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Demeshkina, N.; Laletina, E. S.; Meschaninova, Mariya I.; Репкова, М. Н.; Ven’yaminova, A. G.; Graifer, D. M.; Карпова, Г. Г.

doi:10.1023/a:1022301300906

Cited by 19 publications

(5 citation statements)

References 19 publications

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“…One of methods applicable to study the positioning of mRNA on both pro- and eukaryotic (including mammalian) ribosomes is site-directed cross-linking ( − ). To date, the nature of the contacts between the components of the A, P, and E sites of human ribosome has been determined using short mRNA analogues, that is, derivatized oligonucleotides in which the nature and site of attachment of the (photo)reactive probe were varied ( − ). A comparison of these results with X-ray crystallographic data of prokaryotic ribosomes led to the conclusion that the mRNA codons in these sites are surrounded by nucleotides located in the same positions of the conserved parts of the small subunit rRNA secondary structure ( , ).…”

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confidence: 99%

The First Position of a Codon Placed in the A Site of the Human 80S Ribosome Contacts Nucleotide C1696 of the 18S rRNA as Well as Proteins S2, S3, S3a, S30, and S15

et al. 2005

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Messenger RNA analogues (42-mers) containing a GAC codon (aspartic acid) in the middle of their sequence followed by a s(4)UGA stop codon were used to identify the components of the human ribosomal A site in direct contact with the photoactivatable 4-thiouridine (s(4)U) residue. We compared the behavior of the nonphased ribosome-mRNA complex, (-)tRNA(Asp), to the one of the phased complex, (+)tRNA(Asp), in the absence and in the presence of eRF1, the eukaryotic class 1 translation termination factor of human origin. The patterns of cross-links obtained for the three complexes were similar to those previously reported for rabbit ribosomes [Chavatte, L., et al. (2001) Eur. J. Biochem. 268, 2896-2904]. Cross-links involving proteins S2, S3, S3a, and S30 were poorly dependent on the presence of tRNA(Asp) and eRF1. Cross-linking to nucleotide C1696 of 18S rRNA occurred in all complexes, but its yield was at least two times higher in the phased complex with an empty A site than in the nonphased complex or when the A site was occupied by eRF1. In contrast, protein S15 cross-linked only in the phased complex in the absence of eRF1. The data obtained point to notable differences in organization of the decoding site between mammalian and prokaryotic ribosomes and to large internal mobility of the components of the tRNA (eRF1)-free A site.

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confidence: 99%

The First Position of a Codon Placed in the A Site of the Human 80S Ribosome Contacts Nucleotide C1696 of the 18S rRNA as Well as Proteins S2, S3, S3a, S30, and S15

et al. 2005

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“…Upper diagram shows the protein environment of mRNA (the main targets of cross-linking are in bold). 22,25,31,34,37 The bacterial counterparts are shown in brackets. Below, the mRNA-rRNA neighborhood 21,22,28,29,59 is presented on the secondary structure of the human rRNA from the small ribosomal subunit taken from www.rna.ccbb.utexas.edu.…”

Section: Organisation Of the Mammalian Translation Machinery As Revea...mentioning

confidence: 99%

“…Identification of the ribosomal proteins cross-linked to mRNA analogs is more complicated than that of the rRNA nucleotides, with the choice of methodology depending on the identity of the cross-linked protein. 22,25,31 To identify crosslinked proteins, modified ribosomes are first dissociated into subunits by centrifugation in a sucrose density gradient, before isolating total ribosomal protein from small subunits. In studies using short mRNA analogs, labeled proteins were identified using one-and two-dimensional PAGE in a variety of electrophoresis systems.…”

Section: Introductionmentioning

confidence: 99%

Photoactivatable RNA derivatives as tools for studying the structural and functional organization of complex cellular ribonucleoprotein machineries

Graifer

Карпова

2013

RSC Adv.

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Ribonucleic acids (RNAs) are biopolymers that play key roles in many processes crucial for the life of cells.Functions of RNAs are generally mediated by their specific interactions with proteins and ribonucleoproteins (supramolecular RNA-protein complexes) that take place within complexes of RNA ligands with proteins or ribonucleoproteins. These interactions are defined by the molecular environment of the RNA ligand in the complex. A beneficial approach for studying such complexes involves site-directed crosslinking: RNA derivatives that contain chemically reactive groups form covalent bonds (cross-links) with those structural elements of the protein or ribonucleoprotein that neighbor the RNA ligand. Such RNA derivatives have been successfully used to study the interaction of messenger RNA (mRNA) with the protein synthesis machinery. By applying this approach to studies of the protein translation machinery of higher organisms, chemically reactive RNA derivatives have provided unique information that could not have been obtained by other approaches to date. This article presents a brief review of the types of RNA derivatives used as mRNA analogs, and their structures and synthesis, together with methods for identification of cross-linking targets. Furthermore, we summarize current data on mRNA interactions occurring during the course of protein synthesis in higher organisms.

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“…Cryo‐electron microscopy (cryo‐EM) and X‐ray crystallography data on the structure of the 40S ribosomal subunit1–4 show that the conserved part of rpS5e is located at a site on the 40S subunit homologous to that of rpS7p site on the 30S subunit,7 thus indicating that rpS5e is a component of the 40S ribosomal E site. Indeed, studies with crosslinking of mRNA analogues bearing 4‐thiouridine, or a nucleotide with a photoactivatable group in selected position, with rabbit8, 9 or human10 ribosomes revealed that rpS5e can be crosslinked to the derivatized mRNA nucleotide at position −3 with respect to the first nucleotide of the P site codon (i.e., the first nucleotide of the E site codon). Notably, in a crosslinking study with the 48S preinitiation complex (PIC),8 it was also found that 4‐thiouridine or 6‐thioguanosine at position −3 is able to crosslink to eIF2α.…”

Section: Introductionmentioning

confidence: 99%

Towards a Zero‐Waste Oxidative Coupling of Nonactivated Aromatics by Supported Gold Nanoparticles

Serna

Corma

2014

ChemSusChem

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We show that gold nanoparticles are able to perform the direct oxidative coupling of nonactivated aromatics with O2 as the only co-reagent. In this reaction, the aromatic acts both as reactant and solvent. Biphenyl, for example, can be obtained from benzene with high selectivity and a turnover number (TON) of 230 per pass. Similarly, several substituted biaryls can be prepared. Pd performs only one TON and even when a second catalytic functionality is introduced, together with strong acidic conditions, TON is always lower than 100. Other catalysts require iodine for performing the reaction, leading to 2 kg of waste for 1 kg of biphenyl formed, whereas no waste is created by the oxidative coupling with gold nanoparticles.

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Untitled

Cited by 19 publications

References 19 publications

The First Position of a Codon Placed in the A Site of the Human 80S Ribosome Contacts Nucleotide C1696 of the 18S rRNA as Well as Proteins S2, S3, S3a, S30, and S15

The First Position of a Codon Placed in the A Site of the Human 80S Ribosome Contacts Nucleotide C1696 of the 18S rRNA as Well as Proteins S2, S3, S3a, S30, and S15

Photoactivatable RNA derivatives as tools for studying the structural and functional organization of complex cellular ribonucleoprotein machineries

Towards a Zero‐Waste Oxidative Coupling of Nonactivated Aromatics by Supported Gold Nanoparticles

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