368,172 research outputs found

    Protein-RNA interactions: a structural analysis

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    A detailed computational analysis of 32 protein-RNA complexes is presented. A number of physical and chemical properties of the intermolecular interfaces are calculated and compared with those observed in protein-double-stranded DNA and protein-single-stranded DNA complexes. The interface properties of the protein-RNA complexes reveal the diverse nature of the binding sites. van der Waals contacts played a more prevalent role than hydrogen bond contacts, and preferential binding to guanine and uracil was observed. The positively charged residue, arginine, and the single aromatic residues, phenylalanine and tyrosine, all played key roles in the RNA binding sites. A comparison between protein-RNA and protein-DNA complexes showed that whilst base and backbone contacts (both hydrogen bonding and van der Waals) were observed with equal frequency in the protein-RNA complexes, backbone contacts were more dominant in the protein-DNA complexes. Although similar modes of secondary structure interactions have been observed in RNA and DNA binding proteins, the current analysis emphasises the differences that exist between the two types of nucleic acid binding protein at the atomic contact level

    Functional domains of the influenza A virus PB2 protein:identification of NP- and PB1-binding sites

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    AbstractInfluenza virus genomic RNA segments are packaged into ribonucleoprotein (RNP) structures by the PB1, PB2, and PA subunits of an RNA polymerase and a single-strand RNA-binding nucleoprotein (NP). Assembly and function of these ribonucleoproteins depend on a complex set of protein–protein and protein–RNA interactions. Here, we identify new functional domains of PB2. We show that PB2 contains two regions that bind NP and also identify a novel PB1 binding site. The regions of PB2 responsible for binding NP and PB1 show considerable overlap, and binding of NP to the PB2 fragments could be outcompeted by PB1. The binding domains of PB2 acted as trans-dominant inhibitors of viral gene expression, and consistent with the in vitro binding data, their inhibitory activity depended on the concentration of wild-type PB2, NP, and PB1. This provides evidence for functionally significant and potentially regulatory interactions between PB2 and NP

    Writing a wrong: Coupled RNA polymerase II transcription and RNA quality control

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    Processing and maturation of precursor RNA species is coupled to RNA polymerase II transcription. Co-transcriptional RNA processing helps to ensure efficient and proper capping, splicing, and 3' end processing of different RNA species to help ensure quality control of the transcriptome. Many improperly processed transcripts are not exported from the nucleus, are restricted to the site of transcription, and are in some cases degraded, which helps to limit any possibility of aberrant RNA causing harm to cellular health. These critical quality control pathways are regulated by the highly dynamic protein-protein interaction network at the site of transcription. Recent work has further revealed the extent to which the processes of transcription and RNA processing and quality control are integrated, and how critically their coupling relies upon the dynamic protein interactions that take place co-transcriptionally. This review focuses specifically on the intricate balance between 3' end processing and RNA decay during transcription termination. This article is categorized under: RNA Turnover and Surveillance > Turnover/Surveillance Mechanisms RNA Processing > 3' End Processing RNA Processing > Splicing Mechanisms RNA Processing > Capping and 5' End Modifications

    Development of chemical tools for imaging RNA and studying RNA and protein interactions

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    Tools for study of RNA are divided into two groups: RNA imaging and RNA crosslinking (Chapter 1). RNA imaging denotes visualization of target RNA by labelling it with fluorophores. RNA crosslinking refers to investigating the function of target RNA by capturing bio-macromolecules the RNA interacts with. In consideration of low abundance of some RNAs in living cells, in chapter 2, we have synthesized a new RNA probe based on previously reported aptamers. which reduces background signal to a large extent. We realized imaging of the RNA aptamer in mammalian cells, and the fluorescence obtained from newly constructed probe was apparently brighter.In chapter 3, we developed two psoralen based length tunable crosslinkers (AMT-NHS and AMT dimer) for studying RNA-RNA interactions or RNA-protein interactions. We have synthesized the crosslinkers and verified in vitro experiment that RNA-RNA interactions could be effectively captured by the AMT dimer, and RNA-protein interactions could be effectively tracked by AMT-NHS. In chapter 4, we proved that AMT-NHS could be applied to study RNA-protein interactions in living cells. We also proved that AMT-NHS CLIP is a stable and efficient method for studying RNA-protein interactions, it captured a large portion of interactions that traditional CLIP method may miss.In chapter 5, we have synthesized and incorporated an unnatural photoactivatable amino acid into a protein on a specific site by expanding genetic code, which paves the way to develop a novel and powerful CLIP method to capture more comprehensively RNA-protein interactions
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