Structural rearrangements on HIV‐1 Tat (32–72) TAR complex formation

Metzger, Armin U.; Schindler, Thomas; Willbold, Dieter; Kraft, Margot; Steegborn, Clemens; Volkmann, Andrea; Frank, Rainer; Rösch, Paul

doi:10.1016/0014-5793(96)00314-6

Cited by 28 publications

(16 citation statements)

References 42 publications

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“…Proteins referred to as 'intrinsically unstructured' or 'natively unfolded' may therefore be well adapted for interaction with diverse partners. This is exactly was has been observed and described for lentiviral Tat [32,[45][46][47][48][49][50][51][52] and Vpr [53][54][55][56]. A welldefined and rigid tertiary structure of these proteins is observed only in complexes with one of their ligands [51,52,57,58].…”

Section: Functional Role Of Protein Flexibilitysupporting

confidence: 83%

NMR structural characterization of HIV‐1 virus protein U cytoplasmic domain in the presence of dodecylphosphatidylcholine micelles

et al. 2009

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The HIV‐1 encoded virus protein U (VpU) is required for efficient viral release from human host cells and for induction of CD4 degradation in the endoplasmic reticulum. The cytoplasmic domain of the membrane protein VpU (VpUcyt) is essential for the latter activity. The structure and dynamics of VpUcyt were characterized in the presence of membrane simulating dodecylphosphatidylcholine (DPC) micelles by high‐resolution liquid state NMR. VpUcyt is unstructured in aqueous buffer. The addition of DPC micelles induces a well‐defined membrane proximal α‐helix (residues I39–E48) and an additional helical segment (residues L64–R70). A tight loop (L73–V78) is observed close to the C‐terminus, whereas the interhelical linker (R49–E63) remains highly flexible. A 3D structure of VpUcyt in the presence of DPC micelles was calculated from a large set of proton–proton distance constraints. The topology of micelle‐associated VpUcyt was derived from paramagnetic relaxation enhancement of protein nuclear spins after the introduction of paramagnetic probes into the interior of the micelle or the aqueous buffer. Qualitative analysis of secondary chemical shift and paramagnetic relaxation enhancement data in conjunction with dynamic information from heteronuclear NOEs and structural insight from homonuclear NOE‐based distance constraints indicated that micelle‐associated VpUcyt retains a substantial degree of structural flexibility.

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Section: Functional Role Of Protein Flexibilitysupporting

confidence: 83%

NMR structural characterization of HIV‐1 virus protein U cytoplasmic domain in the presence of dodecylphosphatidylcholine micelles

et al. 2009

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“…Negligible CD intensity in the 200- to 350-nm region was observed, suggesting the lack of any structuration or secondary shape. In contrast, the CD spectrum of TAR alone is characteristic of an A-form double helix, with strong positive and negative bands at 260 nm and 210 nm, respectively, and a weak negative band at 240 nm (40,41). While the 260-nm CD band, very sensitive to base stacking, may vary on binding of a ligand without affecting the general nucleic acid structure, the 210-nm band is more related to the A-form RNA helical structure.…”

Section: Resultsmentioning

confidence: 93%

Thermodynamic studies of a series of homologous HIV-1 TAR RNA ligands reveal that loose binders are stronger Tat competitors than tight ones

Pascale

Azoulay

Giorgio

et al. 2013

Nucleic Acids Research

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RNA is a major drug target, but the design of small molecules that modulate RNA function remains a great challenge. In this context, a series of structurally homologous ‘polyamide amino acids’ (PAA) was studied as HIV-1 trans-activating response (TAR) RNA ligands. An extensive thermodynamic study revealed the occurence of an enthalpy–entropy compensation phenomenon resulting in very close TAR affinities for all PAA. However, their binding modes and their ability to compete with the Tat fragment strongly differ according to their structure. Surprisingly, PAA that form loose complexes with TAR were shown to be stronger Tat competitors than those forming tight ones, and thermal denaturation studies demonstrated that loose complexes are more stable than tight ones. This could be correlated to the fact that loose and tight ligands induce distinct RNA conformational changes as revealed by circular dichroism experiments, although nuclear magnetic resonance (NMR) experiments showed that the TAR binding site is the same in all cases. Finally, some loose PAA also display promising inhibitory activities on HIV-infected cells. Altogether, these results lead to a better understanding of RNA interaction modes that could be very useful for devising new ligands of relevant RNA targets.

