘要
Understanding lipid dynamics and function, from the level of single, isolated molecules to large assemblies, is more than ever an intensive area of research. The interactions of lipids with other molecules, particularly membrane proteins, are now extensively studied. With advances in the development of force fields for molecular dynamics simulations (MD) and increases in computational resources, the creation of realistic and complex membrane systems is now common. In this perspective, we will review four decades of the history of molecular dynamics simulations applied to membranes and lipids through the prism of molecular graphics.
引用
收藏
页数:11
相关论文
共 153 条
[1]   Martini 3 Coarse-Grained Force Field: Small Molecules [J].
Alessandri, Riccardo ;
Barnoud, Jonathan ;
Gertsen, Anders S. ;
Patmanidis, Ilias ;
de Vries, Alex H. ;
Souza, Paulo C. T. ;
Marrink, Siewert J. .
ADVANCED THEORY AND SIMULATIONS, 2022, 5 (01)
[2]   The Martini Model in Materials Science [J].
Alessandri, Riccardo ;
Grunewald, Fabian ;
Marrink, Siewert J. .
ADVANCED MATERIALS, 2021, 33 (24)
[3]  
Alharbi N., 2019, Eurographics
[4]   GridMAT-MD: A Grid-Based Membrane Analysis Tool for Use With Molecular Dynamics [J].
Allen, William J. ;
Lemkul, Justin A. ;
Bevan, David R. .
JOURNAL OF COMPUTATIONAL CHEMISTRY, 2009, 30 (12) :1952-1958
[5]   Molecular mechanism of cardiolipin-mediated assembly of respiratory chain supercomplexes [J].
Arnarez, C. ;
Marrink, S. J. ;
Periole, X. .
CHEMICAL SCIENCE, 2016, 7 (07) :4435-4443
[6]  
Baaden M, 2022, VIRTUAL REALITY INTE, V4, P324, DOI DOI 10.1016/J.VRIH.2022.03.001
[7]   Visualizing Biological Membrane Organization and Dynamics [J].
Baaden, Marc .
JOURNAL OF MOLECULAR BIOLOGY, 2019, 431 (10) :1889-1919
[8]   Composition Fluctuations in Lipid Bilayers [J].
Baoukina, Svetlana ;
Rozmanov, Dmitri ;
Tieleman, D. Peter .
BIOPHYSICAL JOURNAL, 2017, 113 (12) :2750-2761
[9]   Fat SIRAH: Coarse-Grained Phospholipids To Explore Membrane-Protein Dynamics [J].
Barrera, Exequiel E. ;
Machado, Matias R. ;
Pantano, Sergio .
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 2019, 15 (10) :5674-5688
[10]   SOLUTE DIFFUSION IN LIPID BILAYER-MEMBRANES - AN ATOMIC-LEVEL STUDY BY MOLECULAR-DYNAMICS SIMULATION [J].
BASSOLINOKLIMAS, D ;
ALPER, HE ;
STOUCH, TR .
BIOCHEMISTRY, 1993, 32 (47) :12624-12637