Crystal Structure of the Principal Neutralization Site of HIV-1

Ghiara, J.B.; Stura, E.A.; Stanfield, Robyn L.; Profy, Albert T.; Wilson, Ian A.

doi:10.1126/science.7511253

Cited by 244 publications

(227 citation statements)

References 38 publications

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“…Since the ␣-amino (or N) terminus of BPTI becomes an amide group after BPTI reaction with SPDP, a relatively large (Ͼ0.2 ppm) shift of the BPTI Arg 1 H␣ resonance occurred after SPDP coupling. Substantial shifts of the BPTI Ala 58 H␣ and HN resonances were also observed upon SPDP coupling and peptide linkage. The simultaneous occurrence of frequency changes involving the backbone Ala 58 and Arg 1 resonances is consistent with disruption of the native BPTI Arg 1 -Ala 58 BPTI salt bridge due to conjugation of peptide to BPTI.…”

Section: Bpti Modification and Peptidementioning

confidence: 87%

“…These effects were seen only after BPTI linkage to SPDP and consisted of substantial changes in the Ala 58 and Arg 1 backbone resonance frequencies. At the pH (4.1) of these studies, a salt bridge exists between the ␣-amino group of Arg 1 and the Cterminal carboxylate group of residue Ala 58 in native BPTI (48,49).…”

Section: Bpti Modification and Peptidementioning

confidence: 96%

“…Very few resonance frequency changes were observed for most BPTI residues regardless of BPTI form and most of these were less than 0.02 ppm. The largest changes (observed after linkage of SPDP to OMIU-modified BPTI) consisted of large frequency shifts involving the following protein resonances: the HN and H␣ of Ala 58 and Arg 8 -Ala 9 , respectively. As observed for the uncoupled peptide, most of the backbone protons of the coupled peptides gave rise to strong d ␣N (i, iϩ1) NOEs (Fig.…”

Section: Protonmentioning

confidence: 99%

See 2 more Smart Citations

The Binding of a Glycoprotein 120 V3 Loop Peptide to HIV-1 Neutralizing Antibodies

Wu¹,

MacKenzie²,

Durda³

et al. 2000

Journal of Biological Chemistry

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The structural and antigenic properties of a peptide ("CRK") derived from the V3 loop of HIV-1 gp120 protein were studied using NMR and SPR techniques. The sequence of CRK corresponds to the central portion of the V3 loop containing the highly conserved "GPGR" residue sequence. Although the biological significance of this conserved sequence is unknown, the adoption of conserved secondary structure (type II ␤-turn) in this region has been proposed. The tendency of CRK (while free or conjugated to protein), to adopt such structure and the influence of such structure upon CRK antigenicity were investigated by NMR and SPR, respectively. Regardless of conjugation, CRK is conformationally averaged in solution but a weak tendency of the CRK "GPGR" residues to adopt a ␤-turn conformation was observed after conjugation. The influence of GPGR structure upon CRK antigenicity was investigated by measuring the affinities of two cognate antibodies: "5023A" and "5025A," for CRK, protein-conjugated CRK and gp120 protein. Each antibody bound to all the antigens with nearly the same affinity. From these data, it appears that: (a) antibody binding most likely involves an induced fit of the peptide and (b) the gp120 V3 loop is probably conformationally heterogeneous. Since 5023A and 5025A are HIV-1 neutralizing antibodies, neutralization in these cases appears to be independent of adopted GPGR ␤-turn structure. The principal neutralizing determinant (PND)1 of HIV-1 has been mapped to the third hypervariable (V3) loop of the HIV-1 envelope protein, gp120 (1). PND-derived peptides are used as immunogens to elicit antibodies that possess HIV-1 virus neutralization capabilities (2, 3). The binding of neutralizing antibodies blocks virus entry into the host cell but does not prevent binding of HIV-1 to its primary cell receptor protein, CD4 (4, 5). Although the V3 loop represents an important target for the development of vaccines against AIDS, its high sequence variability also makes it a very problematic one (6). Nonetheless, the occurrence of the highly conserved residue sequence, "GPGR," at the tip of the V3 loop has raised the possibility that these residues make up a conserved secondary structural element in gp120. The function of such a structural element, if one exists, is presently unknown, however. The precise predicted secondary structure adopted by the GPGR residues is a type II ␤-turn (6, 7).In order to determine whether the conserved GPGR sequence confers certain secondary structural tendencies upon this region of the V3 loop, numerous NMR studies were conducted upon a variety of V3 loop-derived peptides (8 -21). These peptides were shown to have only low density populations of folded structure and to be conformationally averaged in solution. Despite the report of a "core" gp120 protein complex crystal structure, this complex was prepared using a form of gp120 which lacked most of the hypervariable loops including V3 (22). Information regarding the actual three-dimensional structure of the V3 loop in native gp120 is theref...

