Academic literature on the topic 'Ribosome binding sites'

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Journal articles on the topic "Ribosome binding sites"

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Márquez, V., D. N. Wilson, and K. H. Nierhaus. "Functions and interplay of the tRNA-binding sites of the ribosome." Biochemical Society Transactions 30, no. 2 (2002): 133–40. http://dx.doi.org/10.1042/bst0300133.

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The ribosome translates the genetic information of an mRNA molecule into a sequence of amino acids. The ribosome utilizes tRNAs to connect elements of the RNA and protein worlds during protein synthesis, i.e. an anticodon as a unit of genetic information with the corresponding amino acid as a building unit of proteins. Three tRNA-binding sites are located on the ribosome, termed the A, P and E sites. In recent years the tRNA-binding sites have been localized on the ribosome by three different techniques, small-angle neutron scattering, cryo-electron microscopy and X-ray analyses of 70 S crysta
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Prinz, Anke, Enno Hartmann, and Kai-Uwe Kalies. "Sec61p Is the Main Ribosome Receptor in the Endoplasmic Reticulum of Saccharomyces cerevisiae." Biological Chemistry 381, no. 9-10 (2000): 1025–28. http://dx.doi.org/10.1515/bc.2000.126.

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Abstract A characteristic feature of the co-translational protein translocation into the endoplasmic reticulum (ER) is the tight association of the translating ribosomes with the translocation sites in the membrane. Biochemical analyses identified the Sec61 complex as the main ribosome receptor in the ER of mammalian cells. Similar experiments using purified homologues from the yeast Saccharomyces cerevisiae, the Sec61p complex and the Ssh1p complex, respectively, demonstrated that they bind ribosomes with an affinity similar to that of the mammalian Sec61 complex. However, these studies did n
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Dorner, S., and A. Barta. "Probing Ribosome Structure by Europium-Induced RNA Cleavage." Biological Chemistry 380, no. 2 (1999): 243–51. http://dx.doi.org/10.1515/bc.1999.032.

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AbstractDivalent metal ions are absolutely required for the structure and catalytic activities of ribosomes. They are partly coordinated to highly structured RNA, which therefore possesses high-affinity metal ion binding pockets. As metalion induced RNA cleavages are useful for characterising metal ion binding sites and RNA structures, we analysed europium (Eu3+) induced specific cleavages in both 16S and 23S rRNA ofE. coli. The cleavage sites were identified by primer extension and compared to those previously identified for calcium, lead, magnesium, and manganese ions. Several Eu3+cleavage s
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Aseev, Leonid V., Ludmila S. Koledinskaya, and Irina V. Boni. "Extraribosomal Functions of Bacterial Ribosomal Proteins—An Update, 2023." International Journal of Molecular Sciences 25, no. 5 (2024): 2957. http://dx.doi.org/10.3390/ijms25052957.

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Ribosomal proteins (r-proteins) are abundant, highly conserved, and multifaceted cellular proteins in all domains of life. Most r-proteins have RNA-binding properties and can form protein–protein contacts. Bacterial r-proteins govern the co-transcriptional rRNA folding during ribosome assembly and participate in the formation of the ribosome functional sites, such as the mRNA-binding site, tRNA-binding sites, the peptidyl transferase center, and the protein exit tunnel. In addition to their primary role in a cell as integral components of the protein synthesis machinery, many r-proteins can fu
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Krüger, Tim, Hanswalter Zentgraf, and Ulrich Scheer. "Intranucleolar sites of ribosome biogenesis defined by the localization of early binding ribosomal proteins." Journal of Cell Biology 177, no. 4 (2007): 573–78. http://dx.doi.org/10.1083/jcb.200612048.

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Considerable efforts are being undertaken to elucidate the processes of ribosome biogenesis. Although various preribosomal RNP complexes have been isolated and molecularly characterized, the order of ribosomal protein (r-protein) addition to the emerging ribosome subunits is largely unknown. Furthermore, the correlation between the ribosome assembly pathway and the structural organization of the dedicated ribosome factory, the nucleolus, is not well established. We have analyzed the nucleolar localization of several early binding r-proteins in human cells, applying various methods, including l
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Schaletzky, Julia, and Tom A. Rapoport. "Ribosome Binding to and Dissociation from Translocation Sites of the Endoplasmic Reticulum Membrane." Molecular Biology of the Cell 17, no. 9 (2006): 3860–69. http://dx.doi.org/10.1091/mbc.e06-05-0439.

