Shedding light on the structural properties of lipid bilayers using molecular dynamics simulation: a review study

被引:71
作者
Moradi, Sajad [1 ]
Nowroozi, Amin [2 ]
Shahlaei, Mohsen [3 ]
机构
[1] Kermanshah Univ Med Sci, Nano Drug Delivery Res Ctr, Kermanshah, Iran
[2] Kermanshah Univ Med Sci, Fac Pharm, Pharmaceut Sci Res Ctr, Kermanshah, Iran
[3] Kermanshah Univ Med Sci, Med Biol Res Ctr, Kermanshah, Iran
来源
RSC ADVANCES | 2019年 / 9卷 / 08期
关键词
FORCE-FIELD; LATERAL DIFFUSION; CONFORMATIONAL-ANALYSIS; PHOSPHOLIPID-BILAYERS; NEUTRON-DIFFRACTION; DEUTERIUM NMR; MEMBRANES; MODEL; PHOSPHATIDYLCHOLINE; CHOLESTEROL;
D O I
10.1039/c8ra08441f
中图分类号
O6 [化学];
学科分类号
0703 ;
摘要
In recent years, a massive increase has been observed in the number of published articles describing accurate and reliable molecular dynamics simulations of lipid bilayers. This is due to several reasons, including the development of fast and efficient methods for treating long-range electrostatic interactions, significant progress in computer hardware, progress in atomistic simulation algorithms and the development of well-validated empirical molecular mechanical force fields. Although molecular dynamics is an effective approach for investigating different aspects of lipid bilayers, to the best of our knowledge, there is no review in the literature that explains the different analyses that can be carried out with membrane simulation. This review gives an overview about the some of the most important possible analyses, technical challenges, and existing protocols that can be performed on the biological membrane by molecular dynamics simulation. The reviewed analyses include the degree of membrane disruption, average area per lipid, probability distributions for the area per lipid molecule, membrane thickness, membrane area compressibility, lateral diffusion, rotational diffusion, order parameters, head group tilt, electron density profile, mass density profile, electrostatic potential profile, ordering of vicinity waters, number of hydrogen bonds, and radial distribution function.
引用
收藏
页码:4644 / 4658
页数:15
相关论文
共 50 条
[31]   Molecular dynamics study of lipid bilayers modeling outer and inner leaflets of plasma membranes of mouse hepatocytes. I. Differences in physicochemical properties between the two leaflets [J].
Andoh, Yoshimichi ;
Hayakawa, Shiho ;
Okazaki, Susumu .
JOURNAL OF CHEMICAL PHYSICS, 2020, 153 (03)
[32]   Free energy of adsorption of supported lipid bilayers from molecular dynamics simulation [J].
Schneemilch, M. ;
Quirke, N. .
CHEMICAL PHYSICS LETTERS, 2016, 664 :199-204
[34]   Dibucaine effects on structural and elastic properties of lipid bilayers [J].
Lorite, G. S. ;
Nobre, T. M. ;
Zaniquelli, M. E. D. ;
de Paula, E. ;
Cotta, M. A. .
BIOPHYSICAL CHEMISTRY, 2009, 139 (2-3) :75-83
[35]   Study of curcumin behavior in two different lipid bilayer models of liposomal curcumin using molecular dynamics simulation [J].
Jalili, Seifollah ;
Saeedi, Marzieh .
JOURNAL OF BIOMOLECULAR STRUCTURE & DYNAMICS, 2016, 34 (02) :327-340
[36]   Understanding Interactions of Curcumin with Lipid Bilayers: A Coarse-Grained Molecular Dynamics Study [J].
Ercan, Nazar Ileri .
JOURNAL OF CHEMICAL INFORMATION AND MODELING, 2019, 59 (10) :4413-4426
[37]   Molecular dynamics study of lipid bilayers modeling the plasma membranes of mouse hepatocytes and hepatomas [J].
Andoh, Yoshimichi ;
Aoki, Noriyuki ;
Okazaki, Susumu .
JOURNAL OF CHEMICAL PHYSICS, 2016, 144 (08)
[38]   Molecular dynamics study of lipid bilayers modeling the plasma membranes of normal murine thymocytes and leukemic GRSL cells [J].
Andoh, Yoshimichi ;
Okazaki, Susumu ;
Ueoka, Ryuichi .
BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES, 2013, 1828 (04) :1259-1270
[39]   Molecular dynamics simulations of carbon nanotube porins in lipid bilayers [J].
Voegele, Martin ;
Koefinger, Juergen ;
Hummer, Gerhard .
FARADAY DISCUSSIONS, 2018, 209 :341-358
[40]   Molecular dynamics simulations of rupture in lipid bilayers [J].
Tomasini, Michael D. ;
Rinaldi, Carlos ;
Tomassone, M. Silvina .
EXPERIMENTAL BIOLOGY AND MEDICINE, 2010, 235 (02) :181-188