title: Clade-specific differences between human immunodeficiency virus type 1 clades B and C: diversity and correlations in C3-V4 regions of gp120.
abstract: Current knowledge of human immunodeficiency virus type 1 envelope (Env) glycoprotein structure and function is based on studies of clade B viruses. We present evidence of sequence and structural differences in viral glycoprotein gp120 between clades B and C. In clade C, the C3 region alpha2-helix exhibits high sequence entropy at the polar face but maintains its amphipathicity, whereas in clade B it accommodates hydrophobic residues. The V4 hypervariable domain in clade C is shorter than that in clade B. Generally, shorter V4 loops are incompatible with a glycine occurring in the alpha2-helix in clade C, an intriguing association that could be exploited to inform Env immunogen design.
authors.affiliation: Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA.
authors.forename: S
authors.initials: S
authors.lastname: Gnanakaran
authors.forename: Dorothy
authors.initials: D
authors.lastname: Lang
authors.forename: Marcus
authors.initials: M
authors.lastname: Daniels
authors.forename: Tanmoy
authors.initials: T
authors.lastname: Bhattacharya
authors.forename: Cynthia A
authors.initials: CA
authors.lastname: Derdeyn
authors.forename: Bette
authors.initials: B
authors.lastname: Korber
mesh_terms: D014644:Genetic Variation; D015699:HIV Envelope Protein gp120 / Q000737:chemistry*; D015497:HIV-1 / Q000145:classification* / Q000235:genetics*; D008958:Models, Molecular; D010802:Phylogeny; D011487:Protein Conformation; D017434:Protein Structure, Tertiary
chemical_list: D015699:HIV Envelope Protein gp120