Abstract
Although the HIV-1 Env gp120 and gp41 ectodomain have been extensively characterized in terms of structure and function, similar characterizations of the C-terminal tail (CTT) of HIV gp41 remain relatively limited and contradictory. The current study was designed to examine in detail CTT sequence conservation relative to gp120 and the gp41 ectodomain and to examine the conservation of predicted physicochemical and structural properties across a number of divergent HIV clades and groups. Results demonstrate that CTT sequences display intermediate levels of sequence evolution and diversity in comparison to the more diverse gp120 and the more conserved gp41 ectodomain. Despite the relatively high level of CTT sequence variation, the physicochemical properties of the lentivirus lytic peptide domains (LLPs) within the CTT are evidently highly conserved across clades/groups. Additionally, predictions using PEP-FOLD indicate a high level of structural similarity in the LLP regions that was confirmed by circular dichroism measurements of secondary structure of LLP peptides from clades B, C, and group O. Results demonstrate that LLP peptides adopt helical structure in the presence of SDS or trifluoroethanol but are predominantly unstructured in aqueous buffer. Thus, these data for the first time demonstrate strong conservations of characteristic CTT physicochemical and structural properties despite substantial sequence diversity, apparently indicating a delicate balance between evolutionary pressures and the conservation of CTT structure and associated functional roles in virus replication.
Highlights
The HIV-1 Env gp120 and gp41 ectodomain have been extensively characterized in terms of structure and function, similar characterizations of the C-terminal tail (CTT) of HIV gp41 remain relatively limited and contradictory
We calculated the hydrophobic moment (H), net charge, and hydrophobicity (H) of the peptide domains derived from the consensus sequences for the membrane proximal external region (MPER), membrane-spanning domain (MSD), and the lentivirus lytic peptide domains (LLPs) regions of the CTT for all clades/groups (Fig. 4). The results of these analyses reveal that the LLP domains have significantly higher hydrophobic moments than the MPER and MSD and that the calculated LLP1 hydrophobic moment is significantly higher than LLP2 and LLP3 (Fig. 4A)
In the present study we examined the conservation of the CTT of HIV-1 gp41 in clades A, B, C, D, F, and G and groups N and O as compared both to gp120 and to the gp41 ectodomain
Summary
Sequence Acquisition and Processing—Sequences were obtained from the Los Alamos National Laboratory HIV sequence data base. PEP-FOLD Structure Prediction for LLP Peptides—LLP and Kennedy epitope (KE) sequences for all clades/groups were extracted from the consensus sequences generated by the global multiple sequence alignments. Average r.m.s.d. was determined for all residues on the STAMP-aligned models. Circular Dichroism (CD) Spectroscopy to Determine Peptide Secondary Structure—LLP sequences for clades B and C and group O were extracted from the consensus sequences generated by the global multiple sequence alignments. In addition to the domains derived from the consensus sequences, we determined the sequence with the lowest average divergence (LAD) from all sequences within each clade/group to select a representative natural isolate for secondary structure characterization. All 17 peptides (LLP2 from clade B consensus and LAD were identical) were synthesized using standard Fmoc (N-(9-fluorenyl)methoxycarbonyl) chemistry with a carboxylated N terminus and amidated C terminus to mimic their native chemistry within a longer polypeptide sequence. Peptide mean residue ellipticity was determined using CDPro [45, 46]
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