Journal articles: 'RNA-binding protein'

1

Sawicka, Kirsty, Martin Bushell, Keith A. Spriggs, and Anne E. Willis. "Polypyrimidine-tract-binding protein: a multifunctional RNA-binding protein." Biochemical Society Transactions 36, no. 4 (July 22, 2008): 641–47. http://dx.doi.org/10.1042/bst0360641.

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PTB (polypyrimidine-tract-binding protein) is a ubiquitous RNA-binding protein. It was originally identified as a protein with a role in splicing but it is now known to function in a large number of diverse cellular processes including polyadenylation, mRNA stability and translation initiation. Specificity of PTB function is achieved by a combination of changes in the cellular localization of this protein (its ability to shuttle from the nucleus to the cytoplasm is tightly controlled) and its interaction with additional proteins. These differences in location and trans-acting factor requirements account for the fact that PTB acts both as a suppressor of splicing and an activator of translation. In the latter case, the role of PTB in translation has been studied extensively and it appears that this protein is required for an alternative form of translation initiation that is mediated by a large RNA structural element termed an IRES (internal ribosome entry site) that allows the synthesis of picornaviral proteins and cellular proteins that function to control cell growth and cell death. In the present review, we discuss how PTB regulates these disparate processes.

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Singh, Arunima. "RNA-binding protein kinetics." Nature Methods 18, no. 4 (April 2021): 335. http://dx.doi.org/10.1038/s41592-021-01122-6.

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Ottoz, Diana S. M., and Luke E. Berchowitz. "The role of disorder in RNA binding affinity and specificity." Open Biology 10, no. 12 (December 2020): 200328. http://dx.doi.org/10.1098/rsob.200328.

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Most RNA-binding modules are small and bind few nucleotides. RNA-binding proteins typically attain the physiological specificity and affinity for their RNA targets by combining several RNA-binding modules. Here, we review how disordered linkers connecting RNA-binding modules govern the specificity and affinity of RNA–protein interactions by regulating the effective concentration of these modules and their relative orientation. RNA-binding proteins also often contain extended intrinsically disordered regions that mediate protein–protein and RNA–protein interactions with multiple partners. We discuss how these regions can connect proteins and RNA resulting in heterogeneous higher-order assemblies such as membrane-less compartments and amyloid-like structures that have the characteristics of multi-modular entities. The assembled state generates additional RNA-binding specificity and affinity properties that contribute to further the function of RNA-binding proteins within the cellular environment.

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Eck, Andrew G., Kevin J. Lopez, and Jeffrey O. Henderson. "RNA-binding Motif Protein 45 (Rbm45)/Developmentally Regulated RNA-binding Protein-1 (Drbp1): Association with Neurodegenerative Disorders." Journal of Student Research 7, no. 2 (December 31, 2018): 33–37. http://dx.doi.org/10.47611/jsr.v7i2.417.

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Neurodegenerative disorders are caused by the progressive loss of the structure and/or function of neurons, often through cell death, contributing significantly to morbidity and mortality. Cytoplasmic aggregation of proteins into inclusion bodies is a pathological characteristic of amyotrophic lateral sclerosis (ALS), frontotemporal lobar degeneration (FTLD), and Alzheimer’s disorder (AD). These inclusion bodies have been shown to contain RNA-binding proteins participating in RNA-dependent and RNA–independent protein:protein interactions. RNA-binding motif protein 45 (RBM45), also known as developmentally regulated RNA-binding protein-1 (Drbp1), was first identified as a novel RNA binding protein in rat that functions in neural development. Advancing research has indicated a connection between the presence of human RBM45 protein cytosolic aggregates and degenerative neurological diseases. This review considers the structure, function, and distribution of RBM45 along with a look into potential future research on this multifunctional RNA-binding protein.

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Popper, Bastian, Tom Scheidt, and Rico Schieweck. "RNA-binding protein dysfunction in neurodegeneration." Essays in Biochemistry 65, no. 7 (December 2021): 975–86. http://dx.doi.org/10.1042/ebc20210024.

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Abstract Protein homeostasis (proteostasis) is a prerequisite for cellular viability and plasticity. In particular, post-mitotic cells such as neurons rely on a tightly regulated safeguard system that allows for regulated protein expression. Previous investigations have identified RNA-binding proteins (RBPs) as crucial regulators of protein expression in nerve cells. However, during neurodegeneration, their ability to control the proteome is progressively disrupted. In this review, we examine the malfunction of key RBPs such as TAR DNA-binding protein 43 (TDP-43), Fused in Sarcoma (FUS), Staufen, Pumilio and fragile-X mental retardation protein (FMRP). Therefore, we focus on two key aspects of RBP dysfunctions in neurodegeneration: protein aggregation and dysregulation of their target RNAs. Moreover, we discuss how the chaperone system responds to changes in the RBP-controlled transcriptome. Based on recent findings, we propose a two-hit model in which both, harmful RBP deposits and target mRNA mistranslation contribute to neurodegeneration observed in RBPathologies.

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Choi, Kwang-Ho, Seong-Ryul Kim, Sung-Wan Kim, Tae-Won Goo, Seok-Woo Kang, and Seoung-Won Park. "Characterization of the RNA binding protein-1 gene promoter of the silkworm silk grands." Journal of Sericultural and Entomological Science 52, no. 1 (April 30, 2014): 39–44. http://dx.doi.org/10.7852/jses.2014.52.1.39.

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7

DeLisle, A. J. "RNA-Binding Protein from Arabidopsis." Plant Physiology 102, no. 1 (May 1, 1993): 313–14. http://dx.doi.org/10.1104/pp.102.1.313.

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8

Strack, Rita. "Predicting RNA–protein binding affinity." Nature Methods 16, no. 6 (May 30, 2019): 460. http://dx.doi.org/10.1038/s41592-019-0445-4.

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9

Purnell, B. A. "Noncoding RNA helps protein binding." Science 350, no. 6263 (November 19, 2015): 923–25. http://dx.doi.org/10.1126/science.350.6263.923-o.

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10

Chen, Xiuzhen, and Christine Mayr. "A working model for condensate RNA-binding proteins as matchmakers for protein complex assembly." RNA 28, no. 1 (October 27, 2021): 76–87. http://dx.doi.org/10.1261/rna.078995.121.

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Most cellular processes are carried out by protein complexes, but it is still largely unknown how the subunits of lowly expressed complexes find each other in the crowded cellular environment. Here, we will describe a working model where RNA-binding proteins in cytoplasmic condensates act as matchmakers between their bound proteins (called protein targets) and newly translated proteins of their RNA targets to promote their assembly into complexes. Different RNA-binding proteins act as scaffolds for various cytoplasmic condensates with several of them supporting translation. mRNAs and proteins are recruited into the cytoplasmic condensates through binding to specific domains in the RNA-binding proteins. Scaffold RNA-binding proteins have a high valency. In our model, they use homotypic interactions to assemble condensates and they use heterotypic interactions to recruit protein targets into the condensates. We propose that unoccupied binding sites in the scaffold RNA-binding proteins transiently retain recruited and newly translated proteins in the condensates, thus promoting their assembly into complexes. Taken together, we propose that lowly expressed subunits of protein complexes combine information in their mRNAs and proteins to colocalize in the cytoplasm. The efficiency of protein complex assembly is increased by transient entrapment accomplished by multivalent RNA-binding proteins within cytoplasmic condensates.

