Structure–function analysis of hepatitis C virus envelope glycoproteins E1 and E2

Abstract

Hepatitis C virus (HCV) is the leading cause of chronic liver disease in humans. The envelope proteins of HCV are potential candidates for vaccine development. The absence of three-dimensional (3D) structures for the functional domain of HCV envelope proteins [E1.E2] monomer complex has hindered overall understanding of the virus infection, and also structure-based drug design initiatives. In this study, we report a 3D model containing both E1 and E2 proteins of HCV using the recently published structure of the core domain of HCV E2 and the functional part of E1, and investigate immunogenic implications of the model. HCV [E1.E2] molecule is modeled by using aa205–319 of E1 to aa421–716 of E2. Published experimental data were used to further refine the [E1.E2] model. Based on the model, we predict 77 exposed residues and several antigenic sites within the [E1.E2] that could serve as vaccine epitopes. This study identifies eight peptides which have antigenic propensity and have two or more sequentially exposed amino acids and 12 singular sites are under negative selection pressure that can serve as vaccine or therapeutic targets. Our special interest is 285FLVGQLFTFSPRRHW299 which has five negatively selected sites (L286, V287, G288, T292, and G303) with three of them sequential and four amino acids exposed (F285, L286, T292, and R296). This peptide in the E1 protein maps to dengue envelope vaccine target identified previously by our group. Our model provides for the first time an overall view of both the HCV envelope proteins thereby allowing researchers explore structure-based drug design approaches.

The unexpected structures of hepatitis C virus envelope proteins

“…Most previous studies that analyzed either the structure of E1 or E2 were required to separate the appropriate glycoprotein from the heterodimer, which may impact the conformation of both glycoproteins ( 30 , 31 , 37 – 39 ). However, the amino acids located between E1 and E2 are partially inserted into the membrane, resulting in great difficulty in acquiring a single full-length crystal of either glycoprotein heterodimer that is free of cellular elements ( 16 ).…”

“…In order to attenuate the difficulty in obtaining the full-length envelope protein (E1 plus E2), a 3D structure of E1-E2 complex monomer ([E1.E2]) of HCV genotype 1 has recently been predicted ( 16 ). Dengue virus, another member of the Flaviviridae family, shares many structural similarities with HCV ( 40 ).…”

“…In the model of E1 and E2 monomer, 35% of the residues formed extended/β-strands, while <6% were helical ( 16 ). Although the percentage for extended/β-strand was 1% higher than in the structure predicted by the GOR4 program ( 41 ), it was predominantly consistent with the data of the solved structure.…”

“…E1 and E2 (aa192-383 and aa384-746, respectively), which assemble to cover the core of the virus particle, consist of a highly glycosylated N-terminal ectodomain and a short C-terminal transmembrane domain ( 16 ). The N-terminal ectodomain is further divided into two parts: A receptor-binding domain and a C-terminal membrane-proximal stem region.…”

“…Significant progress in understanding E1 and E2 structures has recently been made: Two crystal structures of the core portion (E2c) of E2 ectodomain (E2e) and one structure of the N-terminal of E1 ectodomain have been successfully established through single-crystal X-ray diffraction methods ( 29 – 31 ). Furthermore, a full-length E1-E2 complex has also been modeled in silico ( 16 ). In the current review, the recent structural progress in E1 and E2 proteins is summarized, and possible explanations for the inconsistent previous findings are proposed.…”