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Relevant bibliographies by topics / Peptidyl transferases. Ribosomes

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Journal articles

Academic literature on the topic 'Peptidyl transferases. Ribosomes'

Author: Grafiati

Published: 4 June 2021

Last updated: 29 January 2023

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Journal articles on the topic "Peptidyl transferases. Ribosomes"

1

Yang, Rui, Luis R. Cruz-Vera, and Charles Yanofsky. "23S rRNA Nucleotides in the Peptidyl Transferase Center Are Essential for Tryptophanase Operon Induction." Journal of Bacteriology 191, no. 11 (2009): 3445–50. http://dx.doi.org/10.1128/jb.00096-09.

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ABSTRACT Distinct features of the ribosomal peptide exit tunnel are known to be essential for recognition of specific amino acids of a nascent peptidyl-tRNA. Thus, a tryptophan residue at position 12 of the peptidyl-tRNA TnaC-tRNAPro leads to the creation of a free tryptophan binding site within the ribosome at which bound tryptophan inhibits normal ribosome functions. The ribosomal processes that are inhibited are hydrolysis of TnaC-tRNAPro by release factor 2 and peptidyl transfer of TnaC of TnaC-tRNAPro to puromycin. These events are normally performed in the ribosomal peptidyl transferase

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2

Cruz-Vera, Luis R., Aaron New, Catherine Squires, and Charles Yanofsky. "Ribosomal Features Essential for tna Operon Induction: Tryptophan Binding at the Peptidyl Transferase Center." Journal of Bacteriology 189, no. 8 (2007): 3140–46. http://dx.doi.org/10.1128/jb.01869-06.

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ABSTRACT Features of the amino acid sequence of the TnaC nascent peptide are recognized by the translating ribosome. Recognition leads to tryptophan binding within the translating ribosome, inhibiting the termination of tnaC translation and preventing Rho-dependent transcription termination in the tna operon leader region. It was previously shown that inserting an adenine residue at position 751 or introducing the U2609C change in 23S rRNA or introducing the K90W replacement in ribosomal protein L22 prevented tryptophan induction of tna operon expression. It was also observed that an adenine a

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3

Agmon, Ilana, Anat Bashan, and Ada Yonath. "On Ribosome Conservation and Evolution." Israel Journal of Ecology and Evolution 52, no. 3-4 (2006): 359–74. http://dx.doi.org/10.1560/ijee_52_3-4_359.

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The ribosome is a ribozyme whose active site, the peptidyl transferase center (PTC), is situated within a highly conserved universal symmetrical region that connects all ribosomal functional centers involved in amino acid polymerization. The linkage between this elaborate architecture and A-site tRNA position revealed that the A-> P-site passage of the tRNA terminus in the peptidyl transferase center is performed by a rotatory motion, synchronized with the overall tRNA/mRNA sideways movement. Guided by the PTC, the rotatory motion leads to stereochemistry suitable for peptide bond formation

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4

Porse, Bo T., Cristina Rodriguez-Fonseca, Ilia Leviev, and Roger A. Garrett. "Antibiotic inhibition of the movement of tRNA substrates through a peptidyl transferase cavity." Biochemistry and Cell Biology 73, no. 11-12 (1995): 877–85. http://dx.doi.org/10.1139/o95-095.

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The present review attempts to deal with movement of tRNA substrates through the peptidyl transferase centre on the large ribosomal subunit and to explain how this movement is interrupted by antibiotics. It builds on the concept of hybrid tRNA states forming on ribosomes and on the observed movement of the 5′ end of P-site-bound tRNA relative to the ribosome that occurs on peptide bond formation. The 3′ ends of the tRNAs enter, and move through, a catalytic cavity where antibiotics are considered to act by at least three primary mechanisms: (i) they interfere with the entry of the aminoacyl mo

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5

Wower, Jacek, Iwona K. Wower, Stanislav V. Kirillov, Kirill V. Rosen, Robert A. Zimmermann, and Stephen S. Hixson. "Peptidyl transferase and beyond." Biochemistry and Cell Biology 73, no. 11-12 (1995): 1041–47. http://dx.doi.org/10.1139/o95-111.