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11

E, Beeram. "Mini review on Protein – Protein and DNA/RNA – protein interactions in biology." Asploro Journal of Biomedical and Clinical Case Reports 2, no. 2 (October 29, 2019): 82–83. http://dx.doi.org/10.36502/2019/asjbccr.6165.

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RNase H1 generally processes the RNA- DNA hybrids through non specific interaction between HBD and the ds RNA/DNA hybrid. There are no direct protein- protein interactions between the hybrid and HBD of RNase H1. The DNA binding region is highly conserved compared to RNA binding region and the Kd for RNA/DNA hybrid is less compared to ds RNA than to that of ds DNA [1]. HBD increases the processivity of RNase H1 and mutations in RNA binding region is tolerated compared to DBR. The RNA interacts between ɑ2 and β3 region with in the loop and with the protein in shallower minor groove.

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12

Ohashi and Shiina. "Cataloguing and Selection of mRNAs Localized to Dendrites in Neurons and Regulated by RNA-Binding Proteins in RNA Granules." Biomolecules 10, no. 2 (January 22, 2020): 167. http://dx.doi.org/10.3390/biom10020167.

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Spatiotemporal translational regulation plays a key role in determining cell fate and function. Specifically, in neurons, local translation in dendrites is essential for synaptic plasticity and long-term memory formation. To achieve local translation, RNA-binding proteins in RNA granules regulate target mRNA stability, localization, and translation. To date, mRNAs localized to dendrites have been identified by comprehensive analyses. In addition, mRNAs associated with and regulated by RNA-binding proteins have been identified using various methods in many studies. However, the results obtained from these numerous studies have not been compiled together. In this review, we have catalogued mRNAs that are localized to dendrites and are associated with and regulated by the RNA-binding proteins fragile X mental retardation protein (FMRP), RNA granule protein 105 (RNG105, also known as Caprin1), Ras-GAP SH3 domain binding protein (G3BP), cytoplasmic polyadenylation element binding protein 1 (CPEB1), and staufen double-stranded RNA binding proteins 1 and 2 (Stau1 and Stau2) in RNA granules. This review provides comprehensive information on dendritic mRNAs, the neuronal functions of mRNA-encoded proteins, the association of dendritic mRNAs with RNA-binding proteins in RNA granules, and the effects of RNA-binding proteins on mRNA regulation. These findings provide insights into the mechanistic basis of protein-synthesis-dependent synaptic plasticity and memory formation and contribute to future efforts to understand the physiological implications of local regulation of dendritic mRNAs in neurons.

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13

Song, Guang, Johnathan Neiswinger, and Heng Zhu. "Characterization of RNA-Binding Proteins Using Protein Microarrays." Cold Spring Harbor Protocols 2016, no. 10 (October 2016): pdb.prot087973. http://dx.doi.org/10.1101/pdb.prot087973.

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14

Matunis, M. J., E. L. Matunis, and G. Dreyfuss. "PUB1: a major yeast poly(A)+ RNA-binding protein." Molecular and Cellular Biology 13, no. 10 (October 1993): 6114–23. http://dx.doi.org/10.1128/mcb.13.10.6114-6123.1993.

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The expression of RNA polymerase II transcripts can be regulated at the posttranscriptional level by RNA-binding proteins. Although extensively characterized in metazoans, relatively few RNA-binding proteins have been characterized in the yeast Saccharomyces cerevisiae. Three major proteins are cross-linked by UV light to poly(A)+ RNA in living S. cerevisiae cells. These are the 72-kDa poly(A)-binding protein and proteins of 60 and 50 kDa (S.A. Adam, T.Y. Nakagawa, M.S. Swanson, T. Woodruff, and G. Dreyfuss, Mol. Cell. Biol. 6:2932-2943, 1986). Here, we describe the 60-kDa protein, one of the major poly(A)+ RNA-binding proteins in S. cerevisiae. This protein, PUB1 [for poly(U)-binding protein 1], was purified by affinity chromatography on immobilized poly(rU), and specific monoclonal antibodies to it were produced. UV cross-linking demonstrated that PUB1 is bound to poly(A)+ RNA (mRNA or pre-mRNA) in living cells, and it was detected primarily in the cytoplasm by indirect immunofluorescence. The gene for PUB1 was cloned and sequenced, and the sequence was found to predict a 51-kDa protein with three ribonucleoprotein consensus RNA-binding domains and three glutamine- and asparagine-rich auxiliary domains. This overall structure is remarkably similar to the structures of the Drosophila melanogaster elav gene product, the human neuronal antigen HuD, and the cytolytic lymphocyte protein TIA-1. Each of these proteins has an important role in development and differentiation, potentially by affecting RNA processing. PUB1 was found to be nonessential in S. cerevisiae by gene replacement; however, further genetic analysis should reveal important features of this class of RNA-binding proteins.

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Matunis, M. J., E. L. Matunis, and G. Dreyfuss. "PUB1: a major yeast poly(A)+ RNA-binding protein." Molecular and Cellular Biology 13, no. 10 (October 1993): 6114–23. http://dx.doi.org/10.1128/mcb.13.10.6114.

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The expression of RNA polymerase II transcripts can be regulated at the posttranscriptional level by RNA-binding proteins. Although extensively characterized in metazoans, relatively few RNA-binding proteins have been characterized in the yeast Saccharomyces cerevisiae. Three major proteins are cross-linked by UV light to poly(A)+ RNA in living S. cerevisiae cells. These are the 72-kDa poly(A)-binding protein and proteins of 60 and 50 kDa (S.A. Adam, T.Y. Nakagawa, M.S. Swanson, T. Woodruff, and G. Dreyfuss, Mol. Cell. Biol. 6:2932-2943, 1986). Here, we describe the 60-kDa protein, one of the major poly(A)+ RNA-binding proteins in S. cerevisiae. This protein, PUB1 [for poly(U)-binding protein 1], was purified by affinity chromatography on immobilized poly(rU), and specific monoclonal antibodies to it were produced. UV cross-linking demonstrated that PUB1 is bound to poly(A)+ RNA (mRNA or pre-mRNA) in living cells, and it was detected primarily in the cytoplasm by indirect immunofluorescence. The gene for PUB1 was cloned and sequenced, and the sequence was found to predict a 51-kDa protein with three ribonucleoprotein consensus RNA-binding domains and three glutamine- and asparagine-rich auxiliary domains. This overall structure is remarkably similar to the structures of the Drosophila melanogaster elav gene product, the human neuronal antigen HuD, and the cytolytic lymphocyte protein TIA-1. Each of these proteins has an important role in development and differentiation, potentially by affecting RNA processing. PUB1 was found to be nonessential in S. cerevisiae by gene replacement; however, further genetic analysis should reveal important features of this class of RNA-binding proteins.

