Molecular recognition in the bovine immunodeficiency virus Tat peptide-TAR RNA complex

Ye, Xiaomei; Kumar, Rupesh; Patel, Dinshaw J.

doi:10.1016/1074-5521(95)90089-6

Cited by 186 publications

(240 citation statements)

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“…In agreement with this observation, Varani and co-workers [14] showed that free TAR contains a large degree of helical discontinuity, leading to a more accessible major groove that forms the contact area with the peptide. The structure of the BIV TAR Tat peptide complex shows that the peptide containing the basic sequence region of the BIV Tat protein adopts a I~-turn conformation and also binds to the widened major groove of the BIV TAR RNA [15,16]. The experimental results on Tat-TAR interactions for BIV and HIV-1 thus seem to become more consistent, and a fuller picture emerges.…”

Section: Discussionmentioning

confidence: 91%

“…As the TAR spectrum was only marginally distorted on TAR binding to Tat, the difference-CD spectrum derived from the TAR-BP1 complex and free TAR (Fig. 5) should provide a rough guess of the CD spectrum of the bound peptide, and previous studies show that difference-CD spectra are well suited to predict the secondary structures correctly [15,16,29]. According to this procedure, the minimum of molar ellipticity is shifted to 217 nm, an effect typical of polypeptides adopting extended conformations, such as 13-strands [28].…”

Section: Spectroscopymentioning

confidence: 92%

“…The extent to which the recognition region of HIV-1 Tat undergoes conformational changes when bound to TAR RNA is still unknown. For the bovine imrnunodeficiency virus (BIV) conformational changes occur in both the TAR RNA and the Tat peptide when they form a complex [15,16]. To gain more insight into the nature of conformational changes of HIV-1 Tat and TAR on complex formation *Corresponding author.…”

Section: Introductionmentioning

confidence: 99%

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

et al. 1996

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Section: Discussionmentioning

confidence: 91%

Section: Spectroscopymentioning

confidence: 92%

Section: Introductionmentioning

confidence: 99%

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

et al. 1996

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“…1A) (17-19). On binding to the TAR site, the Tat peptide adopts a ␤-hairpin conformation nestled deep within the major groove of the TAR RNA (20,21). Using structural information as a guide, a permuted BIV-1 TAR site was placed near the 5Ј-end of every molecule within an RNA pool.…”

Section: Resultsmentioning

confidence: 99%

A ribozyme that ligates RNA to protein

Baskerville

Bartel

2002

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

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We have used a combination of in vitro selection and rational design to generate ribozymes that form a stable phosphoamide bond between the 5 terminus of an RNA and a specific polypeptide. This reaction differs from that of previously identified ribozymes, although the product is analogous to the enzymenucleotidyl intermediates isolated during the reactions of certain proteinaceous enzymes, such as guanyltransferase, DNA ligase, and RNA ligase. Comparative sequence analysis of the isolated ribozymes revealed that they share a compact secondary structure containing six stems arranged in a four-helix junction and branched pseudoknot. An optimized version of the ribozyme reacts with substrate-fusion proteins, allowing it to be used to attach RNA tags to proteins both in vitro and within bacterial cells, suggesting a simple way to tag a specific protein with amplifiable information.in vitro selection ͉ nucleic acid tag ͉ phosphoamide ͉ Tat ͉ TAR I n vitro selection has been used in combination with rational design to identify and optimize numerous ribozymes and binding motifs (1-3). The results of these experiments continue to give insight into the capacity of RNA and DNA to catalyze a variety of chemical reactions and the ability of nucleic acids to recognize an array of substrates. Some of these catalysts are being developed into effective tools for use in molecular biology. These include allosteric ribozymes, used as detectors of small molecules and proteins, and DNA enzymes that efficiently cleave target sequences (4-6).Here we use in vitro selection coupled with rational design to produce a new ribozyme that ligates RNA to protein through the formation of a phosphoamide bond. This is similar to a reaction found in naturally occurring proteins such as guanyltransferase, and DNA and RNA ligases that form phosphoamide bonds as enzyme-nucleotidyl intermediates during cap formation and ligation events (7-9). The selection of this new ribozyme expands the repertoire of RNA-catalyzed chemistry and further illustrates the ability of RNA to chemically modify a variety of substrates. Moreover, this ribozyme might be used to synthesize oligonucleotide-tagged proteins in vitro and in vivo. These attached oligonucleotides might be useful as affinity tags or could function as amplifiable identifying markers. For example, this ribozyme might be used to attach mRNAs to the proteins that they encode. A diverse library of mRNA-protein fusions could be used in conjunction with in vitro selection strategies to identify previously undescribed proteins with unique or enhanced properties, as has been shown previously by using phage display, ribosome display, and mRNA display (10-13). Materials and MethodsPool Construction. The double-stranded DNA pool was constructed from two 110-nt DNA fragments, each containing 76 completely randomized positions (14). Each fragment was amplified separately in 110 ml PCR reactions and ligated through BanI sites to generate a final pool with the sequence: TTCTAATACGACTCACTATAG-GACAGCTCCGAGCATTCTCGTGT...

