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 889 for “"Binding site"”.
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Targeting the CD4 Binding Site of HIV
… in mice. 3BNC60 is a bNAb that targets the CD4 binding site (CD4bs) of HIV-1 and belongs to the IgHV1-2 class of broadly neutralizing CD4bs antibodies. In the first part of my thesis I will describe the evolution of the HIV-1 antibody response in GLVH and MuVH mice upon immunization. We …
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Improving protein docking with binding site prediction
… for protein-ligand and protein-protein binding site prediction and applying these predictions to improve protein-protein docking. First, we develop an automated approach LIGSITEcs to predict protein-ligand binding site, based on the notion of surface-solvent-surface events and the degree …
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Novel pharmacophore clustering methods for protein binding site comparison
… with other entities (ligands) through specific binding sites on their surface. Comparison of protein binding sites has potential benefits in many research fields, including drug promiscuity studies, polypharmacology and immunology. While multiple methods have been proposed for comparing binding …
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Conformational analysis of antibody binding site using EDMA methods /
… in three-loop assembly, CDR loops of antibody binding site, are described using EDMA and distance geometry (DGEOM). To the best of our knowledge, it is the first time the EDMA methods are used to analyze conformational samples of molecules obtained from Monte Carlo simulations. Therefore, …
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Molecular characterization of the binding site of nematode GABA-A receptors
… be linked to differences in the putative GABA binding domains. Mutational analysis conducted in this study identified at least one amino acid, positioned near the GABA binding domain, which may partially account for differences in nematode GABA sensitivity. In addition, positions reported to be …
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Systematic determination of a transcription factor/binding site functional interaction landscape
… underlying this hub of regulation. What binding site sequences functionally interact with a given regulator? How does the regulon sample from available functional sequences? How independent is each half of a two part binding site? How do mutations in the regulator impact the regulon? …
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A peptide model for the heparin binding site on Antithrombin III
Thesis: Ph. D., Massachusetts Institute of Technology, Department of Chemistry, 1992
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Sequence Specific Interaction of R17 Coat Protein With Its Rna Binding Site
… RNA bacteriophage R17 coat protein and its RNA binding site for translational repression was studied as an example of a sequence-specific RNA-protein interaction. The binding site consists of fewer than 20 contiguous nucleotides which form a small hairpin. The thermodynamic validity of a simple …
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Identification of Protein-Phosphate Contacts in the R17 Coat Protein Binding Site
Small RNAs of defined length and sequence can be synthesized enzymatically using T7 RNA polymerase and synthetic DNA templates which contain the T7 promoter. The templates are base paired from $-17$ to +1 and contain a long 5$\sp\prime$ overhang. The products of the transcription reactions have the …
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Site-directed mutagenesis of the ATP-binding site in spinach rubisco activase
… the enzyme activity and/or substrate (ATP) binding.
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The role of Orc6 in ORC binding-site switching during helicase loading
… loading of two Mcm2-7 hexameric helicases in opposite orientations to form the Mcm2-7 double hexamer. These Mcm2-7 double hexamers mark sites of eventual bidirectional replication initiation upon entering S-phase, when activation of these helicases and recruitment of DNA polymerases leads to new …
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Analysis of a Proposed Cell Binding Site on Caenorhabditis Elegans Collagen Type Iv
… support and regulation of cell migration and binding. C. elegans body wall muscle col IV consists of two alpha 1 chains and one alpha 2 chain. The human col IV molecule has a cell binding site (CBS) composed of aspartate (D) on each alpha 1 chain and arginine (R) on the alpha 2 chain that form …
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An Analysis of Bacteriophage Lambda Site-Specific Recombination Using IHF Binding Site Mutants
… of bacteriophage lambda. Mutations of the three sites to which this protein binds within the lambda attachment site were constructed using oligonucleotide-directed site-specific mutagenesis and were ananlysed for their effects on site-specific recombination. One group of mutations had alterations …
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Changing protein-DNA interactions promote ORC binding site exchange during replication origin licensing
… replication. ORC initiates this process by binding to a high-affinity DNA binding site to load the first Mcm2-7 hexamer. Subsequently, ORC transitions to bind a secondary, inverted binding site to load the second Mcm2-7 in the opposite orientation. The precise molecular mechanism of this …
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Application of simulation methods for the identification of allosteric binding site in human glucokinase
Allosteric binding site, in generic terms, refers to a binding site distinct from the active site, where binding of an effector can enhance or decrease enzyme's activity. From a drug design point of view targeting allosteric binding sites can offer advantages in terms of selectivity, saturability, …
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New insights into the binding site formation and the performance of molecularly imprinted polymers
… process. This research focuses on understanding binding site formation and performance, and improvement of the MIPs. Chapter 1 introduces the concept of the MIPs, and binding isotherm and affinity distribution of heterogeneous binding sites in the MIPs. Chapter 2 describes fundamental studies …
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De Novo Transcription Factor Binding Site Discovery: A Machine Learning And Model Selection Approach
… positional distribution of transcription factor binding sites (TFBS) to the problem of TFBS discovery. As alternate measures of positional specificity, log-likelihood ratios for the three models are calculated and treated as features to classify TFBSs as biologically relevant or irrelevant. As a …
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Molecular characterization of a sphingomyelin binding site in the vacuolating cytotoxin of H. pylori
… unknown. Molecular modeling of unrelated SM-binding proteins suggests that specific binding occurs through tryptophan rich aromatic clusters located in solvent exposed peptide loops between β-sheet domains. Structural comparison of these proteins with VacA led to the identification of a …
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Pyridoxylation of the essential lysines in the heparin-binding site of bovine platelet factor 4.
… of bovine platelet factor 4 essential to heparin-binding activity have been determined. The protein was labelled by pyridoxal 5$\sp\prime$-phosphate and reduced by sodium borohydride. Three moles of lysine residues are labelled per mole of platelet factor 4. This resulting modified protein …
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