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16

Brentano, Liana, Diana L. Noah, Earl G. Brown, and Barbara Sherry. "The Reovirus Protein μ2, Encoded by the M1 Gene, Is an RNA-Binding Protein." Journal of Virology 72, no. 10 (October 1, 1998): 8354–57. http://dx.doi.org/10.1128/jvi.72.10.8354-8357.1998.

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ABSTRACT The reovirus M1, L1, and L2 genes encode proteins found at each vertex of the viral core and are likely to form a structural unit involved in RNA synthesis. Genetic analyses have implicated the M1 gene in viral RNA synthesis and core nucleoside triphosphatase activity, but there have been no direct biochemical studies of μ2 function. Here, we expressed μ2 in vitro and assessed its RNA-binding activity. The expressed μ2 binds both poly(I-C)- and poly(U)-Sepharose, and binding activity is greater in Mn2+ than in Mg2+. Heterologous RNA competes for μ2 binding to reovirus RNA transcripts as effectively as homologous reovirus RNA does, providing no evidence for sequence-specific RNA binding by μ2. Protein μ2 is now the sixth reovirus protein demonstrated to have RNA-binding activity.

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Pérez-Cano, Laura, and Juan Fernández-Recio. "Dissection and prediction of RNA-binding sites on proteins." BioMolecular Concepts 1, no. 5-6 (December 1, 2010): 345–55. http://dx.doi.org/10.1515/bmc.2010.037.

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AbstractRNA-binding proteins are involved in many important regulatory processes in cells and their study is essential for a complete understanding of living organisms. They show a large variability from both structural and functional points of view. However, several recent studies performed on protein-RNA crystal structures have revealed interesting common properties. RNA-binding sites usually constitute patches of positively charged or polar residues that make most of the specific and non-specific contacts with RNA. Negatively charged or aliphatic residues are less frequent at protein-RNA interfaces, although they can also be found either forming aliphatic and positive-negative pairs in protein RNA-binding sites or contacting RNA through their main chains. Aromatic residues found within these interfaces are usually involved in specific base recognition at RNA single-strand regions. This specific recognition, in combination with structural complementarity, represents the key source for specificity in protein-RNA association. From all this knowledge, a variety of computational methods for prediction of RNA-binding sites have been developed based either on protein sequence or on protein structure. Some reported methods are really successful in the identification of RNA-binding proteins or the prediction of RNA-binding sites. Given the growing interest in the field, all these studies and prediction methods will undoubtedly contribute to the identification and comprehension of protein-RNA interactions.

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18

Gwack, Yousang, Hyouna Yoo, Inyoung Song, Joonho Choe, and Jang H. Han. "RNA-Stimulated ATPase and RNA Helicase Activities and RNA Binding Domain of Hepatitis G Virus Nonstructural Protein 3." Journal of Virology 73, no. 4 (April 1, 1999): 2909–15. http://dx.doi.org/10.1128/jvi.73.4.2909-2915.1999.

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ABSTRACT Hepatitis G virus (HGV) nonstructural protein 3 (NS3) contains amino acid sequence motifs typical of ATPase and RNA helicase proteins. In order to examine the RNA helicase activity of the HGV NS3 protein, the NS3 region (amino acids 904 to 1580) was fused with maltose-binding protein (MBP), and the fusion protein was expressed inEscherichia coli and purified with amylose resin and anion-exchange chromatography. The purified MBP-HGV/NS3 protein possessed RNA-stimulated ATPase and RNA helicase activities. Characterization of the ATPase and RNA helicase activities of MBP-HGV/NS3 showed that the optimal reaction conditions were similar to those of other Flaviviridae viral NS3 proteins. However, the kinetic analysis of NTPase activity showed that the MBP-HGV/NS3 protein had several unique properties compared to the otherFlaviviridae NS3 proteins. The HGV NS3 helicase unwinds RNA-RNA duplexes in a 3′-to-5′ direction and can unwind RNA-DNA heteroduplexes and DNA-DNA duplexes as well. In a gel retardation assay, the MBP-HGV/NS3 helicase bound to RNA, RNA/DNA, and DNA duplexes with 5′ and 3′ overhangs but not to blunt-ended RNA duplexes. We also found that the conserved motif VI was important for RNA binding. Further deletion mapping showed that the RNA binding domain was located between residues 1383 and 1395, QRRGRTGRGRSGR. Our data showed that the MBP-HCV/NS3 protein also contains the RNA binding domain in the similar domain.

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Clerch, L. B., A. Wright, and D. Massaro. "Dinucleotide-binding site of bovine liver catalase mimics a catalase mRNA-binding protein domain." American Journal of Physiology-Lung Cellular and Molecular Physiology 270, no. 5 (May 1, 1996): L790—L794. http://dx.doi.org/10.1152/ajplung.1996.270.5.l790.

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Rat lung contains protein that interacts with catalase mRNA to form specific, redox-sensitive RNA-protein complexes. The studies in this report were aimed at determining whether catalase protein binds its own RNA. We found that rat catalase RNA binds NADPH-depleted bovine liver catalase (Sigma) but does not bind bovine liver catalase in the presence of NADPH. Complex formation between liver catalase and catalase RNA is competitively eliminated by a CA dinucleotide repeat. These data suggest the dinucleotide binding site of catalase mimics or is homologous to a catalase RNA-binding protein domain. These findings support the hypothesis that a class of RNA-binding proteins may have evolved from (di)nucleotide binding enzymes (M. W. Hentze. Trends Biol. Sci. 19: 101, 1994). When bovine liver catalase from two other commercial sources (Calbiochem and Boehringer) was used, we could not detect binding to catalase RNA. We have not yet been able to identify the basis for this difference. Thus the physiological importance of our observation of the NADPH-sensitive protein binding to catalase RNA cannot be assessed at this time.

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Barton, N. R., E. M. Bonder, D. J. Fishkind, R. H. Warren, and M. M. Pratt. "A novel vesicle-associated protein (VAP-1) in sea urchin eggs containing multiple RNA-binding consensus sequences." Journal of Cell Science 103, no. 3 (November 1, 1992): 797–809. http://dx.doi.org/10.1242/jcs.103.3.797.

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We have identified a novel high molecular weight, vesicle-associated protein (VAP-1) in the eggs of the sea urchin Strongylocentrotus purpuratus. Biochemical fractionation and immunofluorescence analysis of unfertilized eggs indicate that VAP-1 is a peripheral membrane protein associated with microsomal membrane fractions. Sequence analysis of partial VAP-1 cDNA clones reveals that the protein contains at least four RNA-binding consensus sequences. The RNA-binding sequences are separated by several glycine rich domains and this organization, RNA-binding domains separated by glycine rich sequences, is common to several RNA-binding proteins including the heterogeneous ribonuclear protein A1 and nucleolin. The characteristics of VAP-1 suggest that the protein may function as a multidomain RNA-binding protein. The possibility that VAP-1 may play a role in nuclear RNA processing is also discussed.

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Huang, Peiyong, and Michael M. C. Lai. "Heterogeneous Nuclear Ribonucleoprotein A1 Binds to the 3′-Untranslated Region and Mediates Potential 5′-3′-End Cross Talks of Mouse Hepatitis Virus RNA." Journal of Virology 75, no. 11 (June 1, 2001): 5009–17. http://dx.doi.org/10.1128/jvi.75.11.5009-5017.2001.

