Abstract—Hepatitis C virus (HCV) nonstructural protein 2 (NS2) is a transmembranal protein with a hydrophobic amino-terminal subdomain containing up to three putative transmembrane segments and a carboxyterminal cytoplasmic domain. It is believed that NS2 plays a crucial role in major processes during the propagation of virus such as viral replication, assembly, regulation of cellular gene expression and in the induction of apoptosis. The present study describes the sequence and mutational analysis of NS2 from Pakistani isolates of 3a genotype (3a GT). A total of 18 amino acid changes were observed out of which fourteen were frequently reported in other genotypes. Our data however revealed 4 rare mutations in NS2. The effects of these mutations were then examined in the secondary and tertiary structures. At secondary structure level, a significant difference in the transmembrane segment 3 helix1 was noticed which is critically involve in viral assembly on the other hand the protease domain was fully conserved. This study revealed that though NS2 is relatively conserved its N terminal transmembranal part exhibit genotype specific variations and need further investigations across all genotypes.

Index Terms—HCV, mutations, structure prediction, secondary structure.

The author are with Atta-ur-Raman School of applied Biosciences; National University of Science and Technology, Islamabad, Pakistan (email: sadiaezza@gmail.com).

Cite:Sadia Anjum, Faryal Mahwish, Tahir Ahmad, and Muhammad Sohail Afzal, "Mutational and Structural Analysis of HCV Non Structural Protein 2 (NS2) Revealed Genotype Specific Motif in TMD3 of the Protein," International Journal of Bioscience, Biochemistry and Bioinformatics vol. 3, no. 4, pp. 384-386, 2013.