Comparative analysis of amino acid sequences from envelope proteins isolated from different hepatitis C virus variants: possible role of conservativeand variable regions
Bn. Sobolev et al., Comparative analysis of amino acid sequences from envelope proteins isolated from different hepatitis C virus variants: possible role of conservativeand variable regions, J VIRAL HEP, 7(5), 2000, pp. 368-374
Sequences of the E1 and E2 envelope proteins of hepatitis C virus (HCV) (82
7 non-identical items) were collected from available sources and aligned. A
nalysis of the alignment identified regions with different sequence variabi
lity. It was found that 33% and 50% of positions within E1 and E2, respecti
vely, were highly conservative. Such conservation can be considered as the
minimum for maintaining stability of the three-dimensional structure and fu
nction of these proteins. Conserved cysteines in E1 and E2 (eight and 18 re
sidues, respectively) were presumed to form intramolecular disulphide bonds
. Both envelope proteins were predicted to contain 14 conservative glycosyl
ation sites. Two additional glycosylation sites were predicted in 58% of E1
and 30% of E2 sequences within the corresponding regions. We describe the
positions of six conservative regions in E1 and E2, which have several char
ged and aromatic residues known to participate frequently in protein-protei
n recognition. Peculiarities in the amino acid content of conservative frag
ments and putative differences in glycosylation were considered with regard
to antigenic specificity and possible binding to surface structures of tar
get cells. We also analysed the hypervariable region 1 (HVR1), located in t
he E2 protein. Aligned positions of HVR1 were described in relation to the
maintenance of conformational stability and recognition of cell receptors.