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ABSTRACT The 3′-untranslated region (3′-UTR) of mouse hepatitis virus (MHV) RNA regulates the replication of and transcription from the viral RNA. Several host cell proteins have previously been shown to interact with this regulatory region. By immunoprecipitation of UV-cross-linked cellular proteins and in vitro binding of the recombinant protein, we have identified the major RNA-binding protein species as heterogeneous nuclear ribonucleoprotein A1 (hnRNP A1). A strong hnRNP A1-binding site was located 90 to 170 nucleotides from the 3′ end of MHV RNA, and a weak binding site was mapped at nucleotides 260 to 350 from the 3′ end. These binding sites are complementary to the sites on the negative-strand RNA that bind another cellular protein, polypyrimidine tract-binding protein (PTB). Mutations that affect PTB binding to the negative strand of the 3′-UTR also inhibited hnRNP A1 binding on the positive strand, indicating a possible relationship between these two proteins. Defective-interfering RNAs containing a mutated hnRNP A1-binding site have reduced RNA transcription and replication activities. Furthermore, hnRNP A1 and PTB, both of which also bind to the complementary strands at the 5′ end of MHV RNA, together mediate the formation of an RNP complex involving the 5′- and 3′-end fragments of MHV RNA in vitro. These studies suggest that hnRNP A1-PTB interactions provide a molecular mechanism for potential 5′-3′ cross talks in MHV RNA, which may be important for RNA replication and transcription.

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Shimada, Naohiko, Reiko Iwase, Tetsuji Yamaoka, and Akira Murakami. "Design of RNA-Binding Oligopeptides Based on Information of RNA-Binding Protein." Polymer Journal 35, no. 6 (June 2003): 507–12. http://dx.doi.org/10.1295/polymj.35.507.

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Gonzalez-Rivera, Juan C., Asuka A. Orr, Sean M. Engels, Joseph M. Jakubowski, Mark W. Sherman, Katherine N. O'Connor, Tomas Matteson, Brendan C. Woodcock, Lydia M. Contreras, and Phanourios Tamamis. "Computational evolution of an RNA-binding protein towards enhanced oxidized-RNA binding." Computational and Structural Biotechnology Journal 18 (2020): 137–52. http://dx.doi.org/10.1016/j.csbj.2019.12.003.

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Mazan-Mamczarz, Krystyna, Ashish Lal, Jennifer L. Martindale, Tomoko Kawai, and Myriam Gorospe. "Translational Repression by RNA-Binding Protein TIAR." Molecular and Cellular Biology 26, no. 7 (April 1, 2006): 2716–27. http://dx.doi.org/10.1128/mcb.26.7.2716-2727.2006.

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ABSTRACT The RNA-binding protein TIAR has been proposed to inhibit protein synthesis transiently by promoting the formation of translationally silent stress granules. Here, we report the selective binding of TIAR to several mRNAs encoding translation factors such as eukaryotic initiation factor 4A (eIF4A) and eIF4E (translation initiation factors), eEF1B (a translation elongation factor), and c-Myc (which transcriptionally controls the expression of numerous translation regulatory proteins). TIAR bound the 3′-untranslated regions of these mRNAs and potently suppressed their translation, particularly in response to low levels of short-wavelength UV (UVC) irradiation. The UVC-imposed global inhibition of the cellular translation machinery was significantly relieved after silencing of TIAR expression. We propose that the TIAR-mediated inhibition of translation factor expression elicits a sustained repression of protein biosynthesis in cells responding to stress.

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Castello, Alfredo. "The emerging universe of RNA-binding proteins." Biochemist 37, no. 2 (April 1, 2015): 33–38. http://dx.doi.org/10.1042/bio03702033.

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RNA associates with RNA-binding proteins (RBPs) from synthesis to decay, forming dynamic ribonucleoproteins that orchestrate gene expression. RBPs mediate crucial functions in RNA metabolism, including RNA synthesis, processing, transport, translation and degradation. Although essential for RNA life cycle, the repertoire of RBPs has remained largely unknown. The very recent development of a novel proteomic-based system-wide approach termed RNA interactome capture revealed the near-complete census of human RBPs. Applying UV cross-linking of proteins to RNA, oligo(dT) selection of poly(A) RNAs and quantitative mass spectrometry, this method not only ‘rediscovered’ most of the proteins already known to bind RNA, but added hundreds of novel members to the previously known repertoire of RBPs. The newly identified RBPs are distributed over a broad variety of protein families, participate in different biological processes and exert distinct protein functions, implying the existence of unprecedented links between RNA biology and intermediary metabolism, signalling, cellular homoeostasis or disease. Although the near-complete atlas of RBPs offered important insights into RNA biology, it also opened new functional and structural questions about protein–RNA interactions that remain to be answered.

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Kühn, Uwe, and Tomas Pieler. "XenopusPoly(A) Binding Protein: Functional Domains in RNA Binding and Protein – Protein Interaction." Journal of Molecular Biology 256, no. 1 (February 1996): 20–30. http://dx.doi.org/10.1006/jmbi.1996.0065.

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YOSHIZAWA, Takuya. "Phase Regulation of RNA Binding Protein." Nihon Kessho Gakkaishi 64, no. 2 (May 31, 2022): 140–47. http://dx.doi.org/10.5940/jcrsj.64.140.

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Abdelmohsen, Kotb, and Myriam Gorospe. "RNA-binding protein nucleolin in disease." RNA Biology 9, no. 6 (June 2012): 799–808. http://dx.doi.org/10.4161/rna.19718.

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Lee, Wook, Byungkyu Park, Daesik Choi, and Kyungsook Han. "Data of protein-RNA binding sites." Data in Brief 10 (February 2017): 561–63. http://dx.doi.org/10.1016/j.dib.2016.12.041.

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Wang, Xinlei. "Double-Strand RNA Binding Protein Profiling." Biophysical Journal 106, no. 2 (January 2014): 696a. http://dx.doi.org/10.1016/j.bpj.2013.11.3853.

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Markus, M. Andrea, and Brian J. Morris. "RBM4: A multifunctional RNA-binding protein." International Journal of Biochemistry & Cell Biology 41, no. 4 (April 2009): 740–43. http://dx.doi.org/10.1016/j.biocel.2008.05.027.

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Le, Siyuan, Rolf Sternglanz, and Carol W. Greider. "Identification of Two RNA-binding Proteins Associated with Human Telomerase RNA." Molecular Biology of the Cell 11, no. 3 (March 2000): 999–1010. http://dx.doi.org/10.1091/mbc.11.3.999.

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Telomerase plays a crucial role in telomere maintenance in vivo. To understand telomerase regulation, we have been characterizing components of the enzyme. To date several components of the mammalian telomerase holoenzyme have been identified: the essential RNA component (human telomerase RNA [hTR]), the catalytic subunit human telomerase reverse transcriptase (hTERT), and telomerase-associated protein 1. Here we describe the identification of two new proteins that interact with hTR: hStau and L22. Antisera against both proteins immunoprecipitated hTR, hTERT, and telomerase activity from cell extracts, suggesting that the proteins are associated with telomerase. Both proteins localized to the nucleolus and cytoplasm. Although these proteins are associated with telomerase, we found no evidence of their association with each other or with telomerase-associated protein 1. Both hStau and L22 are more abundant than TERT. This, together with their localization, suggests that they may be associated with other ribonucleoprotein complexes in cells. We propose that these two hTR-associated proteins may play a role in hTR processing, telomerase assembly, or localization in vivo.