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Section: Bpti Modification and Peptidementioning

confidence: 87%

Section: Bpti Modification and Peptidementioning

confidence: 96%

Section: Protonmentioning

confidence: 99%

See 1 more Smart Citation

The Binding of a Glycoprotein 120 V3 Loop Peptide to HIV-1 Neutralizing Antibodies

Wu¹,

MacKenzie²,

Durda³

et al. 2000

Journal of Biological Chemistry

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“…Similarly, Ab maturation sometimes leads to the introduction of disulfide bonds, which may stabilize the Ig fold or result in subtle conformational changes that lead to higher affinity. An example may be the anti-gp120 peptide complex structure (1ACY), where an additional disulfide is formed between CDR H1 and H2, which actually contacts the Ag (33). It is also notable that many of the excess tyrosines on the Ab-Ag interface of the germline chains are converted to glycines (see Fig.…”

Section: Discussionmentioning

confidence: 99%

Trends in Antibody Sequence Changes during the Somatic Hypermutation Process

Clark

Ganesan

Papp

et al. 2006

The Journal of Immunology

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Probable germline gene sequences from thousands of aligned mature Ab sequences are inferred using simple computational matching to known V(D)J genes. Comparison of the germline to mature sequences in a structural region-dependent fashion allows insights into the methods that nature uses to mature Abs during the somatic hypermutation process. Four factors determine the residue type mutation patterns: biases in the germline, accessibility from single base permutations, location of mutation hotspots, and functional pressures during selection. Germline repertoires at positions that commonly contact the Ag are biased with tyrosine, serine, and tryptophan. These residue types have a high tendency to be present in mutation hotspot motifs, and their abundance is decreased during maturation by a net conversion to other types. The heavy use of tyrosines on mature Ab interfaces is thus a reflection of the germline composition rather than being due to selection during maturation. Potentially stabilizing changes such as increased proline usage and a small number of double cysteine mutations capable of forming disulfide bonds are ascribed to somatic hypermutation. Histidine is the only residue type for which usage increases in each of the interface, core, and surface regions. The net overall effect is a conversion from residue types that could provide nonspecific initial binding into a diversity of types that improve affinity and stability. Average mutation probabilities are ∼4% for core residues, ∼5% for surface residues, and ∼12% for residues in common Ag-contacting positions, excepting the those coded by the D gene.

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“…Cryo-EM studies have provided evidence that in the prefusion conformation V2 and V3 are spatially contiguous and account for most of the density at the apex of the trimeric envelope spike (12)(13)(14)(15)(16)(17). Although various fragments of V2 and V3 were crystallized separately using antibody-complexed synthetic peptides (28,29), scaffolded chimeric constructs of the first and second variable loops (V1V2) (30,31), or a V3-containing gp120 core monomer (8), the only study in which the two loops were visualized simultaneously is the recent report of the BG505 SOSIP.664 trimer crystal structure (18). In this artificially stabilized trimer, which displays several antigenic features of the native envelope (32), V2 and V3 appear to interact directly at the trimer apex with the V3 β-hairpin extensively buried under the V1V2 four-stranded Greekkey β-sheet (18).…”

mentioning

confidence: 99%

Tyrosine sulfation in the second variable loop (V2) of HIV-1 gp120 stabilizes V2–V3 interaction and modulates neutralization sensitivity

Cimbro¹,

Gallant²,

Dolan

et al. 2014

Proc. Natl. Acad. Sci. U.S.A.

