https://scholars.lib.ntu.edu.tw/handle/123456789/576859
標題: | Investigating ion transport inside the pentameric ion channel encoded in COVID-19 e protein | 作者: | Saurabh K Solovchuk M Sheu T.W.-H. TONY W. H. SHEU |
關鍵字: | Ions; Lennard-Jones potential; Program processors; Viruses; Channel geometry; Current-voltage relations; Immersed boundary; Lattice Boltzmann method; Poisson-nernst-planck; Protein data bank; Structural proteins; System of equations; Proteins; envelope protein, SARS-CoV-2; chemistry; metabolism; molecular model; protein multimerization; protein quaternary structure; transport at the cellular level; Biological Transport; Coronavirus Envelope Proteins; Models, Molecular; Protein Multimerization; Protein Structure, Quaternary | 公開日期: | 2020 | 卷: | 102 | 期: | 5 | 來源出版物: | Physical Review E | 摘要: | Ion flow inside an ion channel can be described through continuum based Born-Poisson-Nernst-Planck (BPNP) equations in conjunction with the Lennard-Jones potential. Keeping in mind the ongoing pandemic, in this study, an attempt has been made to understand the selectivity and the current voltage relation of the COVID-19 E protein pentameric ion channel. Two ionic species, namely Na+ and Cl-, have been considered here. E protein is one of the smallest structural protein which is embedded in the outer membrane of the virus. Once the virus is inside the host cell, this protein is expressed abundantly and is responsible for activities such as replication and budding of the virus. In the literature, we can find a few experimental studies focusing on understanding the activity of the channel formed by E proteins of different viruses. Here, we attempt the same study for the COVID-19 E protein ion channel through mathematical modeling. The channel geometry is calculated from the protein data bank file which was provided by NARLabs, Taiwan, using the hole program. Further, it was used to obtain the charge distribution using the pdbtopqr online program. The immersed boundary-lattice Boltzmann method (IB-LBM) has been implemented to numerically solve the system of equations in the channel generated by the protein data bank file. Further, an in-house code which operates on multiple GPUs and uses the cuda platform has been developed to achieve the goal of performing the current investigation. ? 2020 American Physical Society. |
URI: | https://www.scopus.com/inward/record.uri?eid=2-s2.0-85096898176&doi=10.1103%2fPhysRevE.102.052408&partnerID=40&md5=3dd13c2edc46bd365585f3b7ea613654 https://scholars.lib.ntu.edu.tw/handle/123456789/576859 |
ISSN: | 24700045 | DOI: | 10.1103/PhysRevE.102.052408 |
顯示於: | 工程科學及海洋工程學系 |
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