# Comprehensive Insights into the Molecular Basis of HIV Glycoprotein
## 2 Proteins Engaged in HIV Entry
### gp120
Earlier high-resolution structural studies often utilized truncated fragments of gp120 and gp41 to facilitate crystallizing and determining atomic structures. These truncated forms typically consist of the gp120 core, which lacks variable regions V1, V2, and V3, as well as the C- and N-terminal segments. The gp120 core was initially crystallized in two forms: a fully glycosylated unliganded state [87] and a CD4-bound deglycosylated form complexed with an antigen-binding fragment (Fab) capable of recognizing the CD4-induced (CD4i) epitope [88]. Subsequent studies have reported HIV-1 gp120 core crystal structures with C- and N-terminal extensions, an intact V3 loop, and unliganded forms. These modifications aim to provide a more comprehensive understanding of the structural dynamics and functional properties of gp120 [89; 90]. gp120 undergoes glycosylation, with approximately half of its molecular mass being glycosylated with N-linked glycans and a smaller fraction bearing O-linked sugars. It harbors 20-35 N-linked glycosylation sites, while gp41 possesses 3-5 N-linked glycosylation sites. These glycosylation sites play crucial roles in host immune recognition, Env folding, and the binding of virions to the host cell surface [31]. Among the 24 N-linked glycosylation sites in gp120, 11 contain hybrid or high-Man structures, while 13 contain complex-type oligosaccharides. Notably, these N-linked glycosylation sites are well conserved in the gp120 amino acid sequence [37]. Additionally, Cysteine (Cys) residues in gp120 and gp41 are highly conserved and play a pivotal role in forming intramolecular disulfide bonds (Figure 2a), which are key components of the Env tertiary structure. gp120 contains nine disulfide bridges formed by covalently bound Cys residues. Among these, two disulfide bonds separate the V1 and V2 loops, while another disulfide bond connects the two loops into a large loop. Additionally, a disulfide bond delineates the V3 and V4 regions. As identified in various studies, the presence and arrangement of Cys residues can significantly impact Env structure and antigenicity by altering their numbers and distribution [31]. Several factors, including deletions, insertions, point mutations, and recombination events, influence the sequence variability of the V domains. Among these, the V1/V2 domain exhibits the highest variability in loop length and number of glycosylation sites [91; 92]. The length of V1/V2 loops can range from 50 to 90 amino acids, while the V3 loop typically spans 35 amino acids. Additionally, the lengths of the V4 and V5 domains vary between 19 to 44 and 14 to 36 amino acids, respectively. In contrast, the lengths of the V3, C2, C3, and C4 loops show relatively slight variation [31]. The increase in length and number of glycosylation sites in the V1/V2 domain correlates with disease progression, suggesting a potential role in evading humoral immunity [93]. Furthermore, the secondary structure is influenced by the number of glycosylation sites, particularly in mediating interactions between the V3 loop and neighboring regions. In the tertiary structure of Env, discontinuous segments containing conserved residues are folded into proximity to form the CD4 receptor binding site. Within gp120, the conserved domains C1, C3, and C4 are responsible for binding to CD4 [94]. The V1, V2, and V3 domains are not directly involved in CD4 binding, as demonstrated by studies where a variant of gp120 with deleted V1, V2, and V3 domains still exhibits high-affinity binding to CD4 [31]. Research has elucidated that the V3 loop plays critical roles in membrane fusion and coreceptor specificity [95] and harbors dominant epitopes recognized by neutralizing antibodies. Mutations within the V3 loop can lead to changes in tropism from R5 to X4, primarily through an increase in net positivity, which facilitates interactions with the negatively charged surface of CXCR4 [31].