# Comprehensive Insights into the Molecular Basis of HIV Glycoprotein
## 2 Proteins Engaged in HIV Entry
### gp41
Similarly, SERINC proteins, particularly SERINC5, play a key role in restricting HIV-1 infectivity by integrating into the viral membrane, altering the viral Env conformation, and disrupting the membrane fusion process. SERINC5 is the most potent of the SERINC family (SERINC5 highest; SERINC3 moderate and SERINC2 zero), significantly reducing HIV-1 infectivity, especially in Neef-deficient viruses. Its action primarily interferes with Env clustering during virus entry, potentially exposing the virus to neutralizing antibodies. These features highlight the importance of SERINC5 in host defense and HIV-1 evasion strategies [116; 117]. The membrane topology of the gp41 CT remains debated, with two primary models: the single membrane-spanning domain (MSD) model, placing the KE sequence (residues 731-744) intracellularly, and an alternative model suggesting multiple MSDs that expose the KE on the virion surface [118, 119, 60, 12]. For instance, an antibody targeting the KS on cells expressing Env does not bind to Env on intact virions [112]. HIV-1 resistance to the cholesterol-binding compound amphoteric B methyl ester (AME) was found to be further enhanced by viral protease (PR) cleavage sites flanking the KS [31]. Recent NMR studies support the single MSD model, showing an unstructured, non-membrane-associated gp41 CT. However, studies indicating that anti-KE antibodies can neutralize HIV-1 suggest surface exposure of the KE sequence during viral entry. This dynamic exposure, possibly occurring during membrane fusion, requires further investigation to fully understand gp41's role in HIV-1 entry [120, 121, 122]. This finding implies that a region of gp41 within virions can be cleaved by PR, supporting the notion that this region is located internally [31]. Figure 5: HIV-1 gp41 CT Topology and Structure. **(a)** gp41 CT topology. Traditional model **(left)**: The conventional model of the gp41 CT posits a single membrane-spanning domain, likely found in virions. This single-pass model places the entire CT inside the virion (internal). Sites of mutation that confer resistance to amprenavir (AME), which subsequently became new HIV-1 protease (PR) cleavage sites, are marked by black arrows. The epitope known as the \"KS,\" recognized by neutralizing antibodies, is shown in blue. Alternative model (**right**): An alternative topology suggests a three-membrane-spanning configuration for the gp41 CT, which exposes portions of the gp41 CT, including the KS, to the extracellular space. This topology may also occur with a detectable frequency in HIV-1 Env-expressing cells alongside the traditional model. Reprinted (adapted) with permission from [31] Copyright Elsevier (2024). (**b**) Segmented EM density map of gp41 trimer. The segmented EM density map of the gp41 trimer, with gp120 removed, shows the structural arrangement: The C-terminal half of HR1 (rust) forms a central three-helix bundle. The C-terminal half of HR2 (yellow) wraps helically around the trimer base. Unassigned density (beige) likely corresponds to the intervening region between HR1 and HR2, including the disulfide loop and elements from gp120 (C1 and C5). Density parallel to HR1 (brown) likely corresponds to the N-terminal half of HR1, the fusion peptide proximal region (FPPR), and the fusion peptide (FP). (**c**) Modeled portion corresponding to EM density maps shows the modeled portion of gp41. (**d**) Three-helix bundle in PGV04-bound trimer. The EM density map illustrates the three-helix bundle formed by HR1 in the structure bound by the PGV04 antibody. (**e**) Overlay of EM densities compares the three-helix bundle EM density (orange) from the PGV04-bound structure, filtered to 9.5 A, with the 9 A reconstruction of a 17b-bound SOSIP gp140 trimer (gray, EMDB-5462). (**f**) Reconstruction of SOSIP trimer with deletions. An 8.2 A reconstruction of a SOSIP trimer from which the last 14 amino acids were deleted (SOSIP.650:PGV04) is shown.