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Lee, Nara, Therese A. Yario, Jessica S. Gao, and Joan A. Steitz. "EBV noncoding RNA EBER2 interacts with host RNA-binding proteins to regulate viral gene expression." Proceedings of the National Academy of Sciences 113, no. 12 (March 7, 2016): 3221–26. http://dx.doi.org/10.1073/pnas.1601773113.

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Epstein–Barr virus (EBV) produces a highly abundant noncoding RNA called EBV-encoded RNA 2 (EBER2) that interacts indirectly with the host transcription factor paired box protein 5 (PAX5) to regulate viral latent membrane protein 1/2 (LMP1/2) gene expression as well as EBV lytic replication. To identify intermediary proteins, we isolated EBER2–PAX5-containing complexes and analyzed the protein components by mass spectrometry. The top candidates include three host proteins splicing factor proline and glutamine rich (SFPQ), non-POU domain-containing octamer-binding protein (NONO), and RNA binding motif protein 14 (RBM14), all reported to be components of nuclear bodies called paraspeckles. In vivo RNA–protein crosslinking indicates that SFPQ and RBM14 contact EBER2 directly. Binding studies using recombinant proteins demonstrate that SFPQ and NONO associate with PAX5, potentially bridging its interaction with EBER2. Similar to EBER2 or PAX5 depletion, knockdown of any of the three host RNA-binding proteins results in the up-regulation of viral LMP2A mRNA levels, supporting a physiologically relevant interaction of these newly identified factors with EBER2 and PAX5. Identification of these EBER2-interacting proteins enables the search for cellular noncoding RNAs that regulate host gene expression in a manner similar to EBER2.

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Nakamura, T., G. Schuster, M. Sugiura, and M. Sugita. "Chloroplast RNA-binding and pentatricopeptide repeat proteins." Biochemical Society Transactions 32, no. 4 (August 1, 2004): 571–74. http://dx.doi.org/10.1042/bst0320571.

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Chloroplast gene expression is mainly regulated at the post-transcriptional level by numerous nuclear-encoded RNA-binding protein factors. In the present study, we focus on two RNA-binding proteins: cpRNP (chloroplast ribonucleoprotein) and PPR (pentatricopeptide repeat) protein. These are suggested to be major contributors to chloroplast RNA metabolism. Tobacco cpRNPs are composed of five different proteins containing two RNA-recognition motifs and an acidic N-terminal domain. The cpRNPs are abundant proteins and form heterogeneous complexes with most ribosome-free mRNAs and the precursors of tRNAs in the stroma. The complexes could function as platforms for various RNA-processing events in chloroplasts. It has been demonstrated that cpRNPs contribute to RNA stabilization, 3′-end formation and editing. The PPR proteins occur as a superfamily only in the higher plant species. They are predicted to be involved in RNA/DNA metabolism in chloroplasts or mitochondria. Nuclear-encoded HCF152 is a chloroplast-localized protein that usually has 12 PPR motifs. The null mutant of Arabidopsis, hcf152, is impaired in the 5′-end processing and splicing of petB transcripts. HCF152 binds the petB exon–intron junctions with high affinity. The number of PPR motifs controls its affinity and specificity for RNA. It has been suggested that each of the highly variable PPR proteins is a gene-specific regulator of plant organellar RNA metabolism.

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Côté, Jocelyn, Franc˛ois-Michel Boisvert, Marie-Chloé Boulanger, Mark T. Bedford, and Stéphane Richard. "Sam68 RNA Binding Protein Is an In Vivo Substrate for Protein Arginine N-Methyltransferase 1." Molecular Biology of the Cell 14, no. 1 (January 2003): 274–87. http://dx.doi.org/10.1091/mbc.e02-08-0484.

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RNA binding proteins often contain multiple arginine glycine repeats, a sequence that is frequently methylated by protein arginine methyltransferases. The role of this posttranslational modification in the life cycle of RNA binding proteins is not well understood. Herein, we report that Sam68, a heteronuclear ribonucleoprotein K homology domain containing RNA binding protein, associates with and is methylated in vivo by the protein arginineN-methyltransferase 1 (PRMT1). Sam68 contains asymmetrical dimethylarginines near its proline motif P3 as assessed by using a novel asymmetrical dimethylarginine-specific antibody and mass spectrometry. Deletion of the methylation sites and the use of methylase inhibitors resulted in Sam68 accumulation in the cytoplasm. Sam68 was also detected in the cytoplasm of PRMT1-deficient embryonic stem cells. Although the cellular function of Sam68 is unknown, it has been shown to export unspliced human immunodeficiency virus RNAs. Cells treated with methylase inhibitors prevented the ability of Sam68 to export unspliced human immunodeficiency virus RNAs. Other K homology domain RNA binding proteins, including SLM-1, SLM-2, QKI-5, GRP33, and heteronuclear ribonucleoprotein K were also methylated in vivo. These findings demonstrate that RNA binding proteins are in vivo substrates for PRMT1, and their methylation is essential for their proper localization and function.

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Ding, Deqiang, Chao Wei, Kunzhe Dong, Jiali Liu, Alexander Stanton, Chao Xu, Jinrong Min, Jian Hu, and Chen Chen. "LOTUS domain is a novel class of G-rich and G-quadruplex RNA binding domain." Nucleic Acids Research 48, no. 16 (August 7, 2020): 9262–72. http://dx.doi.org/10.1093/nar/gkaa652.

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Abstract LOTUS domains are helix-turn-helix protein folds identified in essential germline proteins and are conserved in prokaryotes and eukaryotes. Despite originally predicted as an RNA binding domain, its molecular binding activity towards RNA and protein is controversial. In particular, the most conserved binding property for the LOTUS domain family remains unknown. Here, we uncovered an unexpected specific interaction of LOTUS domains with G-rich RNA sequences. Intriguingly, LOTUS domains exhibit high affinity to RNA G-quadruplex tertiary structures implicated in diverse cellular processes including piRNA biogenesis. This novel LOTUS domain-RNA interaction is conserved in bacteria, plants and animals, comprising the most ancient binding feature of the LOTUS domain family. By contrast, LOTUS domains do not preferentially interact with DNA G-quadruplexes. We further show that a subset of LOTUS domains display both RNA and protein binding activities. These findings identify the LOTUS domain as a specialized RNA binding domain across phyla and underscore the molecular mechanism underlying the function of LOTUS domain-containing proteins in RNA metabolism and regulation.

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Tsuji, Yoshiaki. "Optimization of Biotinylated RNA or DNA Pull-Down Assays for Detection of Binding Proteins: Examples of IRP1, IRP2, HuR, AUF1, and Nrf2." International Journal of Molecular Sciences 24, no. 4 (February 10, 2023): 3604. http://dx.doi.org/10.3390/ijms24043604.