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We have addressed how ribosome-nascent chain complexes (RNCs), associated with the signal recognition particle (SRP), can be targeted to Sec61 translocation channels of the endoplasmic reticulum (ER) membrane when all binding sites are occupied by nontranslating ribosomes. These competing ribosomes are known to be bound with high affinity to tetramers of the Sec61 complex. We found that the membrane binding of RNC–SRP complexes does not require or cause the dissociation of prebound nontranslating ribosomes, a process that is extremely slow. SRP and its receptor target RNCs to a free population
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Auerbach, Tamar, Inbal Mermershtain, Chen Davidovich, et al. "The structure of ribosome-lankacidin complex reveals ribosomal sites for synergistic antibiotics." Proceedings of the National Academy of Sciences 107, no. 5 (2010): 1983–88. http://dx.doi.org/10.1073/pnas.0914100107.

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Crystallographic analysis revealed that the 17-member polyketide antibiotic lankacidin produced by Streptomyces rochei binds at the peptidyl transferase center of the eubacterial large ribosomal subunit. Biochemical and functional studies verified this finding and showed interference with peptide bond formation. Chemical probing indicated that the macrolide lankamycin, a second antibiotic produced by the same species, binds at a neighboring site, at the ribosome exit tunnel. These two antibiotics can bind to the ribosome simultaneously and display synergy in inhibiting bacterial growth. The bi
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Wittmann-Liebold, Brigitte, Monika Ühlein, Henning Urlaub, Eva-Christina Müller, Albrecht Otto, and Oliver Bischof. "Structural and functional implications in the eubacterial ribosome as revealed by protein–rRNA and antibiotic contact sites." Biochemistry and Cell Biology 73, no. 11-12 (1995): 1187–97. http://dx.doi.org/10.1139/o95-128.

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Contact sites between protein and rRNA in 30S and 50S ribosomal subunits of Escherichia coli and Bacillus stearothermophilus were investigated at the molecular level using UV and 2–iminothiolane as cross-linkers. Thirteen ribosomal proteins (S3, S4, S7, S14, S17, L2, L4, L6, L14, L27, L28, L29, andL36) from these organisms were cross-linked in direct contact with the RNAs, and the peptide stretches as well as amino acids involved were identified. Further, the binding sites of puromycin and spiramycin were established at die peptide level in several proteins that were found to constitute me ant
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Kalies, K. U., D. Görlich, and T. A. Rapoport. "Binding of ribosomes to the rough endoplasmic reticulum mediated by the Sec61p-complex." Journal of Cell Biology 126, no. 4 (1994): 925–34. http://dx.doi.org/10.1083/jcb.126.4.925.

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The cotranslational translocation of proteins across the ER membrane involves the tight binding of translating ribosomes to the membrane, presumably to ribosome receptors. The identity of the latter has been controversial. One putative receptor candidate is Sec61 alpha, a multi-spanning membrane protein that is associated with two additional membrane proteins (Sec61 beta and gamma) to form the Sec61p-complex. Other receptors of 34 and 180 kD have also been proposed on the basis of their ability to bind at low salt concentration ribosomes lacking nascent chains. We now show that the Sec61p-comp
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Lytle, J. Robin, Lily Wu, and Hugh D. Robertson. "The Ribosome Binding Site of Hepatitis C Virus mRNA." Journal of Virology 75, no. 16 (2001): 7629–36. http://dx.doi.org/10.1128/jvi.75.16.7629-7636.2001.

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ABSTRACT Hepatitis C virus (HCV) infects an estimated 170 million people worldwide, the majority of whom develop a chronic infection which can lead to severe liver disease, and for which no generally effective treatment yet exists. A promising target for treatment is the internal ribosome entry site (IRES) of HCV, a highly conserved domain within a highly variable RNA. Never before have the ribosome binding sites of any IRES domains, cellular or viral, been directly characterized. Here, we reveal that the HCV IRES sequences most closely associated with 80S ribosomes during protein synthesis in
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Dissertations / Theses on the topic "Ribosome binding sites"

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Berg, Emily Katherine. "Thermodynamics of λ-PCR Primer Design and Effective Ribosome Binding Sites". Thesis, Virginia Tech, 2019. http://hdl.handle.net/10919/89900.

