Phylogenetic Analysis and Secondary and Tertiary (3D) Structure Prediction of the p7 Protein of Hepatitis C Virus

Abstract

The p7 protein of Hepatitis C virus (HCV) is a small integral membrane protein consists of 63 amino acids that is crucial for assembly and release of infectious virions. The p7 protein forms viral ion channels that can change membrane permeability, and could thus be considered as an antiviral target for drug design.The present study was designed to carry out a phylogenetic analysis and secondary and 3-D structure prediction of the p7 protein in the HCV genotype 4a detected in different countries. This is to examine the diversity of this genotype in different geographical regions and determine conserved regions that can be considered as a potential antiviral target for drug design. Molecular evolutionary and phylogenetic analysis using Jalview program showed that the HCV p7 gene of the genotype 4a isolates detected in Egypt was closely related to their counterpart in Germany. The phylogenetic analysis of HCV p7 genotype isolates from several parts of the world showing high genomic diversity of genotype 4 where the HCV-p7 protein genotype 4a dendrogram illustrates that the Egyptian isolates were classified into four clusters. Secondary structure predictions using JNetpred algorithm suggested that the p7 protein of the HCV genotype 4 contain one alpha Helix at 20-34(HPRLVRHLLHLHC amino acids) and three β-sheets at 5-7(GSVamino acids), 13-16(QCCF amino acids) and 43-47(CCYLR amino acids. The 3-D structure prediction model for the p7 protein of different HCV genotype 4a isolates (using J.mol) showed two coiled-coils. The α-helical coiled coil is a principal subunit oligomerization motifs in approximately 10% of all protein sequences.