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“…These general recognition principles could also be common to proteins that contain other motifs enriched in arginine and glycines. For example, the NMR structures of a complex between a bovine immunodeficiency virus (BIV) transactivation response element (TAR) and a peptide from a transactivating protein (Tat) showed that the peptide adopts a β-turn conformation and sits in the major grove of the RNA, where it forms base-specific contacts with RNA using glycines and arginines (54,55).…”

Section: Discussionmentioning

confidence: 99%

Crystal structure reveals specific recognition of a G-quadruplex RNA by a β-turn in the RGG motif of FMRP

Vasilyev

Polonskaia

Darnell

et al. 2015

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

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Fragile X Mental Retardation Protein (FMRP) is a regulatory RNA binding protein that plays a central role in the development of several human disorders including Fragile X Syndrome (FXS) and autism. FMRP uses an arginine-glycine-rich (RGG) motif for specific interactions with guanine (G)-quadruplexes, mRNA elements implicated in the disease-associated regulation of specific mRNAs. Here we report the 2.8-Å crystal structure of the complex between the human FMRP RGG peptide bound to the in vitro selected G-rich RNA. In this model system, the RNA adopts an intramolecular K + -stabilized G-quadruplex structure composed of three G-quartets and a mixed tetrad connected to an RNA duplex. The RGG peptide specifically binds to the duplex-quadruplex junction, the mixed tetrad, and the duplex region of the RNA through shape complementarity, cation-π interactions, and multiple hydrogen bonds. Many of these interactions critically depend on a type I β-turn, a secondary structure element whose formation was not previously recognized in the RGG motif of FMRP. RNA mutagenesis and footprinting experiments indicate that interactions of the peptide with the duplex-quadruplex junction and the duplex of RNA are equally important for affinity and specificity of the RGG-RNA complex formation. These results suggest that specific binding of cellular RNAs by FMRP may involve hydrogen bonding with RNA duplexes and that RNA duplex recognition can be a characteristic RNA binding feature for RGG motifs in other proteins.R NA-binding proteins (RBPs) control all aspects of RNA metabolism and are fundamental to core cellular processes. ∼14% of identified human RBPs are implicated in a broad spectrum of human pathologies, including neurodegenerative and muscular diseases, metabolic disorders, and cancers (1, 2). Fragile X Mental Retardation Protein (FMRP) is among the most important RBPs because of its central role in several human diseases (3). Loss of FMRP function due to CGG triplet repeat expansion-associated transcriptional silencing or missense mutations in the protein (4, 5) lead to fragile X syndrome (FXS), the most common cause of inherited intellectual disability. Mutations in FMRP are also the leading monogenic cause of autism (6, 7). Intermediate length repeat expansions in the FMR1 gene are linked to fragile X-associated tremor ataxia syndrome (8) and fragile X-associated primary ovarian insufficiency (9).FMRP contains four canonical nucleic acid-binding motifs, three KH domains and one arginine-glycine-rich (RGG) box, which mediate interactions with RNAs in mRNA transport, storage, stability, and regulation of translation (Fig. 1A) (3, 10). Each KH domain has been reported to have a mutation either causing FXS or found in patients with intellectual disability (4, 5, 11). In neurons, FMRP associates with a subset of mRNAs and represses their translation both in the cell body and near synapses (12). Loss of repression of these mRNAs is associated with alterations in synaptic plasticity and dendritic spine dynamics thought to underlie...

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Molecular recognition in the bovine immunodeficiency virus Tat peptide-TAR RNA complex

Cited by 186 publications

References 23 publications

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

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

A ribozyme that ligates RNA to protein

Crystal structure reveals specific recognition of a G-quadruplex RNA by a β-turn in the RGG motif of FMRP

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