title: Positional effect of phosphorylation sites 266 and 267 in the cytoplasmic domain of the E2 protein of hepatitis C virus 3a genotype: interferon resistance analysis via sequence alignment.
abstract: BACKGROUND
  Interferon is well thought-out as the key defence against all infections including HCV. The only treatment for HCV infection is pegylated interferon alpha (IFN-α) but unluckily more than half of the infected individuals do not act in response to the cure and become chronic HCV carriers. The mechanism how HCV induce interferon resistance is still elusive. It is recently reported that HCV envelope protein 2 interacts with PKR which is the interferon-inducible protein kinase and which in turn blocks the activity of its target molecule called eukaryotic initiation factor elF2. Sequence analysis of Envelope protein reveals it contains a domain homologous to phosphorylation sites of PKR andthe translation initiation factor eIF2alpha. Envelope protein competes for phosphorylation with PKR. Inhibition of kinase activity of PKR is postulated as a mechanism of to interferon (IFN) resistance.
  
  
  RESULTS
  Present study involves the insilico investigation of possible role of potential phosphorylation in envelope 2 protein of 3a genotype in interferon resistance. Envelope protein coding genes were isolated from local HCV isolates, cloned and sequenced. Phylogenetic analysis was done and tertiary structure of envelope gene was predicted. Visualization of phosphorylation in tertiary structure reveals that residue 266 and 267 of envelope gene 2 are surface exposed and their phosphorylation may compete with the phosphorylation of PKR protein and possibly involved in mediating Interferon Resistance.
  
  
  CONCLUSIONS
  A hybrid in-silico and wet laboratory approach of motif prediction, evolutionary and structural analysis has pointed out serine 266 and 267 of the HCV E2 gene as a hopeful claimant for the serine phosphorylation. Recognition of these nucleotide variations may assist to propose genotype precise therapy to avoid and resolve HCV infections.
authors.affiliation: Division of Molecular Virology & Molecular Diagnostics, National Centre of Excellence in Molecular Biology, Thokar Niaz Baig Lahore-53700, University of the Punjab Lahore, Pakistan.
authors.forename: Shazia
authors.initials: S
authors.lastname: Rafique
authors.forename: Muhammad
authors.initials: M
authors.lastname: Idrees
authors.forename: Muhammad
authors.initials: M
authors.lastname: Ilyas
authors.forename: Abrar
authors.initials: A
authors.lastname: Hussain
authors.forename: Muhammad
authors.initials: M
authors.lastname: Ali
authors.forename: Liaqat
authors.initials: L
authors.lastname: Ali
authors.forename: Sadia
authors.initials: S
authors.lastname: Butt
authors.forename: Samia
authors.initials: S
authors.lastname: Afzal
authors.forename: Irshad
authors.initials: I
authors.lastname: Ur Rehman
authors.forename: Sana
authors.initials: S
authors.lastname: Saleem
mesh_terms: D020816:Amino Acid Motifs; D003001:Cloning, Molecular; D019295:Computational Biology; D005838:Genotype; D016174:Hepacivirus / Q000235:genetics / Q000276:immunology* / Q000472:pathogenicity; D006801:Humans; D057131:Immune Evasion; D007372:Interferons / Q000037:antagonists & inhibitors* / Q000276:immunology*; D010766:Phosphorylation; D010802:Phylogeny; D017434:Protein Structure, Tertiary; D012367:RNA, Viral / Q000235:genetics; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA; D014759:Viral Envelope Proteins / Q000235:genetics / Q000378:metabolism*; D019892:eIF-2 Kinase / Q000378:metabolism*
chemical_list: D012367:RNA, Viral; D014759:Viral Envelope Proteins; C091015:glycoprotein E2, Hepatitis C virus; D007372:Interferons; D019892:eIF-2 Kinase