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Elicitation of broadly neutralizing antibodies is essential for the development of a protective vaccine against HIV-1. However, the native HIV-1 envelope adopts a protected conformation that conceals highly conserved sites of vulnerability from antibody recognition. Although high-definition structures of the monomeric core of the envelope glycoprotein subunit gp120 and, more recently, of a stabilized soluble gp140 trimer have been solved, fundamental aspects related to the conformation and function of the native envelope remain unresolved. Here, we show that the conserved central region of the second variable loop (V2) of gp120 contains sulfated tyrosines (Tys173 and Tys177) that in the CD4-unbound prefusion state mediate intramolecular interaction between V2 and the conserved base of the third variable loop (V3), functionally mimicking sulfated tyrosines in CCR5 and anti-coreceptor-binding-site antibodies such as 412d. Recombinant gp120 expressed in continuous cell lines displays low constitutive levels of V2 tyrosine sulfation, which can be enhanced markedly by overexpression of the tyrosyl sulfotransferase TPST2. In contrast, virion-associated gp120 produced by primary CD4 + T cells is inherently highly sulfated. Consistent with a functional role of the V2 sulfotyrosines, enhancement of tyrosine sulfation decreased binding and neutralization of HIV-1 BaL by monomeric soluble CD4, 412d, and anti-V3 antibodies and increased recognition by the trimer-preferring antibodies PG9, PG16, CH01, and PGT145. Conversely, inhibition of tyrosine sulfation increased sensitivity to soluble CD4, 412d, and anti-V3 antibodies and diminished recognition by trimer-preferring antibodies. These results identify the sulfotyrosine-mediated V2-V3 interaction as a critical constraint that stabilizes the native HIV-1 envelope trimer and modulates its sensitivity to neutralization.T he development of a protective vaccine remains a high priority for the global control of the HIV/AIDS epidemic (1). However, the unique biological features of HIV-1 make this task extremely challenging. The main obstacles include the ability of the virus to integrate into the host chromosomes, a remarkable degree of genetic variability, and the cryptic, antibody-shielded conformation adopted by the viral envelope in the native spikes that protrude from the virion surface (2). These spikes are composed of homotrimers of heterodimers of the envelope glycoprotein subunits gp120 and gp41 maintained in an energetically unfavorable, metastable conformation (3, 4). Upon binding to CD4 and a coreceptor such as CCR5 or CXCR4, gp120 undergoes dramatic conformational changes that lead to a low-energy state, creating permissive conditions for activation of the gp41 fusogenic mechanism (3). In the prefusion conformation, gp120 effectively conceals its highly conserved receptor-and coreceptor-binding sites from antibody recognition, imposing a high-entropy penalty for interaction with CD4 or antibodies to the coreceptor-binding site such as 17b; in contrast, in the open, l...

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Crystal Structure of the Principal Neutralization Site of HIV-1

Cited by 244 publications

References 38 publications

The Binding of a Glycoprotein 120 V3 Loop Peptide to HIV-1 Neutralizing Antibodies

The Binding of a Glycoprotein 120 V3 Loop Peptide to HIV-1 Neutralizing Antibodies

Trends in Antibody Sequence Changes during the Somatic Hypermutation Process

Tyrosine sulfation in the second variable loop (V2) of HIV-1 gp120 stabilizes V2–V3 interaction and modulates neutralization sensitivity

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