Molecular dynamics simulations of glyphosate in a DPPC lipid bilayer

被引:12
|
作者
Frigini, Ezequiel N. [1 ,2 ]
Lopez Cascales, J. J. [3 ]
Porasso, Rodolfo D. [1 ,2 ]
机构
[1] Univ Nacl San Luis, IMASL, Ejercito Los Andes 950,D5700HHW, San Luis, Argentina
[2] Consejo Nacl Invest Cient & Tecn, Ejercito Los Andes 950,D5700HHW, San Luis, Argentina
[3] Univ Politecn Cartagena, Grp Bioinformat & Macromol BioMac, Area Quim Fis, Aulario 2,Campus Alfonso 13, Murcia 30203, Spain
关键词
Glyphosate; Lipid bilayer; Molecular dynamics; Free energy; PARTICLE MESH EWALD; COMPUTER-SIMULATIONS; FREE-ENERGY; DIPALMITOYLPHOSPHATIDYLCHOLINE; DIFFUSION; MEMBRANES; MODEL; DISTRIBUTIONS; MECHANISM; INTERIOR;
D O I
10.1016/j.chemphyslip.2018.04.003
中图分类号
Q5 [生物化学]; Q7 [分子生物学];
学科分类号
071010 ; 081704 ;
摘要
Extensive molecular dynamics simulations have been performed to study the effect of glyphosate (in their neutral and charged forms, GLYP and GLYP(2-), respectively) on fully hydrated DiPalmitoylPhosphatidylCholine (DPPC) lipid bilayer. First, we calculated the free energy profile (using the Umbrella Sampling technique) for both states of charge of glyphosate. The minimum value for the free energy for GLYP is similar to-60 kJ mol(-1) located at z = +/- 1.7 nm (from the lipid bilayer center), and there is almost no maximum at the center of the lipid bilayer. By contrast, the minimum for GLYP(2-) is similar to-35 kJ mol(-1) located at z = +/- 1.4 nm (from the lipid bilayer center), and the maximum reaches similar to 35 kJ mol(-1) at the center of the lipid bilayer. Then, different lipid bilayer properties were analyzed for different glyphosate:lipid (G:L) ratios. The mean area per lipid was slightly affected, increasing only 5% (in the presence of glyphosate at high concentrations), which is in agreement with the slight decrease in deuterium order parameters. As for the thickness of the bilayer, it is observed that the state of charge produces opposite effects. On one hand, the neutral state produces an increase in the thickness of the lipid bilayer; on the other, the charged form produces a decrease in the thickness, which not depend linearly on the G:L ratios, either. The orientation of the DPPC head groups is practically unaffected throughout the range of the G:L ratios studied. Finally, the mobility of the lipids of the bilayer is strongly affected by the presence of glyphosate, considerably increasing its lateral diffusion coefficient noteworthy (one order of magnitude), with increasing G:L ratio.
引用
收藏
页码:111 / 117
页数:7
相关论文
共 50 条
  • [21] Molecular dynamics simulations and free energy profile of Paracetamol in DPPC and DMPC lipid bilayers
    YOUSEF NADEMI
    SEPIDEH AMJAD IRANAGH
    ABBAS YOUSEFPOUR
    SEYEDEH ZAHRA MOUSAVI
    HAMID MODARRESS
    Journal of Chemical Sciences, 2014, 126 : 637 - 647
  • [22] Molecular dynamics simulations of the effects of sodium dodecyl sulfate on lipid bilayer
    徐斌
    林文强
    汪小刚
    曾松伟
    周国泉
    陈均朗
    Chinese Physics B, 2017, 26 (03) : 307 - 311
  • [23] Molecular Dynamics Simulations of Cholesterol Effects on the Interaction of hIAPP with Lipid Bilayer
    Liu, Yonglan
    Zhang, Dong
    Zhang, Yanxian
    Tang, Yijing
    Xu, Lijian
    He, Huacheng
    Wu, Jiang
    Zheng, Jie
    JOURNAL OF PHYSICAL CHEMISTRY B, 2020, 124 (36): : 7830 - 7841
  • [24] Atomistic Molecular Dynamics Simulations of Drosophila Orai in a Hydrated Lipid Bilayer
    Wood, Mona L.
    Amcheslavsky, Anna
    Wong, Eric
    Freites, J. Alfredo
    Cahalan, Michael D.
    Tobias, Douglas J.
    BIOPHYSICAL JOURNAL, 2014, 106 (02) : 316A - 316A
  • [25] Molecular dynamics simulations of the effects of sodium dodecyl sulfate on lipid bilayer
    Xu, Bin
    Lin, Wen-Qiang
    Wang, Xiao-Gang
    Zeng, Song-wei
    Zhou, Guo-Quan
    Chen, Jun-Lang
    CHINESE PHYSICS B, 2017, 26 (03)
  • [26] Study of lipid heterogeneity on bilayer membranes using molecular dynamics simulations
    Kumar, Nandan
    Sastry, G. Narahari
    JOURNAL OF MOLECULAR GRAPHICS & MODELLING, 2021, 108 (108):
  • [27] Molecular dynamics simulations of dialkyl carbocyanine dyes in a DPPC bilayer: Atomistic insights into single molecule fluorescence
    Gullapalli, Ramachandra
    Demirel, Mellk
    Butler, Peter J.
    PROCEEDING OF THE ASME SUMMER BIOENGINEERING CONFERENCE - 2007, 2007, : 787 - 788
  • [28] Investigation of benzodiazepines (BZDs) in a DPPC lipid bilayer: Insights from molecular dynamics simulation and DFT calculations
    Koli, Mokhtar Ganjali
    Azizi, Khaled
    JOURNAL OF MOLECULAR GRAPHICS & MODELLING, 2019, 90 : 171 - 179
  • [29] Molecular dynamics simulations of negatively charged DPPC/DPPI lipid bilayers at two levels of resolution
    Stanishneva-Konovalova, T. B.
    Sokolova, O. S.
    COMPUTATIONAL AND THEORETICAL CHEMISTRY, 2015, 1058 : 61 - 66
  • [30] Molecular dynamics simulations of a DPPC/DPPG monolayer.
    Kaznessis, YN
    Kim, S
    Larson, RG
    BIOPHYSICAL JOURNAL, 2000, 78 (01) : 331A - 331A