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Dissertations / Theses on the topic 'Ribosome binding sites'

Author: Grafiati

Published: 4 June 2021

Last updated: 25 July 2025

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1

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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2

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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3

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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4

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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5

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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6

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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7

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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8

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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9

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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10

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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11

Mawn, Mary V. "Inhibition of protein synthesis in Escherichia coli by expression of RNAs containing multiple ribosome binding sites." 2000. https://scholarworks.umass.edu/dissertations/AAI9978525.

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Biologically synthesized poly(α,L-glutamic acid) (PLGA) can be chemically modified to form monodisperse poly(γ-benzyl α,L-glutamate) (PBLG). This material shows rare smectic ordering where macromolecular rods organize into highly-ordered layers. Analysis of PBLG has been hindered by low level biosynthesis of PLGA. An unusual feature of PLGA expression is that its accumulation is inversely related to the levels of its mRNA. This phenomenon has been investigated with the objective of improving the bioproduction of PLGA. PLGA was expressed as a C-terminal fusion with dihydrofolate reductase (DHFR

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12

Kung, Yu An, and 龔俞安. "Roles of far upstream element binding protein 1 and 2 on viral versus cellular internal ribosome entry sites." Thesis, 2009. http://ndltd.ncl.edu.tw/handle/19171670844609235153.

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碩士<br>長庚大學<br>醫學生物技術研究所<br>97<br>The 5’ untranslation region (5’UTR) of enterovirus 71 (EV71) contains internal ribosome entry site (IRES) that directs the initiation of viral protein translation. In addition to viral IRES, numerous cellular mRNAs , such as cellular human immunoglobulin heavy chain-binding protein (BiP), c-myc and cyclin D1 have been reported to contain IRES . Furthermore, many cellular IRES have also been found to be activated upon stress, such as virus infection. Several IRES trans-acting factors (ITAFs) for EV71 have been identified in our previous study, including far upst

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13

Zhang, Houjin. "Nucleotide analog interference mapping of TFIIIA and ribosomal protein L5 binding sites on 5S rRNA." 2005. http://etd.nd.edu/ETD-db/theses/available/etd-11282005-220114/.

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Thesis (Ph. D.)--University of Notre Dame, 2005.<br>Thesis directed by Paul W. Huber for the Department of Chemistry and Biochemistry. "November 2005." Includes bibliographical references (leaves 120-130).

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14

Dieterich, Christoph, Steffen Grossmann, Andrea Tanzer, et al. "Comparative promoter region analysis powered by CORG." 2005. https://ul.qucosa.de/id/qucosa%3A32449.

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Background Promoters are key players in gene regulation. They receive signals from various sources (e.g. cell surface receptors) and control the level of transcription initiation, which largely determines gene expression. In vertebrates, transcription start sites and surrounding regulatory elements are often poorly defined. To support promoter analysis, we present CORG http://corg.molgen.mpg.de, a framework for studying upstream regions including untranslated exons (5' UTR). Description The automated annotation of promoter regions integrates information of two kinds. First, statistically sig

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15

Kung, Yu An, and 龔俞安. "Downregulation of Enterovirus 71 Internal Ribosome Entry Site-driven Translation via Far Upstream Element Binding Protein 2 Ubiquitination." Thesis, 2017. http://ndltd.ncl.edu.tw/handle/29112406638423496908.

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16

Romanowska, Julia. "Comparing physical properties of aminoglycoside antibiotics' binding sites in RNA and proteins." Doctoral thesis, 2012. http://depotuw.ceon.pl/handle/item/79.

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Aminoglycoside antibiotics have been in use for more than 60 years, helping combat severe bacterial infections. Due to this long time of usage, more and more bacteria become resistant to one or several drugs from this group. This spread of resistant species is alarming and additionally, there is little knowledge about the mechanisms of bacterial resistance. In order to broaden our understanding of how bacteria combat aminoglycosides, we performed computer simulations of various molecules that bind aminoglycosides in a bacterial cell: (i) the primary binding site, called the A-site and located

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17

Arandkar, Sharath Chandra. "Characterization of the Cis and Trans Acting Factors that Influence p53 IRES Function." Thesis, 2012. http://etd.iisc.ac.in/handle/2005/3243.

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p53 is a nodal tumor suppressor protein that acts as a major defense against cancers. Approximately 50% of human tumours have mutations in p53 gene. Among its myriad features, the most distinctive is the ability to elicit both apoptotic death and cell cycle arrest. p53 has several isoforms. Most of them are produced by either internal promoter activity of the gene or alternate splicing of the pre-mRNA. Apart from these mechanisms, p53 mRNA has also been shown to be translated into two isoforms, the full-length p53 (FL-p53) and a truncated isoform ΔN-p53, which acts as a dominant-negative inhib

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18

Arandkar, Sharath Chandra. "Characterization of the Cis and Trans Acting Factors that Influence p53 IRES Function." Thesis, 2012. http://hdl.handle.net/2005/3243.

