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^*

^*Corresponding author for this work

Institute of Biophotonics

Research output: Contribution to journal › Article › peer-review

3 Scopus citations

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 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.

Original language	English
Pages (from-to)	85-91
Number of pages	7
Journal	Biochemical and Biophysical Research Communications
Volume	442
Issue number	1-2
DOIs	https://doi.org/10.1016/j.bbrc.2013.11.017
State	Published - 6 Dec 2013

Keywords

Assembly
Docking approach
HIV-1
Membrane protein
Molecular dynamics simulations
Vpu protein

UN SDGs

This output contributes to the following UN Sustainable Development Goals (SDGs)

Access to Document

10.1016/j.bbrc.2013.11.017

Cite this

@article{81295e2591f648839b9c727e9a55d556,

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. ",

year = "2013",

month = dec,

day = "6",

doi = "10.1016/j.bbrc.2013.11.017",

language = "English",

volume = "442",

pages = "85--91",

journal = "Biochemical and Biophysical Research Communications",

issn = "0006-291X",

publisher = "Academic Press Inc.",

number = "1-2",

}

TY - JOUR

T1 - Qualitative computational bioanalytics

T2 - Assembly of viral channel-forming peptides around mono and divalent ions

AU - Li, Li Hua

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

Y1 - 2013/12/6

N2 - 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.

AB - 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.

KW - Assembly

KW - Docking approach

KW - HIV-1

KW - Membrane protein

KW - Molecular dynamics simulations

KW - Vpu protein

UR - http://www.scopus.com/inward/record.url?scp=84889660179&partnerID=8YFLogxK

U2 - 10.1016/j.bbrc.2013.11.017

DO - 10.1016/j.bbrc.2013.11.017

M3 - Article

C2 - 24239548

AN - SCOPUS:84889660179

SN - 0006-291X

VL - 442

SP - 85

EP - 91

JO - Biochemical and Biophysical Research Communications

JF - Biochemical and Biophysical Research Communications

IS - 1-2

ER -

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

Abstract

Keywords

UN SDGs

Access to Document

Other files and links

Fingerprint

Cite this