Conformational Features of a Synthetic Cyclic Peptide Corresponding to the Complete V3 Loop of the ELI HIV-1 Strain in Water

Vranken, Wim; Budêšínský, Miloś; Fant, Franky; Boulez, Kris; Gras‐Masse, Hélène; Borremans, Frans

doi:10.1135/cccc19960742

Cited by 4 publications

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“…If they can still adopt the conformation preferred by M‐tropic V3 loops despite having a higher positive charge, they could possess the putative features of both M‐ and T‐tropic strains. The structural studies on V3 loops from dual‐tropic and T‐tropic strains confirm this: some have a tendency to form a C‐terminal helix (MN [33,35] or RF [36,39]), but this is not a necessary requirement (IIIB [40] or ELI [38]). The ambiguous character of the HIV‐1 strains toward tropism might thus be based on their ability to form a C‐terminal amphipathic helix, which is in turn directed by the number and location of basic amino acid residues.…”

Section: Discussionmentioning

confidence: 92%

“…Despite its importance, relatively little is known about the conformation of the V3 loop. Free V3 loop peptides in aqueous solution are highly flexible, with some tendency towards helical conformations in their C‐terminal region [33–42]. The central residues of V3 loop peptides in complex with anti‐(gp120 V3 loop) Ig adopt a short β hairpin with a type II turn for the central GPGR region [43–46].…”

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confidence: 99%

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Conformational model for the consensus V3 loop of the envelope protein gp120 of HIV‐1 in a 20% trifluoroethanol/water solution

Vranken

Fant

Budêšínský

et al. 2001

European Journal of Biochemistry

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Based on experimental NMR data, a model was generated for the conformation of the disulfide-bond-closed cyclic peptide corresponding to the whole V3 loop of the consensus HIV-1 strain in a 20% trifluoroethanol/water solution. The obtained family of structures shows a prominent and well-defined amphipathic alpha helix at the C-terminal end of the peptide from Thr23 to Gln32. A series of turns characterizes the central Gly15-Tyr21 region, while the N-terminal region is poorly defined. Independent experimental data confirms the features of this model, and suggests that this type of conformation can be readily adopted when the V3 loop is in contact with a membrane. The examined V3 loop belongs to a macrophage tropic strain, and using the model, a structural explanation is proposed for the different requirements of V3 loops belonging to macrophage and T-cell line tropic HIV-1 strains.

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Section: Discussionmentioning

confidence: 92%

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confidence: 99%

Conformational model for the consensus V3 loop of the envelope protein gp120 of HIV‐1 in a 20% trifluoroethanol/water solution

Vranken

Fant

Budêšínský

et al. 2001

European Journal of Biochemistry

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Confronting the degeneracy of convergent combinatorial immunogens, or ‘mixotopes’, with the specificity of recognition of the target sequences

Gras‐Masse

Boutillon

Diesis

et al. 1997

Vaccine

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Conformational Preferences of the HIV-1 Principal Neutralizing Determinant

Andrianov

2005

Journal of Biomolecular Structure and Dynamics

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The model describing the conformational properties of the HIV-1 principal neutralizing determinant in the geometric space of dihedrals was generated in terms of NMR spectroscopy data published in literature. To gain an object in view, the following successive steps were put into effect: (i) the NMR-based local structures for the HIV(MN) V3 loop were determined in water and in a mixed water/trifluoroethanol (TFE) solvent (7:3), (ii) in either case, the conformations of its irregular segments were analyzed and the secondary structure elements identified, (iii) to appreciate the degree of conformational mobility of the stretch of interest, the simulated structures were compared with each other, (iv) to detect the amino acids retaining their conformations inside the diverse HIV-1 isolates, the structures computed were collated with the one derived previously for the V3 loop from Thailand isolate, and (v) as a matter of record, the structurally rigid residues, that may present the forward-looking targets for AIDS drug researches, were revealed. Summing up the principal results arising from these studies, the following conclusions were drawn: I. The HIV(MN) V3 loop offers the highly mobile fragment of gp120 sensitive to its environment whose changes trigger the large-scale structural reforms, bringing in substantial altering the secondary structure of this functionally important site of the virus envelope. II. In water, it exhibits extended site 1-14 separated by double beta-turn 15-20 with unordered region 21-35. III. Adding the TFE gives rise to destruction of the regular structure in the V3 loop N-terminal, stimulates the formation of 3(10)-helix in site 24-31, and affects also its central region 20-25 forming the HIV-1 immunogenic crown. IV. Regardless of statistically significant differences between local structures of the HIV(MN) V3 loop in water and in water/TFE solution, over one-third of residues keeps their conformational states; the register of these amino acids comprises Asn-25 critical for virus binding with primary cell receptor CD4 as well as Arg-3 critical for utilization of CCR5 coreceptor. V. There are no conserved structural motifs within the V3 loops from Minnesota and Thailand HIV-1 strains. However, perceptible portion of amino acids (more than 35%), including those appearing in the functionally important regions of gp120, holds the values of dihedral angles in which case. The implications are discussed in conjunction with the data on the experimental observations for the HIV-1 principal neutralizing determinant.

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Conformational Features of a Synthetic Cyclic Peptide Corresponding to the Complete V3 Loop of the ELI HIV-1 Strain in Water

Cited by 4 publications

References 0 publications

Conformational model for the consensus V3 loop of the envelope protein gp120 of HIV‐1 in a 20% trifluoroethanol/water solution

Conformational model for the consensus V3 loop of the envelope protein gp120 of HIV‐1 in a 20% trifluoroethanol/water solution

Confronting the degeneracy of convergent combinatorial immunogens, or ‘mixotopes’, with the specificity of recognition of the target sequences

Conformational Preferences of the HIV-1 Principal Neutralizing Determinant

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