RNABindR: a server for analyzing and predicting RNA-binding sites in proteins

Terribilini, Michael; Sander, Jeffry D.; Lee, Jae Hyung; Zaback, Peter; Jernigan, Robert L.; Honavar, Vasant; Dobbs, Drena

doi:10.1093/nar/gkm294

Cited by 168 publications

(175 citation statements)

References 22 publications

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“…As the LBD does not have an obvious nucleic acid binding domain, we used two prediction tools, RNABindR and BindN (28,29), to identify putative RNA binding motifs in the RAR␣ LBD. These tools predicted an RNA-binding region in the C terminus of RAR␣ (i.e., the F-domain) that is immediately downstream of helix 12 (H12; Fig.…”

Section: Rar␣ Regulates the Translation Of A Reporter Construct Contamentioning

confidence: 99%

Retinoic acid-gated sequence-specific translational control by RARα

Poon¹,

Chen

2008

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

117

170

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Retinoic acid (RA) plays important roles in development by modulating gene transcription through nuclear receptor activation. Increasing evidence supports a role for RA and RA receptors (RARs) in synaptic plasticity in the brain. We have recently reported that RA mediates a type of homeostatic synaptic plasticity through activation of dendritic protein synthesis, a process that requires dendritically localized RARα and is independent of transcriptional regulation. The molecular basis of this translational regulation by RA/RARα signaling, however, is unknown. Here we show that RARα is actively exported from the nucleus. Cytoplasmic RARα acts as an RNA-binding protein that associates with a subset of mRNAs, including dendritically localized glutamate receptor 1 (GluR1) mRNA. This binding is mediated by the RARα carboxyl terminal F-domain and specific sequence motifs in the 5′UTR of the GluR1 mRNA. Moreover, RARα association with the GluR1 mRNA directly underlies the translational control of GluR1 by RA: RARα represses GluR1 translation, while RA binding to RARα reduces its association with the GluR1 mRNA and relieves translational repression. Taken together, our results demonstrate a ligand-gated translational regulation mechanism mediated by a non-genomic function of RA/RARα signaling.

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Section: Rar␣ Regulates the Translation Of A Reporter Construct Contamentioning

confidence: 99%

Retinoic acid-gated sequence-specific translational control by RARα

Poon¹,

Chen

2008

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

117

170

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“…The TbADAT2 sequence was also further analyzed for potential RNA binding residues with the RNABindR program (Terribilini et al 2007) (http://bindr.gdcb.iastate.edu/ RNABindR/), and the KR-domain showed high probability for a potential RNA binding domain (Fig. 4B).…”

Section: Resultsmentioning

confidence: 99%

“…The minor differences seen at various points in the scans for the mutants compared to the wild type are within the experimental error of the machine on which the circular dichroism experiments were performed. Each protein sample was scanned at least three times, and raw data from each scan are averaged to give the data used to create each plot in The amino acid sequence of TbADAT2 was also analyzed for potential RNA binding domains by the RNAbindR program, which uses a naive Bayesian classifier for all predictions, as described by Terribilini (Terribilini et al 2007). Potential domains are denoted by plus (+) signs under the sequence, and boldface letters denote the KR-domain which has been analyzed further in this study.…”

Section: Resultsmentioning

confidence: 99%

The C-terminal end of the Trypanosoma brucei editing deaminase plays a critical role in tRNA binding

Ragone

Spears²,

Wohlgamuth-Benedum³

et al. 2011

RNA

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Adenosine to inosine editing at the wobble position allows decoding of multiple codons by a single tRNA. This reaction is catalyzed by adenosine deaminases acting on tRNA (ADATs) and is essential for viability. In bacteria, the anticodon-specific enzyme is a homodimer that recognizes a single tRNA substrate (tRNA Arg ACG ) and can efficiently deaminate short anticodon stem-loop mimics of this tRNA in vitro. The eukaryal enzyme is composed of two nonidentical subunits, ADAT2 and ADAT3, which upon heterodimerization, recognize seven to eight different tRNAs as substrates, depending on the organism, and require a full-length tRNA for activity. Although crystallographic data have provided clues to why the bacterial deaminase can utilize short substrates, residues that provide substrate binding and recognition with the eukaryotic enzymes are not currently known. In the present study, we have used a combination of mutagenesis, binding studies, and kinetic analysis to explore the contribution of individual residues in Trypanosoma brucei ADAT2 (TbADAT2) to tRNA recognition. We show that deletion of the last 10 amino acids at the C terminus of TbADAT2 abolishes tRNA binding. In addition, single alanine replacements of a string of positively charged amino acids (KRKRK) lead to binding defects that correlate with losses in enzyme activity. This region, which we have termed the KR-domain, provides a first glance at key residues involved in tRNA binding by eukaryotic tRNA editing deaminases.

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“…Several recent studies have focused on the development of machine learning approaches to amino acid sequence-based prediction of RNA-binding residues in proteins [21,20,8,9]. The predictions obtained using such methods have already contributed to the design of wetlab experiments to decipher mechanisms of protein-RNA recognition [19,1].…”

Section: Introductionmentioning

confidence: 99%

“…We describe an analysis of the structural features of protein chains from RNA-binding proteins that explores this question using a non-redundant dataset of 147 protein chains from the RB147 dataset [21]. We focus on three of the six structural properties of amino acid residues used in a recent analysis of protein-protein interfaces by Wu et al [22], namely, surface roughness [14], solid angle [4] and CX value [18].…”

Section: Introductionmentioning

confidence: 99%

Structural characterization of RNA-binding sites of proteins: Preliminary results

Towfic

Caragea

Dobbs

et al. 2007

2007 IEEE International Conference on Bioinformatics and Biomedicine Workshops

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We explore whether protein-RNA interfaces differ from non-interfaces in terms of their structural features and whether structural features vary according to the type of the bound RNA (e.g., mRNA, siRNA...etc.), using a nonredundant dataset of 147 protein chains extracted from protein-RNA complexes in the protein data bank. Our analysis of surface roughness, solid angle and CX value of amino acid residues for each of the protein chains in the dataset shows that: The protein-RNA interface residues tend to be protruding compared to non-interface residues and tend to have higher surface roughness and exhibit moderately convex or concave solid angles. Furthermore, the protein chains in protein-RNA interfaces that contain Viral RNA and rRNA significantly differ from those that contain dsRNA, mRNA siRNA, snRNA, SRP RNA and tRNA with respect to their CX values. The results of this analysis suggests the possibility of using such structural features to reliably identify protein-RNA interface residues when the structure of the protein is available but the structures of complexes formed by the protein with RNA are not.

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RNABindR: a server for analyzing and predicting RNA-binding sites in proteins

Cited by 168 publications

References 22 publications

Retinoic acid-gated sequence-specific translational control by RARα

Retinoic acid-gated sequence-specific translational control by RARα

The C-terminal end of the Trypanosoma brucei editing deaminase plays a critical role in tRNA binding

Structural characterization of RNA-binding sites of proteins: Preliminary results

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