Qualitative computational bioanalytics: Assembly of viral channel-forming peptides around mono and divalent ions

Li Hua Li; Hao Jen Hsu; Wolfgang B. Fischer

doi:10.1016/j.bbrc.2013.11.017

Qualitative computational bioanalytics: Assembly of viral channel-forming peptides around mono and divalent ions

Li Hua Li, Hao Jen Hsu, Wolfgang B. Fischer^*

^*此作品的通信作者

生醫光電研究所

研究成果: Article › 同行評審

3 引文斯高帕斯（Scopus）

摘要

A fine-grained docking protocol was used to generate a bundle-like structure of the bitopic membrane protein Vpu from HIV-1. Vpu is a type I membrane protein with 81 amino acids. It is proposed that Vpu forms ion- and substrate-conducting bundles, which are located at the plasma membrane in the infected cell. The Vpu_1-32 peptide that includes the transmembrane domain (TMD) is assembled into homo-pentameric bundles around prepositioned Na, K, Ca or Cl ions. For bundles with the lowest energy, the TMDs generate a hydrophobic pore. Bundles in which Ser-24 faces the pore have higher energy. The tilt of the helices in the lowest energy bundles is larger than bundles with serines facing the pore. Left-handed bundles are lowest in energy where the ions are located at the serines.

原文	English
頁（從 - 到）	85-91
頁數	7
期刊	Biochemical and Biophysical Research Communications
卷	442
發行號	1-2
DOIs	https://doi.org/10.1016/j.bbrc.2013.11.017
出版狀態	Published - 6 12月 2013

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title = "Qualitative computational bioanalytics: Assembly of viral channel-forming peptides around mono and divalent ions",

abstract = "A fine-grained docking protocol was used to generate a bundle-like structure of the bitopic membrane protein Vpu from HIV-1. Vpu is a type I membrane protein with 81 amino acids. It is proposed that Vpu forms ion- and substrate-conducting bundles, which are located at the plasma membrane in the infected cell. The Vpu1-32 peptide that includes the transmembrane domain (TMD) is assembled into homo-pentameric bundles around prepositioned Na, K, Ca or Cl ions. For bundles with the lowest energy, the TMDs generate a hydrophobic pore. Bundles in which Ser-24 faces the pore have higher energy. The tilt of the helices in the lowest energy bundles is larger than bundles with serines facing the pore. Left-handed bundles are lowest in energy where the ions are located at the serines.",

keywords = "Assembly, Docking approach, HIV-1, Membrane protein, Molecular dynamics simulations, Vpu protein",

author = "Li, {Li Hua} and Hsu, {Hao Jen} and Fischer, {Wolfgang B.}",

note = "Funding Information: WBF thanks the National Science Council of Taiwan ( NSC98-2112-M-010-002-MY3 ) for financial support. We acknowledge the National Center for High-Performance Computing (NCHC) , TW for providing computer time and services. ",

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AU - Hsu, Hao Jen

AU - Fischer, Wolfgang B.

N1 - Funding Information: WBF thanks the National Science Council of Taiwan ( NSC98-2112-M-010-002-MY3 ) for financial support. We acknowledge the National Center for High-Performance Computing (NCHC) , TW for providing computer time and services.

PY - 2013/12/6

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KW - Assembly

KW - Docking approach

KW - HIV-1

KW - Membrane protein

KW - Molecular dynamics simulations

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Qualitative computational bioanalytics: Assembly of viral channel-forming peptides around mono and divalent ions

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