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“…Neomycin Inhibits Tat Binding to TAR-The Tat-derived peptides BP1 and BP1 SW have been shown to have very similar properties with respect to TAR binding as full-length Tat (29,30). The BP1 SW -derived peptide BP3 with the amino acid sequence YHSQVWFITKGLGISYGRKKRGQSLTPSQGGQT-HQDPIPKQ has been selected by phage display as a high affinity TAR-binding peptide (31).…”

Section: Resultsmentioning

confidence: 99%

Structural Rearrangements of HIV-1 Tat-responsive RNA upon Binding of Neomycin B

Faber

Sticht

Schweimer

et al. 2000

Journal of Biological Chemistry

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Binding of human immunodeficiency virus type 1 (HIV-1) transactivator (Tat) protein to Tat-responsive RNA (TAR) is essential for viral replication and is considered a promising starting point for the design of anti-HIV drugs. NMR spectroscopy indicated that the aminoglycosides neomycin B and ribostamycin bind to TAR and that neomycin is able to inhibit Tat binding to TAR. The solution structure of the neomycin-bound TAR has been determined by NMR spectroscopy. Chemical shift mapping and intermolecular nuclear Overhauser effects define the binding region of the aminoglycosides on TAR and give strong evidence for minor groove binding. Based on 15 nuclear Overhauser effect-derived intermolecular distance restraints, a model structure of the TAR-neomycin complex was calculated. Neomycin is bound in a binding pocket formed by the minor groove of the lower stem and the uridine-rich bulge of TAR, which adopts a conformation different from those known. The neamine core of the aminoglycoside (rings I and II) is covered with the bulge, explaining the inhibition of Tat by an allosteric mechanism. Neomycin reduces the volume of the major groove in which Tat is bound and thus impedes essential protein-RNA contacts.Antibiotics are chemicals that are active against microorganisms, exerting their function in different ways at various cellular locations. Aminoglycoside antibiotics, for example, target the 30 S subunit of ribosomal RNA and cause mistranslation. Molecules of the neomycin family of aminoglycosides ( Fig. 1a) bind directly to the A site of 16 S ribosomal RNA (1) and efficiently disturb protein biosynthesis of prokaryotes. Structural studies on the interaction of aminoglycosides with RNAs provided insights into the mechanisms of miscoding (2-4). The antibiotic distorts the structure of the RNA and thus leads to errors in protein biosynthesis. Variations in eukaryotic ribosomal RNA prevent high affinity binding of aminoglycosides to the ribosomes of higher organisms, making them less prone to antibiotic influence and thus rendering the antibiotics valuable medical drugs. Due to the growing problem of antibiotic resistance, caused by only a small number of mutations in the microorganisms, the determinants for antibiotic binding to RNA are of major interest in structural biology. Only a few structures of antibiotic-RNA complexes have been determined experimentally to date, among them the structure of paromomycin in complex with a model oligonucleotide comprising the A site of 16 S rRNA (2) and a low resolution and two high resolution structures of complexes between RNA aptamers and tobramycin or neomycin (5-7).Aminoglycosides have also been found to bind to group I introns (8), to hammerhead RNA (9), and to human hepatitis ␦ virus ribozymes (10). These antibiotics also bind to the Rev (regulator of expression of the virion) and Tat (transactivator of transcription) binding regions of human immunodeficiency virus type 1 (HIV-1) 1 RNA, Rev response element (11), and Tat-responsive element (TAR) (12). Different modeling ap...

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Structural rearrangements on HIV‐1 Tat (32–72) TAR complex formation

Cited by 28 publications

References 42 publications

NMR structural characterization of HIV‐1 virus protein U cytoplasmic domain in the presence of dodecylphosphatidylcholine micelles

NMR structural characterization of HIV‐1 virus protein U cytoplasmic domain in the presence of dodecylphosphatidylcholine micelles

Thermodynamic studies of a series of homologous HIV-1 TAR RNA ligands reveal that loose binders are stronger Tat competitors than tight ones

Structural Rearrangements of HIV-1 Tat-responsive RNA upon Binding of Neomycin B

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