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Investigation of RNA- and DNA-binding proteins to a defined regulatory sequence, such as an AU-rich RNA and a DNA enhancer element, is important for understanding gene regulation through their interactions. For in vitro binding studies, an electrophoretic mobility shift assay (EMSA) was widely used in the past. In line with the trend toward using non-radioactive materials in various bioassays, end-labeled biotinylated RNA and DNA oligonucleotides can be more practical probes to study protein–RNA and protein–DNA interactions; thereby, the binding complexes can be pulled down with streptavidin-conjugated resins and identified by Western blotting. However, setting up RNA and DNA pull-down assays with biotinylated probes in optimum protein binding conditions remains challenging. Here, we demonstrate the step-by step optimization of pull-down for IRP (iron-responsive-element-binding protein) with a 5′-biotinylated stem-loop IRE (iron-responsive element) RNA, HuR, and AUF1 with an AU-rich RNA element and Nrf2 binding to an antioxidant-responsive element (ARE) enhancer in the human ferritin H gene. This study was designed to address key technical questions in RNA and DNA pull-down assays: (1) how much RNA and DNA probes we should use; (2) what binding buffer and cell lysis buffer we can use; (3) how to verify the specific interaction; (4) what streptavidin resin (agarose or magnetic beads) works; and (5) what Western blotting results we can expect from varying to optimum conditions. We anticipate that our optimized pull-down conditions can be applicable to other RNA- and DNA-binding proteins along with emerging non-coding small RNA-binding proteins for their in vitro characterization.

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Li, Xinyi, Wenchen Pu, Song Chen, and Yong Peng. "Therapeutic targeting of RNA-binding protein by RNA-PROTAC." Molecular Therapy 29, no. 6 (June 2021): 1940–42. http://dx.doi.org/10.1016/j.ymthe.2021.04.032.

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Fung, P. A., R. Labrecque, and T. Pederson. "RNA-dependent phosphorylation of a nuclear RNA binding protein." Proceedings of the National Academy of Sciences 94, no. 4 (February 18, 1997): 1064–68. http://dx.doi.org/10.1073/pnas.94.4.1064.

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de Moor, C. H., M. Jansen, E. J. Bonte, A. A. M. Thomas, J. S. Sussenbach, and J. L. Van Den Brande. "Proteins binding to the leader of the 6.0 kb mRNA of human insulin-like growth factor 2 influence translation." Biochemical Journal 307, no. 1 (April 1, 1995): 225–31. http://dx.doi.org/10.1042/bj3070225.

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The leader of the 6.0 kb human insulin-like growth factor 2 (IGF-2) mRNA, leader 3, has been reported to partially repress translation. In the regulation of this phenomenon, RNA-binding proteins may play a role. Using UV-irradiation crosslinking, we found specific binding of four proteins (57, 43, 37 and 36 kDa) to this leader. Binding of these proteins to RNA proved to be highly sensitive to the potassium chloride concentration in the buffer solution, each protein having its own optimum. The 57 kDa protein was indistinguishable by size, binding properties and immunoprecipitation from the polypyrimidine tract binding protein (PTB), first described as a nuclear protein binding to the polypyrimidine tracts (PPTs) in introns. Cross-competition experiments showed that leader 3 has a much higher affinity for this 57 kDa protein than the PPT on which PTB was originally characterized. By competition with different fragments of leader 3, we were able to localize the binding of the 57 kDa protein to a 162 nt RNA fragment (AsnI-PvuII) in the 3′-part of the leader. When placed before a chloramphenicol acetyltransferase (CAT) open reading frame, this RNA fragment stimulated translation in reticulocyte lysate 3-fold, while other fragments of leader 3 repressed translation. The efficient translation directed by the 162 nt AsnI-PvuII fragment fused to CAT could be repressed by adding free AsnI-PvuII RNA fragment, indicating that the high translation efficiency of the AsnI-PvuII-CAT synthetic mRNA was due to the binding of protein and not to the structure of the RNA itself.

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Zhang, Jian, Zhiqiang Ma, and Lukasz Kurgan. "Comprehensive review and empirical analysis of hallmarks of DNA-, RNA- and protein-binding residues in protein chains." Briefings in Bioinformatics 20, no. 4 (December 15, 2017): 1250–68. http://dx.doi.org/10.1093/bib/bbx168.

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Abstract Proteins interact with a variety of molecules including proteins and nucleic acids. We review a comprehensive collection of over 50 studies that analyze and/or predict these interactions. While majority of these studies address either solely protein–DNA or protein–RNA binding, only a few have a wider scope that covers both protein–protein and protein–nucleic acid binding. Our analysis reveals that binding residues are typically characterized with three hallmarks: relative solvent accessibility (RSA), evolutionary conservation and propensity of amino acids (AAs) for binding. Motivated by drawbacks of the prior studies, we perform a large-scale analysis to quantify and contrast the three hallmarks for residues that bind DNA-, RNA-, protein- and (for the first time) multi-ligand-binding residues that interact with DNA and proteins, and with RNA and proteins. Results generated on a well-annotated data set of over 23 000 proteins show that conservation of binding residues is higher for nucleic acid- than protein-binding residues. Multi-ligand-binding residues are more conserved and have higher RSA than single-ligand-binding residues. We empirically show that each hallmark discriminates between binding and nonbinding residues, even predicted RSA, and that combining them improves discriminatory power for each of the five types of interactions. Linear scoring functions that combine these hallmarks offer good predictive performance of residue-level propensity for binding and provide intuitive interpretation of predictions. Better understanding of these residue-level interactions will facilitate development of methods that accurately predict binding in the exponentially growing databases of protein sequences.

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Bentley, R. C., and J. D. Keene. "Recognition of U1 and U2 small nuclear RNAs can be altered by a 5-amino-acid segment in the U2 small nuclear ribonucleoprotein particle (snRNP) B" protein and through interactions with U2 snRNP-A' protein." Molecular and Cellular Biology 11, no. 4 (April 1991): 1829–39. http://dx.doi.org/10.1128/mcb.11.4.1829-1839.1991.

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We have investigated the sequence elements influencing RNA recognition in two closely related small nuclear ribonucleoprotein particle (snRNP) proteins, U1 snRNP-A and U2 snRNP-B". A 5-amino-acid segment in the RNA-binding domain of the U2 snRNP-B" protein was found to confer U2 RNA recognition when substituted into the corresponding position in the U1 snRNP-A protein. In addition, B", but not A, was found to require the U2 snRNP-A' protein as an accessory factor for high-affinity binding to U2 RNA. The pentamer segment in B" that conferred U2 RNA recognition was not sufficient to allow the A' enhancement of U2 RNA binding by B", thus implicating other sequences in this protein-protein interaction. Sequence elements involved in these interactions have been localized to variable loops of the RNA-binding domain as determined by nuclear magnetic resonance spectroscopy (D. Hoffman, C.C. Query, B. Golden, S.W. White, and J.D. Keene, Proc. Natl. Acad. Sci. USA, in press). These findings suggest a role for accessory proteins in the formation of RNP complexes and pinpoint amino acid sequences that affect the specificity of RNA recognition in two members of a large family of proteins involved in RNA processing.

