Global ETD Search
Search theses and dissertations gathered from participating repositories worldwide. Every result links back to the library that holds it. No account is needed.
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Showing 1 to 20 of 22 for “"Cooperative binding"”.
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Enhancing the cooperative binding properties of1,1'-bis(1,2,3,4-tetrahydroisoquinolines)
… ligands with unusual but predictable ligand binding properties, particularly cooperativity. The introduction of ω-aminoalkyl, ω-azidoalkyl, ω-alkynyl and ω-alkenyl groups onto the nitrogens of the reduced bisisoquinoline core was conducted with the intention of broadening the scope of the …
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Regulation of DnaA as a transcription factor by modulation of cooperative binding, and by arrA, an antisense RNA
DnaA is both the bacterial replication initiator and a transcription factor. Both activities are highly conserved and closely regulated. The mechanisms regulating its replication initiation activity have been well studied. Most organisms regulate both the abundance DnaA protein and its activity …
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Studies on the operator-repressor-effector interactions in the glp regulon of Escherichia Coli K-12
… repressor (GlpR). Comparison of the repressor binding affinity for consensus and altered consensus operator regions showed that positions 3, 4, 5, 7 and 8 bp removed from the center of operator symmetry are most important for repressor binding. Cooperative binding of repressors to tandem …
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Analysis of the roles of ligand and DNA binding in estrogen receptor action
… and ER concentration, and is likely due to the cooperative binding of ER to adjacent estrogen response elements (EREs).
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Progress towards a highly efficient and accurate platform for enantiomeric excess determination
… error was observed. Additionally, potential cooperative binding to the multicomponent assembly was investigated. Furthermore, this work included some preliminary results for a concurrent sensing platform for molecules with chiral amine and alcohol moieties.
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Action at a distance for specific repression of the glpD and glpTQ genes, and organization of the glpEGR genes of Escherichia coli K-12
… respectively. The glpD operon is controlled by cooperative binding of glp repressor (GlpR) to tandem operators that cover the -10 promoter element and 30 bp downstream of the transcription start site. The glpACB-glpTQ operons operons are controlled by GlpR binding to operators that overlap the …
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Regulation of DNA replication and the replication initiator, DnaA, in Bacillus subtilis
… inhibitor, YabA, binds to DnaA and prevents its cooperative binding at the origin. In addition to its role in replication initiation, DnaA also directly regulates expression of several genes. YabA has been shown to inhibit DnaA binding at several promoters but its effect on DnaA-mediated gene …
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Oct4 and Sox2 regulate methylation at the Igf2/H19 imprinting control region
… with mutations in one of the pair of octamer binding sites within the ICR. Using a tissue culture system, we found that both octamers were required for transgene hypomethylation in F9 cells and that Oct4 was present at the endogenous ICR. In addition, each of the octamers is flanked by a …
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Calorimetric studies of small-molecule adsorption to carbon nanotubes
… agrees with previous studies indicating that CNT binding energy depends upon the polarizability of the ligand. Molecules with large CNT binding affinity have potential for use in CNT-based sensing applications, serving to anchor analyte receptors to the surface of CNTs. In this context, a …
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Analysis of Structure-Function Relationships in *Lambda and HK022 Site -Specific Recombination
… a three-dimensional model of the Lambda Int core-binding (CB) domain. The model suggests that all prokaryotic Tyrosine recombinases share a common CB domain fold, and facilitates interpretation of pre-existing genetic and biochemical data by providing a structural framework within which mutant …
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X-Ray crystal structure of a ribosomal protein S6, S15, S18 : rRNA complex from T. thermophilus, and investigation of conformational changes in 16S rRNA fragments from B. stearothermophilus during ribonucleoprotein assembly
… proteins S6, S15, S18, and a minimal rRNA binding site (T4 RNP) containing two different three-helix junctions was solved to 2.6 A. The protein S15 contains four bundled a-helices and binds the rRNA along the minor groove of helix 22 and contacts elements of both three-helix rRNA junctions. …
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Estimating transcription factor binding properties in human cell lines using statistical methods and genomics datasets
… chromatin accessibility, CpG methylation and cooperative binding with other transcription factors or themselves also impacts transcription factor binding. The era of high throughput sequencing has brought large amounts of genomic data, including chromatin immunoprecipitation and sequencing …
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Computational Models of Function and Evolution of cis-Regulatory Sequences
… blocks of CRMs, called transcription factor binding sites (TFBSs), coordinate to drive gene expression is unclear. My thesis is focused on predicting the location of CRMs in genomes and understanding their function and evolution through computational methods. The first part of my thesis …
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Dissecting Roles for the Macromolecular Machinery Involved in Neurotransmitter Release
… and activating/inhibiting properties. I observed cooperative interactions between Complexin, the SNARE complex, and lipids by forming SNARE complexes anchored on nanodiscs and liposomes. Such cooperative binding of Complexin to membranes and SNAREs may be critical for releasing the inhibition …
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Weak intermolecular interactions as binding probes and analytical tools
… supramolecular structures are often involved in cooperative binding events to guest molecules in which they display enhanced affinity. This dissertation describes a series of studies aimed at gaining a deeper understanding of the fundamental intermolecular interactions involved in these binding …
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Using Chemically Modified Oligonucleotides to Modulate Gene Expression, Treat Genetic Diseases, and Probe Novel Mechanisms of RNA Interference
… Selectivity is achieved through preferential cooperative binding of multiple RISC units to the longer poly-CAG tract on the mutant HTT mRNA versus that of the wild-type. Structural-activity relationship (SAR) studies showed that several ss-siRNAs tolerated significant structural modifications …
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Computational Studies on R67 Dihydrofolate Reductase: An Investigation Into Its Unique Binding Patterns
… of the productive complex, this enzyme exhibits binding cooperativity. Unlike other allosteric enzymes which achieve binding cooperativity through conformational changes, this enzyme does not appear to undergo any backbone alterations upon ligand binding. Therefore, a different mechanism must be …
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Mirroring Enzymes: The Role of H-Bonding In HQuin-BAM Catalyzed Asymmetric Aza-Henry Reactions: A DFT Study into the Reactivity, Mechanism, and Origins of Selectivity
… governed the relative orientation of substrate binding. Attracted by this well-defined mechanistic investigation, the other important aspect of my PhD research addressed a detailed theoretical analysis accounting for the observed selectivity in diastereoselective versions of this reaction. A …
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Methods to program and to probe RNA tertiary structure with nucleic acid origami
… sites. For this complex, I verified stable, cooperative binding, and characterized the 3D structure with cryo-EM, which confirmed binding at all three sites and yielded a 17-Å resolution reconstruction of the tRNA. I also outlined a high-throughput workflow to probe the unknown tertiary …
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Stochastic Modeling and Simulation of Multiscale Biochemical Systems
… this dissertation simplifies the fundamental cooperative binding mechanism by a stochastic Hill equation model with optimized system parameters. Considering that many parameter vectors generate similar system dynamics and results, this dissertation proposes a general α-β-γ rule to return an …
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