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Recombinant DNA technology has been commonly used in a number of fields to synthesize new products or generate products with a new pathway. Conventional cloning methods are expensive and require significant time and labor; λ-PCR, a new cloning method developed in the Senger lab, has a number of advantages compared to other cloning processes due to its employment of relatively inexpensive and widely available materials and time-efficiency. While the amount of lab work required for the cloning process is minimal, the importance of accurate primer design cannot be overstated. The target of this s
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Collins, Paula Grosse. "Ribosome Binding to the Mammalian Endoplasmic Reticulum: A Thesis." eScholarship@UMMS, 1991. https://escholarship.umassmed.edu/gsbs_diss/155.

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Investigators have been attempting to identify the receptor for ribosomes on the rough endoplasmic reticulum (RER) for almost 20 years, yet the ribosome receptor has remained elusive. Rough microsomal membranes contain endogenous ribosomes bound in at least two types of interactions. Loosely associated ribosomes can be removed by extraction with a high ionic strength solution, but ribosomes that were actively engaged in translocation when the membranes were isolated remain tethered to the membrane by a nascent polypeptide (Adelman et al., 1973). The original assay for the ribosome receptor inv
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Tuck, Laura. "Structural and synthetic biology study of bacterial microcompartments." Thesis, University of Edinburgh, 2018. http://hdl.handle.net/1842/33180.

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Bacterial microcompartments (BMCs) are proteinaceous metabolic compartments found in a wide range of bacteria, whose function it is to encapsulate pathways for the breakdown of various carbon sources, whilst retaining toxic and volatile intermediates formed from substrate breakdown. Examples of these metabolic processes are the 1,2- propanediol-breakdown pathway in Salmonella enterica (Pdu microcompartment), as well as the ethanolamine breakdown pathway in Clostridium difficile (Eut microcompartment). Some of the major challenges to exploiting BMCs as a tool in biotechnology are understanding
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Kaminishi, Tatsuya, Andreas Schedlbauer, Attilio Fabbretti, et al. "Crystallographic characterization of the ribosomal binding site and molecular mechanism of action of Hygromycin A." Oxford University Press, 2015. http://hdl.handle.net/10757/608247.

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Hygromycin A (HygA) binds to the large ribosomal subunit and inhibits its peptidyl transferase (PT) activity. The presented structural and biochemical data indicate that HygA does not interfere with the initial binding of aminoacyl-tRNA to the A site, but prevents its subsequent adjustment such that it fails to act as a substrate in the PT reaction. Structurally we demonstrate that HygA binds within the peptidyl transferase center (PTC) and induces a unique conformation. Specifically in its ribosomal binding site HygA would overlap and clash with aminoacyl-A76 ribose moiety and, therefore, its
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Phelps, Steven Scott. "tRNA interactions in the ribosomal A-site that are important for binding, decoding, and translocation /." Diss., Connect to a 24 p. preview or request complete full text in PDF format. Access restricted to UC campuses, 2003. http://wwwlib.umi.com/cr/ucsd/fullcit?p3112867.

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Mao, Hongyuan 1969. "Structure determination of a yeast ribosomal protein L30 and pre-mRNA binding site complex by NMR spectroscopy." Thesis, Massachusetts Institute of Technology, 1998. http://hdl.handle.net/1721.1/49674.

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Thesis (Ph.D.)--Massachusetts Institute of Technology, Dept. of Chemistry, 1998.<br>Includes bibliographical references (p. 342-353).<br>The yeast (Saccharomyces cerevisiae) ribosomal protein L30 and its auto-regulatory pre-mRNA binding site provide one of the best examples the critical role of protein-RNA interactions in regulation of RNA processing and control of gene translation. A model system for this interaction, which includes the ribosomal L30 protein and the phylogenetically conserved RNA segment for auto-regulation, was studied using nuclear magnetic resonance (NMR) spectroscopy. The
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Yang, Grace. "Application of the Adaptive Poisson Boltzmann Solver on the investigation of the small oligonucleotide A-site model and 30S ribosomal subunit binding to aminoglycosidic antibiotics /." Diss., Connect to a 24 p. preview or request complete full text in PDF format. Access restricted to UC campuses, 2005. http://wwwlib.umi.com/cr/ucsd/fullcit?p3170239.

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Toddo, Stephen. "Engineering membrane proteins for production and topology." Doctoral thesis, Stockholms universitet, Institutionen för biokemi och biofysik, 2015. http://urn.kb.se/resolve?urn=urn:nbn:se:su:diva-116598.