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Bentley, R. C., and J. D. Keene. "Recognition of U1 and U2 small nuclear RNAs can be altered by a 5-amino-acid segment in the U2 small nuclear ribonucleoprotein particle (snRNP) B" protein and through interactions with U2 snRNP-A' protein." Molecular and Cellular Biology 11, no. 4 (April 1991): 1829–39. http://dx.doi.org/10.1128/mcb.11.4.1829.

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We have investigated the sequence elements influencing RNA recognition in two closely related small nuclear ribonucleoprotein particle (snRNP) proteins, U1 snRNP-A and U2 snRNP-B". A 5-amino-acid segment in the RNA-binding domain of the U2 snRNP-B" protein was found to confer U2 RNA recognition when substituted into the corresponding position in the U1 snRNP-A protein. In addition, B", but not A, was found to require the U2 snRNP-A' protein as an accessory factor for high-affinity binding to U2 RNA. The pentamer segment in B" that conferred U2 RNA recognition was not sufficient to allow the A' enhancement of U2 RNA binding by B", thus implicating other sequences in this protein-protein interaction. Sequence elements involved in these interactions have been localized to variable loops of the RNA-binding domain as determined by nuclear magnetic resonance spectroscopy (D. Hoffman, C.C. Query, B. Golden, S.W. White, and J.D. Keene, Proc. Natl. Acad. Sci. USA, in press). These findings suggest a role for accessory proteins in the formation of RNP complexes and pinpoint amino acid sequences that affect the specificity of RNA recognition in two members of a large family of proteins involved in RNA processing.

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Khan, Mateen A. "Analysis of Ion and pH Effects on Iron Response Element (IRE) and mRNA-Iron Regulatory Protein (IRP1) Interactions." Current Chemical Biology 14, no. 2 (November 19, 2020): 88–99. http://dx.doi.org/10.2174/2212796814999200604121937.

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Background: Cellular iron uptake, utilization, and storage are tightly controlled through the action of iron regulatory proteins (IRPs). IRPs achieve this control by binding to IREs-mRNA in the 5'- or 3'-end of mRNAs that encode proteins involved in iron metabolism. The interaction of iron regulatory proteins with mRNAs containing an iron responsive element plays a central role in this regulation. The IRE RNA family of mRNA regulatory structures combines absolutely conserved protein binding sites with phylogenetically conserved base pairs that are specific to each IREs and influence RNA/protein stability. Our previous result revealed the binding and kinetics of IRE RNA with IRP1. The aim of the present study is to gain further insight into the differences in protein/RNA stability as a function of pH and ionic strength. Objective: To determine the extent to which the binding affinity and stability of protein/RNA complex was affected by ionic strength and pH. Methods: Fluorescence spectroscopy was used to characterize IRE RNA-IRP protein interaction. Results: Scatchard analysis revealed that the IRP1 protein binds to a single IRE RNA molecule. The binding affinity of two IRE RNA/IRP was significantly changed with the change in pH. The data suggests that the optimum binding of RNA/IRP complex occurred at pH 7.6. Dissociation constant for two IRE RNA/IRP increased with an increase in ionic strength, with a larger effect for FRT IRE RNA. This suggests that numerous electrostatic interactions occur in the ferritin IRE RNA/IRP than ACO2 IRE RNA/IRP complex. Iodide quenching shows that the majority of the tryptophan residues in IRP1 are solvent-accessible, assuming that most of the tryptophan residues contribute to protein fluorescence. Conclusion: The results obtained from this study clearly indicate that IRE RNA/IRP complex is destabilized by the change in pH and ionic strength. These observations suggest that both pH and ion are important for the assembly and stability of the IRE RNA/IRP complex formation.

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Swanson, Maud M., Patricia Ansel-McKinney, Felicia Houser-Scott, Vidadi Yusibov, L. Sue Loesch-Fries, and Lee Gehrke. "Viral Coat Protein Peptides with Limited Sequence Homology Bind Similar Domains of Alfalfa Mosaic Virus and Tobacco Streak Virus RNAs." Journal of Virology 72, no. 4 (April 1, 1998): 3227–34. http://dx.doi.org/10.1128/jvi.72.4.3227-3234.1998.

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ABSTRACT An unusual and distinguishing feature of alfalfa mosaic virus (AMV) and ilarviruses such as tobacco streak virus (TSV) is that the viral coat protein is required to activate the early stages of viral RNA replication, a phenomenon known as genome activation. AMV-TSV coat protein homology is limited; however, they are functionally interchangeable in activating virus replication. For example, TSV coat protein will activate AMV RNA replication and vice versa. Although AMV and TSV coat proteins have little obvious amino acid homology, we recently reported that they share an N-terminal RNA binding consensus sequence (Ansel-McKinney et al., EMBO J. 15:5077–5084, 1996). Here, we biochemically compare the binding of chemically synthesized peptides that include the consensus RNA binding sequence and lysine-rich (AMV) or arginine-rich (TSV) environment to 3′-terminal TSV and AMV RNA fragments. The arginine-rich TSV coat protein peptide binds viral RNA with lower affinity than the lysine-rich AMV coat protein peptides; however, the ribose moieties protected from hydroxyl radical attack by the two different peptides are localized in the same area of the predicted RNA structures. When included in an infectious inoculum, both AMV and TSV 3′-terminal RNA fragments inhibited AMV RNA replication, while variant RNAs unable to bind coat protein did not affect replication significantly. The data suggest that RNA binding and genome activation functions may reside in the consensus RNA binding sequence that is apparently unique to AMV and ilarvirus coat proteins.

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Zhang, Jing, Fanghui Ding, Dan Jiao, Qiaozhi Li, and Hong Ma. "The Aberrant Expression of MicroRNA-125a-5p/IGF2BP3 Axis in Advanced Gastric Cancer and Its Clinical Relevance." Technology in Cancer Research & Treatment 19 (January 1, 2020): 153303382091733. http://dx.doi.org/10.1177/1533033820917332.

