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一项关于一氧化碳通过水通道蛋白5渗透的新型分子动力学研究。

A novel molecular dynamics study of CO permeation through aquaporin-5.

作者信息

Alishahi Marzieh, Kamali Reza

机构信息

Department of Mechanical Engineering, Shiraz University, Shiraz, Iran.

出版信息

Eur Phys J E Soft Matter. 2019 Nov 27;42(11):151. doi: 10.1140/epje/i2019-11912-x.

Abstract

Aquaporins (AQPs) are protein channels which facilitate rapid water permeation across cell membrane. The AQPs are very vital for biological organs, as their malfunction causes severe diseases in human body. A particular family of AQPs, that is AQP5, has a significant role in lung fluid transport due to submucosal glands structure. However, it has not been yet well understood whether these protein channels can conduct gas molecules. Here, Molecular Dynamics (MD) simulations are used to investigate the CO permeability and diffusion in AQP5 during a 40-nanosecond period. For the first time, equilibrium and Steered MD (SMD) are used to simulate self and force-induced diffusion of CO molecules across AQP5 and POPE lipid bilayer. According to PMFs profile associated to CO permeation, the hydrophobic central pore provides a more suitable pathway for gas molecules compared to other AQP5 channels. Although CO molecules can also permeate across AQP5 water channels, the rate of CO permeation through four channels of the AQP5 monomers is much lower than the central pore. The rate of CO permeation through four AQP5 water channels is even lower than CO diffusion through POPE lipid membrane. The results reported in this investigation demonstrate that MD simulations of human AQP5 provide valuable insights into the gas permeation mechanism for both the equilibrium self-diffusion, and quasi-equilibrium condition.

摘要

水通道蛋白(AQPs)是促进水快速透过细胞膜的蛋白质通道。水通道蛋白对生物器官非常重要,因为其功能异常会导致人体患上严重疾病。水通道蛋白的一个特定家族,即水通道蛋白5(AQP5),由于黏膜下腺结构,在肺液运输中具有重要作用。然而,这些蛋白质通道是否能传导气体分子尚未得到充分了解。在此,利用分子动力学(MD)模拟研究了40纳秒内一氧化碳(CO)在水通道蛋白5中的渗透性和扩散情况。首次使用平衡态和引导分子动力学(SMD)来模拟CO分子在水通道蛋白5和1-棕榈酰-2-油酰磷脂酰乙醇胺(POPE)脂质双层中的自扩散和力诱导扩散。根据与CO渗透相关的势能面(PMFs)分布,与水通道蛋白5的其他通道相比,疏水中心孔为气体分子提供了更合适的通道。尽管CO分子也能透过水通道蛋白5的水通道,但CO通过水通道蛋白5单体的四个通道的渗透速率远低于中心孔。CO通过水通道蛋白5的四个水通道的渗透速率甚至低于其在POPE脂质膜中的扩散速率。本研究报告的结果表明,对人类水通道蛋白5的MD模拟为平衡态自扩散和准平衡态的气体渗透机制提供了有价值的见解。

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