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
[91]   UnityMol prototype for FAIR sharing of molecular-visualization experiences: from pictures in the cloud to collaborative virtual reality exploration in immersive 3D environments [J].
Martinez, Xavier ;
Baaden, Marc .
ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY, 2021, 77 :746-754
[92]   Visualizing protein structures - tools and trends [J].
Martinez, Xavier ;
Chavent, Matthieu ;
Baaden, Marc .
BIOCHEMICAL SOCIETY TRANSACTIONS, 2020, 48 (02) :499-506
[93]   Molecular Graphics: Bridging Structural Biologists and Computer Scientists [J].
Martinez, Xavier ;
Krone, Michael ;
Alharbi, Naif ;
Rose, Alexander S. ;
Laramee, Robert S. ;
O'Donoghue, Sean ;
Baaden, Marc ;
Chavent, Matthieu .
STRUCTURE, 2019, 27 (11) :1617-1623
[94]   Structure of lateral heterogeneities in a coarse-grained model for multicomponent membranes [J].
Meinhardt, Sebastian ;
Schmid, Friederike .
SOFT MATTER, 2019, 15 (09) :1942-1952
[95]   RASTER3D VERSION-2.0 - A PROGRAM FOR PHOTOREALISTIC MOLECULAR GRAPHICS [J].
MERRITT, EA ;
MURPHY, MEP .
ACTA CRYSTALLOGRAPHICA SECTION D-BIOLOGICAL CRYSTALLOGRAPHY, 1994, 50 :869-873
[96]   The MARTINI coarse-grained force field: Extension to proteins [J].
Monticelli, Luca ;
Kandasamy, Senthil K. ;
Periole, Xavier ;
Larson, Ronald G. ;
Tieleman, D. Peter ;
Marrink, Siewert-Jan .
JOURNAL OF CHEMICAL THEORY AND COMPUTATION, 2008, 4 (05) :819-834
[97]   Characterization of Lipid-Protein Interactions and Lipid-Mediated Modulation of Membrane Protein Function through Molecular Simulation [J].
Muller, Melanie P. ;
Jiang, Tao ;
Sun, Chang ;
Lihan, Muyun ;
Pant, Shashank ;
Mahinthichaichan, Paween ;
Trifan, Anda ;
Tajkhorshid, Emad .
CHEMICAL REVIEWS, 2019, 119 (09) :6086-6161
[98]   The MemProtMD database: a resource for membrane-embedded protein structures and their lipid interactions [J].
Newport, Thomas D. ;
Sansom, Mark S. P. ;
Stansfeld, Phillip J. .
NUCLEIC ACIDS RESEARCH, 2019, 47 (D1) :D390-D397
[99]   Interactive molecular dynamics in virtual reality from quantum chemistry to drug binding: An open-source multi-person framework [J].
O'Connor, Michael B. ;
Bennie, Simon J. ;
Deeks, Helen M. ;
Jamieson-Binnie, Alexander ;
Jones, Alex J. ;
Shannon, Robin J. ;
Walters, Rebecca ;
Mitchell, Thomas J. ;
Mulholland, Adrian J. ;
Glowacki, David R. .
JOURNAL OF CHEMICAL PHYSICS, 2019, 150 (22)
[100]  
O'Donoghue SI, 2010, NAT METHODS, V7, pS42, DOI [10.1038/NMETH.1427, 10.1038/nmeth.1427]