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The peptidyl transferase center of the Escherichia coli ribosome encompasses a number of 50S-subunit proteins as well as several specific segments of the 23S rRNA. Although our knowledge of the role that both ribosomal proteins and 23S rRNA play in peptide bond formation has steadily increased, the location, organization, and molecular structure of the peptidyl transferase center remain poorly defined. Over the past 10 years, we have developed a variety of photoaffinity reagents and strategies for investigating the topography of tRNA binding sites on the ribosome. In particular, we have used t

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6

Dorner, S., N. Polacek, U. Schulmeister, C. Panuschka, and A. Barta. "Molecular aspects of the ribosomal peptidyl transferase." Biochemical Society Transactions 30, no. 6 (2002): 1131–37. http://dx.doi.org/10.1042/bst0301131.

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The proteins in a living cell are synthesized on a large bipartite ribonucleoprotein complex termed the ribosome. The peptidyl transferase, which polymerizes amino acids to yield peptides, is localized on the large subunit. Biochemical investigations over the past 35 years have led to the hypothesis that rRNA has a major role in all ribosomal functions. The recent high resolution X-ray structures of the ribosomal subunits clearly demonstrated that peptidyl transfer is an RNA-mediated process. As all ribosomal activities are dependent on bivalent metal ions, as is the case for most ribozymes, w

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7

Agmon, Ilana. "Hypothesis: Spontaneous Advent of the Prebiotic Translation System via the Accumulation of L-Shaped RNA Elements." International Journal of Molecular Sciences 19, no. 12 (2018): 4021. http://dx.doi.org/10.3390/ijms19124021.

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The feasibility of self-assembly of a translation system from prebiotic random RNA chains is a question that is central to the ability to conceive life emerging by natural processes. The spontaneous materialization of a translation system would have required the autonomous formation of proto-transfer RNA (tRNA) and proto-ribosome molecules that are indispensable for translating an RNA chain into a polypeptide. Currently, the vestiges of a non-coded proto-ribosome, which could have only catalyzed the formation of a peptide bond between random amino acids, is consensually localized in the region

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8

Powers, Kyle T., Flint Stevenson-Jones, Sathish K. N. Yadav, et al. "Blasticidin S inhibits mammalian translation and enhances production of protein encoded by nonsense mRNA." Nucleic Acids Research 49, no. 13 (2021): 7665–79. http://dx.doi.org/10.1093/nar/gkab532.

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Abstract Deciphering translation is of paramount importance for the understanding of many diseases, and antibiotics played a pivotal role in this endeavour. Blasticidin S (BlaS) targets translation by binding to the peptidyl transferase center of the large ribosomal subunit. Using biochemical, structural and cellular approaches, we show here that BlaS inhibits both translation elongation and termination in Mammalia. Bound to mammalian terminating ribosomes, BlaS distorts the 3′CCA tail of the P-site tRNA to a larger extent than previously reported for bacterial ribosomes, thus delaying both, p

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9

Marks, James, Krishna Kannan, Emily J. Roncase, et al. "Context-specific inhibition of translation by ribosomal antibiotics targeting the peptidyl transferase center." Proceedings of the National Academy of Sciences 113, no. 43 (2016): 12150–55. http://dx.doi.org/10.1073/pnas.1613055113.

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The first broad-spectrum antibiotic chloramphenicol and one of the newest clinically important antibacterials, linezolid, inhibit protein synthesis by targeting the peptidyl transferase center of the bacterial ribosome. Because antibiotic binding should prevent the placement of aminoacyl-tRNA in the catalytic site, it is commonly assumed that these drugs are universal inhibitors of peptidyl transfer and should readily block the formation of every peptide bond. However, our in vitro experiments showed that chloramphenicol and linezolid stall ribosomes at specific mRNA locations. Treatment of ba

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10

Swaney, Steven, Mark McCroskey, Dean Shinabarger, Zhigang Wang, Benjamin A. Turner, and Christian N. Parker. "Characterization of a High-Throughput Screening Assay for Inhibitors of Elongation Factor P and Ribosomal Peptidyl Transferase Activity." Journal of Biomolecular Screening 11, no. 7 (2006): 736–42. http://dx.doi.org/10.1177/1087057106291634.

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Elongation Factor P (EF-P) is an essential component of bacterial protein synthesis, enhancing the rate of translation by facilitating the addition of amino acids to the growing peptide chain. Using purified Staphylococcus aureus EF-P and a reconstituted Escherichia coli ribosomal system, an assay monitoring the addition of radiolabeled N-formyl methionine to biotinylated puromycin was developed. Reaction products were captured with streptavidin-coated scintillation proximity assay (SPA) beads and quantified by scintillation counting. Data from the assay were used to create a kinetic model of

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