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The genomes of diverse organisms are predicted to contain 20 – 30% membrane protein encoding genes and more than half of all therapeutics target membrane proteins. However, only 2% of crystal structures deposited in the protein data bank represent integral membrane proteins. This reflects the difficulties in studying them using standard biochemical and crystallographic methods. The first problem frequently encountered when investigating membrane proteins is their low natural abundance, which is insufficient for biochemical and structural studies. The aim of my thesis was to provide a simple me
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Bandmann, Nina. "Rational and combinatorial genetic engineering approaches for improved recombinant protein production and purification." Doctoral thesis, Stockholm : Bioteknologi, Kungliga Tekniska högskolan, 2007. http://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-4318.

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Tang, Shiyuyun. "Improving algorithms of gene prediction in prokaryotic genomes, metagenomes, and eukaryotic transcriptomes." Diss., Georgia Institute of Technology, 2016. http://hdl.handle.net/1853/54998.

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Next-generation sequencing has generated enormous amount of DNA and RNA sequences that potentially carry volumes of genetic information, e.g. protein-coding genes. The thesis is divided into three main parts describing i) GeneMarkS-2, ii) GeneMarkS-T, and iii) MetaGeneTack. In prokaryotic genomes, ab initio gene finders can predict genes with high accuracy. However, the error rate is not negligible and largely species-specific. Most errors in gene prediction are made in genes located in genomic regions with atypical GC composition, e.g. genes in pathogenicity islands. We describe a new algorit
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Books on the topic "Ribosome binding sites"

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Looman, Alfred Cornelis. Effects of heterologous ribosomal binding sites on the expression of the lacz gene of Escherichia coli. A.C. Looman, 1986.

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Book chapters on the topic "Ribosome binding sites"

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Wower, Jacek, Lee A. Sylvers, Kirill V. Rosen, Stephen S. Hixson, and Robert A. Zimmermann. "A Model of the tRNA Binding Sites on the Escherichia Coli Ribosome." In The Translational Apparatus. Springer US, 1993. http://dx.doi.org/10.1007/978-1-4615-2407-6_43.

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Mazen, Alice, Daniel Lamarre, Guy Poirier, Gérard Gradwohl, and Gilbert de Murcia. "Localization of the Zinc-Binding Sites in the DNA-Binding Domain of the Bovine Poly(ADP-Ribose) Polymerase." In ADP-Ribose Transfer Reactions. Springer US, 1989. http://dx.doi.org/10.1007/978-1-4615-8507-7_17.

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Srivastava, Swati, and Himansu Kumar. "Recent Advancements in Ribosome Binding Site Prediction, Ribosome Profiling, and Structural Analysis in Prokaryotes." In Microbial Omics in Environment and Health. Springer Nature Singapore, 2024. http://dx.doi.org/10.1007/978-981-97-1769-9_14.

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Ballesta, Juan P. G. "The Structure of the Antibiotic Binding Sites in Bacterial Ribosomes." In The Translational Apparatus of Photosynthetic Organelles. Springer Berlin Heidelberg, 1991. http://dx.doi.org/10.1007/978-3-642-75145-5_15.

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Nierhaus, K. H., H. J. Rheinberger, U. Geigenmüller, et al. "Three tRNA Binding Sites Involved in the Ribosomal Elongation Cycle." In Springer Series in Molecular Biology. Springer New York, 1986. http://dx.doi.org/10.1007/978-1-4612-4884-2_26.

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Rheinberger, H. J., A. Gnirke, H. Saruyama, P. Wurmbach, and K. H. Nierhaus. "Three Ribosomal tRNA-Binding Sites Involved in the Elongation Process." In Gene Manipulation and Expression. Springer Netherlands, 1985. http://dx.doi.org/10.1007/978-94-011-6565-5_33.

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Rodnina, Marina V., Rainer Fricke, and Wolfgang Wintermeyer. "Kinetic Fluorescence Study on EF-Tu-Dependent Binding of Phe-tRNAPhe to the Ribosomal a Site." In The Translational Apparatus. Springer US, 1993. http://dx.doi.org/10.1007/978-1-4615-2407-6_30.

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Draper, David E. "RNA-protein interactions in ribosotnes." In RNA-Protein Interactions. Oxford University PressOxford, 1995. http://dx.doi.org/10.1093/oso/9780199635054.003.0004.