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p53 is a nodal tumor suppressor protein that acts as a major defense against cancers. Approximately 50% of human tumours have mutations in p53 gene. Among its myriad features, the most distinctive is the ability to elicit both apoptotic death and cell cycle arrest. p53 has several isoforms. Most of them are produced by either internal promoter activity of the gene or alternate splicing of the pre-mRNA. Apart from these mechanisms, p53 mRNA has also been shown to be translated into two isoforms, the full-length p53 (FL-p53) and a truncated isoform ΔN-p53, which acts as a dominant-negative inhib

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19

Hung, Chuan Tien, and 洪傳典. "Additive Promotion of Viral Internal Ribosome Entry Site-Mediated Translation by Far Upstream Element-Binding Protein 1 and an Enterovirus 71-Induced Cleavage Product." Thesis, 2017. http://ndltd.ncl.edu.tw/handle/71127200117644629146.

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20

Drygin, Denis. "Studies of the complex of ribosomal protein L1 with its binding site in 23S rRNA: Modification -interference, mutagenesis and crosslinking." 2002. https://scholarworks.umass.edu/dissertations/AAI3039352.

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Interaction of ribosomal protein L1 and the 23S rRNA plays an important role in both the structure and biological activity of the Escherichia coli ribosome. We have minimized the binding site for protein L1 on the 23S rRNA to a 32-nucleotide fragment consisting of helix 77, helix 78, and the conserved sequences that interconnect them. Filter-binding, modification-interference and manganese rescue experiments were used do demonstrate (1) that the absence of a 2′-OH group at position 2122 can disrupt protein L1-23S rRNA interaction, but only if certain other deoxyribonucleotides are present in t

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21

Chen, Shih-Yuan, and 陳仕元. "Molecular Dynamics Study and Binding Free Energy Calculation on Recognition and Interaction Between Antibiotics and Oligonucleotides: (I) Mithramycin and DNA (II) Aminoglycosides and Ribosomal RNA A-Site." Thesis, 2009. http://ndltd.ncl.edu.tw/handle/87189327231034454761.

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博士<br>國立清華大學<br>分子醫學研究所<br>98<br>Molecular dynamics (MD) simulations allow detail analysis of structural dynamics of atomic–level phenomena such as binding recognition fundamental in Biology field. Binding interaction involved between (bio) –molecules can be evaluated by binding free energy calculation base on the law of thermodynamics. Conformational flexibility essential for investigating dynamic property can be estimated by calculating conformational entropy such as principal components analysis. Combination with these techniques can provide reasonable explanations for atomic–level phenomen

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22

Dhar, Debojyoti. "Regulation Of Interferon Regulatory Factor-2 mRNA Translation By 'IRES' Element : Possible Role Of trans Acting Factors." Thesis, 2007. http://etd.iisc.ac.in/handle/2005/607.

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Cellular response to various stress conditions involves regulation of gene expression by different mechanisms. Translation is the final step in the flow of genetic information and regulation at this level allows an early response to changes in physiological conditions. Initiation of translation is the rate-limiting step of protein synthesis and hence is tightly regulated. Translation initiation in mammalian cells is mainly by “cap dependent pathway” wherein the 5’methyl guanosine “cap” structure is recognized by certain canonical initiation factors along with 40S ribosomal subunit and the comp

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23

Dhar, Debojyoti. "Regulation Of Interferon Regulatory Factor-2 mRNA Translation By 'IRES' Element : Possible Role Of trans Acting Factors." Thesis, 2007. http://hdl.handle.net/2005/607.

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Cellular response to various stress conditions involves regulation of gene expression by different mechanisms. Translation is the final step in the flow of genetic information and regulation at this level allows an early response to changes in physiological conditions. Initiation of translation is the rate-limiting step of protein synthesis and hence is tightly regulated. Translation initiation in mammalian cells is mainly by “cap dependent pathway” wherein the 5’methyl guanosine “cap” structure is recognized by certain canonical initiation factors along with 40S ribosomal subunit and the comp

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24

Shwetha, S. "Host-Pathogen Interactions in Hepatitis C Virus Infection : Deciphering the Role of Host Proteins and MicroRNAs." Thesis, 2015. http://etd.iisc.ac.in/handle/2005/3858.

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Host-pathogen interactions in Hepatitis C Virus infection: Deciphering the role of host proteins and microRNAs Hepatitis C virus (HCV) is a positive sense single stranded RNA virus belonging to the Hepacivirus genus of the Flaviviridae family. HCV genome consists of a single open reading frame flanked by highly structured 5‟ and 3‟ untranslated regions (UTRs) at both ends. Unlike cellular mRNAs, HCV RNA translation is independent of the cap structure and is mediated by an internal ribosomal entry site (IRES) present in the 5‟UTR. HCV replication begins with the synthesis of a complementary ne

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25

Shwetha, S. "Host-Pathogen Interactions in Hepatitis C Virus Infection : Deciphering the Role of Host Proteins and MicroRNAs." Thesis, 2015. http://etd.iisc.ernet.in/2005/3858.

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Host-pathogen interactions in Hepatitis C Virus infection: Deciphering the role of host proteins and microRNAs Hepatitis C virus (HCV) is a positive sense single stranded RNA virus belonging to the Hepacivirus genus of the Flaviviridae family. HCV genome consists of a single open reading frame flanked by highly structured 5‟ and 3‟ untranslated regions (UTRs) at both ends. Unlike cellular mRNAs, HCV RNA translation is independent of the cap structure and is mediated by an internal ribosomal entry site (IRES) present in the 5‟UTR. HCV replication begins with the synthesis of a complementary ne

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