通过原子级模拟研究三油酰甘油两层和脂肪体横截面模拟四层系统。

IF 2.3 2区 物理与天体物理 Q3 CHEMISTRY, PHYSICAL Structural Dynamics-Us Pub Date : 2022-12-05 eCollection Date: 2022-11-01 DOI:10.1063/4.0000168
Ahmed Hammad Mirza
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引用次数: 0

摘要

脂肪体是人工制备的仿脂滴(LD)结构,与 LD 不同,它不含有蛋白质。脂肪体中的三酰甘油(TAG)、药物分子和磷脂之间的相互作用动力学目前尚未得到很好的证实。三油酰甘油(TOG)分子被分为三部分:两个油酰尾和一个 2-单油酰甘油(MOG)。两个油酰基尾部的力场参数来自 AMBER18 数据库,而 MOG 力场的参数则来自文献。在使用 MOG 力场之前对其进行了电荷校正。经过电荷校正后,得到的 TOG 分子电荷为零。制备并模拟了 TOG 双层(2L)和四层(4L)系统。从两种不同的初始构象(TOG3构象和TOG2:1构象)模拟的TOG双分子层(2L)系统显示,无论初始构象如何,TOG2:1构象都更为普遍,因此被用于进一步的模拟。水合 TOG 2L 系统显示 TOG 水溶液溶解度为 0.051 mol L-1,接近实验值。这验证了对 TOG 分子参数化的正确性。4L 系统的模拟结果表明,在模拟的最后阶段,膜的行为比较稳定。还观察到在 4L 系统中,TOG 分子与药物分子形成胶束。在整个模拟过程中,近六个 TOG 始终与药物分子保持接触。电荷校正 TOG 参数化的可用性有望为今后的研究提供原子水平的脂肪体和/或 LD 的分子动力学模拟框架。
本文章由计算机程序翻译,如有差异,请以英文原文为准。

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Study of trioleoylglycerol two-layer and adiposome cross-section mimicking four-layer systems through atomic-level simulations.

Adiposomes are artificially prepared lipid droplet (LD)-mimetic structures, which, unlike LDs, do not harbor proteins. The dynamics of interaction between triacylglycerols (TAGs), drug molecule, and phospholipids in adiposomes is currently not well-established. Trioleoylglycerol (TOG) molecule was divided into three parts: two oleoyl tails and one 2-monooleoylglycerol (MOG). Forcefield parameters for two oleoyl tails were adopted from the AMBER18 repository while that of the MOG forcefield was taken from the literature. Charge correction was performed on the MOG forcefield before its utilization. After charge correction, the resulting TOG molecule had zero charge. TOG bilayer (2L) and tetralayer (4L) systems were prepared and simulated. TOG bilayer (2L) systems-modeled from two different initial conformations, the TOG3 conformation and the TOG2:1 conformation-showed that TOG2:1 conformation was more prevailing irrespective of the starting conformation and was subsequently used in further simulations. The hydrated TOG 2L system showed TOG-water solution solubility of 0.051 mol L-1 which is near experimental values. This validated the correct parameterization of the TOG molecule. The simulations of 4L systems showed stable membrane behaviors toward the end of simulations. It was also observed that in the 4L system, the TOG molecules showed the formation of micelles with the drug molecule. Almost six TOGs remained continuously in contact with the drug molecule throughout the simulation. The availability of charge-corrected TOG parameterization is expected to equip future studies with a framework for molecular dynamics simulations of adiposomes and/or LDs at the atomic level.

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来源期刊
Structural Dynamics-Us
Structural Dynamics-Us CHEMISTRY, PHYSICALPHYSICS, ATOMIC, MOLECU-PHYSICS, ATOMIC, MOLECULAR & CHEMICAL
CiteScore
5.50
自引率
3.60%
发文量
24
审稿时长
16 weeks
期刊介绍: Structural Dynamics focuses on the recent developments in experimental and theoretical methods and techniques that allow a visualization of the electronic and geometric structural changes in real time of chemical, biological, and condensed-matter systems. The community of scientists and engineers working on structural dynamics in such diverse systems often use similar instrumentation and methods. The journal welcomes articles dealing with fundamental problems of electronic and structural dynamics that are tackled by new methods, such as: Time-resolved X-ray and electron diffraction and scattering, Coherent diffractive imaging, Time-resolved X-ray spectroscopies (absorption, emission, resonant inelastic scattering, etc.), Time-resolved electron energy loss spectroscopy (EELS) and electron microscopy, Time-resolved photoelectron spectroscopies (UPS, XPS, ARPES, etc.), Multidimensional spectroscopies in the infrared, the visible and the ultraviolet, Nonlinear spectroscopies in the VUV, the soft and the hard X-ray domains, Theory and computational methods and algorithms for the analysis and description of structuraldynamics and their associated experimental signals. These new methods are enabled by new instrumentation, such as: X-ray free electron lasers, which provide flux, coherence, and time resolution, New sources of ultrashort electron pulses, New sources of ultrashort vacuum ultraviolet (VUV) to hard X-ray pulses, such as high-harmonic generation (HHG) sources or plasma-based sources, New sources of ultrashort infrared and terahertz (THz) radiation, New detectors for X-rays and electrons, New sample handling and delivery schemes, New computational capabilities.
期刊最新文献
Laser-induced electron diffraction: Imaging of a single gas-phase molecular structure with one of its own electrons. Deconvolution of dynamic heterogeneity in protein structure. Role of crystal orientation in attosecond photoinjection dynamics of germanium. CrysFormer: Protein structure determination via Patterson maps, deep learning, and partial structure attention. Introduction to the Special Issue Tribute to Olga Kennard (1924-2023).
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