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Abstract In recent years, the functional role of ribosomal RNAs in protein synthesis has received a great deal of attention, as domains of highly conserved structure have been identified with the decoding site, the peptidyl transferase active centre, binding sites for the elongation factors, and other functional centres of the ribosome (1). Now that a large database of ribosomal protein sequences is available, it is also apparent that many of the ribosomal proteins are as highly conserved as the rRNAs, including many of the proteins which bind directly and independently to the RNA (2-4). The b
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Liljas, A. "Ribosome Binding Site." In Encyclopedia of Genetics. Elsevier, 2001. http://dx.doi.org/10.1006/rwgn.2001.1127.

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Liljas, A. "Ribosome Binding Site." In Brenner's Encyclopedia of Genetics. Elsevier, 2013. http://dx.doi.org/10.1016/b978-0-12-374984-0.01338-3.

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Conference papers on the topic "Ribosome binding sites"

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Małkiewicz, A. J., M. Marszałek, A. B. Miśkiewicz, E. Sochacka, R. Guenther, and P. F. Agris. "Site-specifically modified sequences of human tRNA3Lys and E. coli tRNALys anticodon arms: synthesis and binding to ribosome." In XIth Symposium on Chemistry of Nucleic Acid Components. Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, 1999. http://dx.doi.org/10.1135/css199902328.

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Singatulina, A. S., M. V. Sukhanova, and O. I. Lavrik. "FACTOR HPF1 REGULATES THE ACTIVITY OF POLY(ADP-RIBOSE)POLYMERASES 1 AND 2 AND THE FORMATION OF POLY(ADP-RIBOSE)-CONTAINING COMPARTMENTS WITH THE PARTICIPATION OF THE RNA-BINDING PROTEIN FUS." In X Международная конференция молодых ученых: биоинформатиков, биотехнологов, биофизиков, вирусологов и молекулярных биологов — 2023. Novosibirsk State University, 2023. http://dx.doi.org/10.25205/978-5-4437-1526-1-281.

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Poly(ADP-ribose) polymerases 1 and 2 (PARP1/2) synthesize poly(ADP-ribose) (PAR) by covalently modifying a number of proteins involved in DNA/RNA metabolism, including themselves. PARP1/2 are key regulators of DNA repair via autopoly(ADP-ribosyl)ation at the site of DNA damage. The study of factors that modulate PARP1/2 activity in response to genotoxic stress is an important task in modern biology.
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Hu, Jun, and Jing Zhang. "Co-occurrence of core of binding sites for transcription factors in intronic region of Saccharomyces cerevisiae ribosomal protein genes." In 2010 International Conference on Bioinformatics and Biomedical Technology. IEEE, 2010. http://dx.doi.org/10.1109/icbbt.2010.5479005.

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Reports on the topic "Ribosome binding sites"

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Ostersetzer-Biran, Oren, and Jeffrey Mower. Novel strategies to induce male sterility and restore fertility in Brassicaceae crops. United States Department of Agriculture, 2016. http://dx.doi.org/10.32747/2016.7604267.bard.

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Abstract Mitochondria are the site of respiration and numerous other metabolic processes required for plant growth and development. Increased demands for metabolic energy are observed during different stages in the plants life cycle, but are particularly ample during germination and reproductive organ development. These activities are dependent upon the tight regulation of the expression and accumulation of various organellar proteins. Plant mitochondria contain their own genomes (mtDNA), which encode for rRNAs, tRNAs and some mitochondrial proteins. Although all mitochondria have probably evo
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Elroy-Stein, Orna, and Dmitry Belostotsky. Mechanism of Internal Initiation of Translation in Plants. United States Department of Agriculture, 2010. http://dx.doi.org/10.32747/2010.7696518.bard.

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Original objectives Elucidation of PABP's role in crTMV148 IRES function in-vitro using wheat germ extract and krebs-2 cells extract. Fully achieved. Elucidation of PABP's role in crTMV148 IRES function in-vivo in Arabidopsis. Characterization of the physical interactions of PABP and other potential ITAFs with crTMV148 IRES. Partly achieved. To conduct search for additional ITAFs using different approaches and evaluate the candidates. Partly achieved. Background of the topic The power of internal translation via the activity of internal ribosomal entry site (IRES) elements allow coordinated sy
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