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RNA-binding proteins have been associated with cancer development. The overexpression of a well-known RNA-binding protein, insulin-like growth factor 2 messenger RNA–binding protein 3, has been identified as an indicator of poor prognosis in patients with various types of cancer. Although gastric cancer is a relatively frequent and potentially fatal malignancy, the mechanism by which insulin-like growth factor 2 messenger RNA–binding protein 3 regulates the development of this cancer remains unclear. This study aimed to investigate the role and regulatory mechanism of insulin-like growth factor 2 messenger RNA–binding protein 3 in gastric cancer. An analysis of IGF2BP3 expression patterns reported in 4 public gastric cancer–related microarray data sets from the Gene Expression Omnibus and The Cancer Genome Atlas-Stomach Adenocarcinoma revealed strong expression of this gene in gastric cancer tissues. Insulin-like growth factor 2 messenger RNA–binding protein 3 expression in gastric cancer was further confirmed via quantitative reverse transcription polymerase chain reaction and immunohistochemistry, respectively, in an in-house gastric cancer cohort (n = 30), and the association of insulin-like growth factor 2 messenger RNA–binding protein 3 expression with clinical parameters and prognosis was analyzed. Notably, stronger IGF2BP3 expression significantly correlated with poor prognosis, and significant changes in insulin-like growth factor 2 messenger RNA–binding protein 3 expression were only confirmed in patients with advanced-stage gastric cancer in an independent cohort. The effects of insulin-like growth factor 2 messenger RNA–binding protein 3 on cell proliferation were confirmed through in vitro experiments involving the HGC-27 gastric cancer cell line. MicroR-125a-5p, a candidate microRNA that target on insulin-like growth factor 2 messenger RNA–binding protein 3, decreased in advanced-stage gastric cancer. Upregulation of microR-125a-5p inhibited insulin-like growth factor 2 messenger RNA–binding protein 3, and dual-luciferase report assay indicated that microR-125a-5p inhibited the translation of IGF2BP3 by directly targeting the 3′ untranslated region. These results indicate that the microR-125a-5p/insulin-like growth factor 2 messenger RNA–binding protein 3 axis contributes to the oncogenesis of advanced gastric cancer.

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Yang, Rui, Haoquan Liu, Liu Yang, Ting Zhou, Xinyao Li, and Yunjie Zhao. "RPpocket: An RNA–Protein Intuitive Database with RNA Pocket Topology Resources." International Journal of Molecular Sciences 23, no. 13 (June 21, 2022): 6903. http://dx.doi.org/10.3390/ijms23136903.

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RNA–protein complexes regulate a variety of biological functions. Thus, it is essential to explore and visualize RNA–protein structural interaction features, especially pocket interactions. In this work, we develop an easy-to-use bioinformatics resource: RPpocket. This database provides RNA–protein complex interactions based on sequence, secondary structure, and pocket topology analysis. We extracted 793 pockets from 74 non-redundant RNA–protein structures. Then, we calculated the binding- and non-binding pocket topological properties and analyzed the binding mechanism of the RNA–protein complex. The results showed that the binding pockets were more extended than the non-binding pockets. We also found that long-range forces were the main interaction for RNA–protein recognition, while short-range forces strengthened and optimized the binding. RPpocket could facilitate RNA–protein engineering for biological or medical applications.

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Goodier, John L., Lili Zhang, Melissa R. Vetter, and Haig H. Kazazian. "LINE-1 ORF1 Protein Localizes in Stress Granules with Other RNA-Binding Proteins, Including Components of RNA Interference RNA-Induced Silencing Complex." Molecular and Cellular Biology 27, no. 18 (June 11, 2007): 6469–83. http://dx.doi.org/10.1128/mcb.00332-07.

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ABSTRACT LINE-1 retrotransposons constitute one-fifth of human DNA and have helped shape our genome. A full-length L1 encodes a 40-kDa RNA-binding protein (ORF1p) and a 150-kDa protein (ORF2p) with endonuclease and reverse transcriptase activities. ORF1p is distinctive in forming large cytoplasmic foci, which we identified as cytoplasmic stress granules. A phylogenetically conserved central region of the protein is critical for wild-type localization and retrotransposition. Yeast two-hybrid screens revealed several RNA-binding proteins that coimmunoprecipitate with ORF1p and colocalize with ORF1p in foci. Two of these proteins, YB-1 and hnRNPA1, were previously reported in stress granules. We identified additional proteins associated with stress granules, including DNA-binding protein A, 9G8, and plasminogen activator inhibitor RNA-binding protein 1 (PAI-RBP1). PAI-RBP1 is a homolog of VIG, a part of the Drosophila melanogaster RNA-induced silencing complex (RISC). Other RISC components, including Ago2 and FMRP, also colocalize with PAI-RBP1 and ORF1p. We suggest that targeting ORF1p, and possibly the L1 RNP, to stress granules is a mechanism for controlling retrotransposition and its associated genetic and cellular damage.

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Kappel, Kalli, Inga Jarmoskaite, Pavanapuresan P. Vaidyanathan, William J. Greenleaf, Daniel Herschlag, and Rhiju Das. "Blind tests of RNA–protein binding affinity prediction." Proceedings of the National Academy of Sciences 116, no. 17 (April 8, 2019): 8336–41. http://dx.doi.org/10.1073/pnas.1819047116.

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Interactions between RNA and proteins are pervasive in biology, driving fundamental processes such as protein translation and participating in the regulation of gene expression. Modeling the energies of RNA–protein interactions is therefore critical for understanding and repurposing living systems but has been hindered by complexities unique to RNA–protein binding. Here, we bring together several advances to complete a calculation framework for RNA–protein binding affinities, including a unified free energy function for bound complexes, automated Rosetta modeling of mutations, and use of secondary structure-based energetic calculations to model unbound RNA states. The resulting Rosetta-Vienna RNP-ΔΔG method achieves root-mean-squared errors (RMSEs) of 1.3 kcal/mol on high-throughput MS2 coat protein–RNA measurements and 1.5 kcal/mol on an independent test set involving the signal recognition particle, human U1A, PUM1, and FOX-1. As a stringent test, the method achieves RMSE accuracy of 1.4 kcal/mol in blind predictions of hundreds of human PUM2–RNA relative binding affinities. Overall, these RMSE accuracies are significantly better than those attained by prior structure-based approaches applied to the same systems. Importantly, Rosetta-Vienna RNP-ΔΔG establishes a framework for further improvements in modeling RNA–protein binding that can be tested by prospective high-throughput measurements on new systems.

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Burd, C. G., E. L. Matunis, and G. Dreyfuss. "The multiple RNA-binding domains of the mRNA poly(A)-binding protein have different RNA-binding activities." Molecular and Cellular Biology 11, no. 7 (July 1991): 3419–24. http://dx.doi.org/10.1128/mcb.11.7.3419-3424.1991.

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The poly(A)-binding protein (PABP) is the major mRNA-binding protein in eukaryotes, and it is essential for viability of the yeast Saccharomyces cerevisiae. The amino acid sequence of the protein indicates that it consists of four ribonucleoprotein consensus sequence-containing RNA-binding domains (RBDs I, II, III, and IV) and a proline-rich auxiliary domain at the carboxyl terminus. We produced different parts of the S. cerevisiae PABP and studied their binding to poly(A) and other ribohomopolymers in vitro. We found that none of the individual RBDs of the protein bind poly(A) specifically or efficiently. Contiguous two-domain combinations were required for efficient RNA binding, and each pairwise combination (I/II, II/III, and III/IV) had a distinct RNA-binding activity. Specific poly(A)-binding activity was found only in the two amino-terminal RBDs (I/II) which, interestingly, are dispensable for viability of yeast cells, whereas the activity that is sufficient to rescue lethality of a PABP-deleted strain is in the carboxyl-terminal RBDs (III/IV). We conclude that the PABP is a multifunctional RNA-binding protein that has at least two distinct and separable activities: RBDs I/II, which most likely function in binding the PABP to mRNA through the poly(A) tail, and RBDs III/IV, which may function through binding either to a different part of the same mRNA molecule or to other RNA(s).

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Journal articles on the topic 'RNA-binding protein'

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