Structure based computational assessment of channel properties of assembled ORF-8a from SARS-CoV

Hao Jen Hsu, Meng Han Lin, Christina Schindler, Wolfgang B. Fischer*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

6 Scopus citations

Abstract

ORF 8a is a short 39 amino acid bitopic membrane protein encoded by severe acute respiratory syndrome causing corona virus (SARS-CoV). It has been identified to increase permeability of the lipid membrane for cations. Permeability is suggested to occur due to the assembly of helical bundles. Computational models of a pentameric assembly of 8a peptides are generated using the first 22 amino acids, which include the transmembrane domain. Low energy structures reveal a hydrophilic pore mantled by residues Thr-8, and -18, Ser-11, Cys-13, and Arg-22. Potential of mean force (PMF) profiles for mono (Na+, K+, Cl-) and divalent (Ca2+) ions along the pore are calculated. The data support experimental findings of a weak cation selectivity of the channel. Calculations on 8a are compared to data derived for a pentameric bundle consisting of the M2 helices of the bacterial pentameric ligand gated ion channel GLIC (3EHZ). PMF curves of both, bundles 8a and M2, show sigmoidal shaped profiles. In comparison to the data for the M2-GLIC model, data of the 8a bundle show lower amplitude of the PMF values between maximum and minimum and less discrimination amongst ions.

Original languageEnglish
Pages (from-to)300-308
Number of pages9
JournalProteins: Structure, Function and Bioinformatics
Volume83
Issue number2
DOIs
StatePublished - Feb 2015

Keywords

  • Ion selectivity
  • Membrane protein
  • Molecular dynamics simulations
  • ORF 8a
  • Protein assembly
  • SARS-CoV
  • Viral ion channel

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