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基于分子动力学模拟的磷脂和整合蛋白的物理性质及其在肺表面活性剂中的生物功能作用

Physical properties of phospholipids and integral proteins and their biofunctional roles in pulmonary surfactant from molecular dynamics simulation.

作者信息

Hadrioui Nourddine, Lemaalem Mohammed, Derouiche Abdelali, Ridouane Hamid

机构信息

Laboratoire de Physique des Polymères et Phénomènes Critiques Sciences Faculty Ben M'Sik, Hassan II University P.O. Box 7955 Casablanca Morocco

出版信息

RSC Adv. 2020 Feb 27;10(14):8568-8579. doi: 10.1039/d0ra00077a. eCollection 2020 Feb 24.

DOI:10.1039/d0ra00077a
PMID:35497816
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC9049990/
Abstract

This work deals with a quantitative investigation of the physical properties of pulmonary surfactant near melting temperature. To this end, we make use of molecular dynamics simulations, using the MARTINI coarse-grained model, for determining the physical properties of the system, such as the potential energy, the specific heat, the microstructure, the diffusion laws, and the elastic properties of the surfactant. The microstructure is studied by computation of the radial-distribution-function upon varying the distance between constituents (lipid molecules or proteins). The diffusion phenomenon is investigated by determination of the mean-squared-displacement and the time dependent velocity-autocorrelation-function for various values of temperature. We show that the dynamics of lipids and proteins exhibit a subdiffusion regime (slow movement) due to the cage effect within pulmonary surfactant. From the obtained mean-squared-displacement, we get the values of the self-diffusion-coefficients and the anomalous exponents at different temperatures close to the melting temperature. For the mathematical description of the cage effect, we make use of the scale relations in terms of the waiting time probability distribution. The last study is concerned with determination of the dependence of the lateral stress upon the strain of pulmonary surfactant, which is found to be linear, and from which we deduce the lateral-elastic-modulus.

摘要

这项工作涉及对接近熔点温度的肺表面活性剂物理性质的定量研究。为此,我们利用分子动力学模拟,采用MARTINI粗粒化模型,来确定系统的物理性质,如势能、比热、微观结构、扩散规律以及表面活性剂的弹性性质。通过计算不同成分(脂质分子或蛋白质)之间距离变化时的径向分布函数来研究微观结构。通过确定不同温度下的均方位移和随时间变化的速度自相关函数来研究扩散现象。我们表明,由于肺表面活性剂中的笼效应,脂质和蛋白质的动力学表现出亚扩散状态(缓慢运动)。从获得的均方位移中,我们得到了不同温度下接近熔点时的自扩散系数和反常指数值。对于笼效应的数学描述,我们利用了等待时间概率分布的尺度关系。最后一项研究涉及确定肺表面活性剂的横向应力对应变的依赖性,发现其为线性关系,并由此推导出横向弹性模量。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/c3a8/9049990/8e66305cffc9/d0ra00077a-f9.jpg
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