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 “"Functional Sites"”.
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Insights into the evolution of protein domains give rise to improvements of function prediction
… of little understood function, as well as on functional sites of protein domains in general. Glucosaminidases (GlcNAcases) represent key enzymes in signal transduction pathways. Together with glucosamine transferases, they serve as molecular switches, similar to kinases and phosphatases. …
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Knowledge discovery and modeling in genomic databases
… the consensus and degeneracy features of the functional sites including protein-translation start sites, mRNA splicing junction donor and acceptor sites in vertebrate genes. The HMM system based on the developed models is fully trained using an expectation maximization (EM) algorithm and the …
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Star Polymers and Dendrimers Based on Highly Functional Resorcin- and Pyrogallolarenes
… with a varying number and varying type of functional sites and their precise characterization by modern NMR techniques and single crystal X-ray diffraction. Second: Synthesis of well-defined star polymers and dendrimers with different number of arms and accordingly dendrons, based on …
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Improving Profile Similarity Search and Alignment of Protein Sequences
… motifs, the same structure folds, and similar functional sites. Current sequence-based homology search methods are still unable to detect many similarities evident from protein spatial structures. We present a new method, COMPADRE, to assess the relationship between the query sequence and a hit …
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Protein structure prediction and structure-based protein function annotation
… usually provide more clues on evolution of functionally related proteins. In this dissertation, I study the design of three bioinformatics modules that form a new hierarchical approach for structure prediction and function annotation of proteins based on sequence-to-structure-to-function …
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Investigations of Local Unfolding Like Conformational Excursions in the Native State of Adenylate Kinase
… distortions connecting the mutated and the functional sites. Secondly, the results reveal a general strategy for thermal adaptation that allows enzymes to modulate binding affinity by controlling the amount of local unfolding in the native-state ensemble. These findings open new avenues for …
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Bioengineered surfaces and hydrogels for specific cell capture and release from whole blood
… presents the development and evaluation of a functional hydrogel coating that supplements microfluidic capture devices to enable both specific capture and release. The hydrogels are formed by ionically crosslinking a microscale pre-functionalized alginate film on top of the capture substrate. …
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Development and Optimization of a Clustering Process that Utilizes Active Site Features to Identify Functionally Relevant Groups Within Protein Superfamilies
… and efficient computational methods to define functional relationships is essential. Protein similarity networks have emerged as a simple, high-throughput method for defining protein relationships, but sequence-based techniques often inaccurately define molecular function details. Active site …
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Examination of HIV-1 diversity and evolution by a bioinformatics approach
… Los Alamos Sequence Database. I identified PS sites, investigated PS patterns, correlated PS with the known functional sites of the two proteins, calculated frequencies of HLA alleles targeting CTL epitopes, and compared PS patterns among major subtypes. The results showed that PS pressure was …
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PLASTICITY IN PROTEIN SEQUENCE-FUNCTION RELATIONSHIPS
Allostery is defined as the functional regulation at one site in a protein by activity at a distant site. Because of the ubiquitous occurrence and diverse cellular roles of allosteric proteins, designing novel allosteric proteins is of great interest for applications in synthetic biological and …
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Insights into protein function from evolutionary and conformational dynamics
… testable hypotheses about proteins with multiple functional sites for the design of non-competitive protein inhibitors. The third study asks, "What is the consequence of allosteric cooperation between the tandem binding sites in a class of proteins that bundle filamentous actin (F-actin)?" Through …
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Biochemical Characterization of CXCR4 Interactions With HIV -1, Natural Ligands and De Novo Designed Inhibitors
… Whereas the overlap between HIV-1 and SDF-1alpha functional sites on the extracellular domains of CXCR4 has been well documented, it is yet to be determined whether there are sites in CXCR4 important for HIV-1 and/or SDF-1alpha functions and, if such sites do exist, whether they are overlapping or …
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Isolation and characterization of latex-specific promoters from Papaver somniferum L.
… its expression pattern. To assess the functional sites within the DIOX promoter, deletions were made 1.5 kb and 0.14 kb upstream of the ATG start codon, fused to GUS, and transformed into opium poppy, Arabidopsis thaliana, and tobacco (Nicotiana tabacum). The 2.5 kb DIOX:GUS and 1.5 kb …
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Amide and Ester-Functionalized Humic Acid for Fuel Combustion Enhancement
… hydrocarbon networks with surface and edge functional groups including phenols, carboxylic acids, and epoxides. These naturally occurring molecules are found in brown coal deposits near lignite formations. Humic acid has gained attention from the scientific community as a precursor for …
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Evolutionary patterns of group B Sox binding and function in Drosophila
… binding makes it difficult to identify true functional binding events. Additionally, externalfactors such as chromatin accessibility are known to play a role in determining binding patterns in Drosophila. A comparative approach to transcription factor binding facilitates the use of …
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Structural studies on enzyme active sites
… and one exploring active site commonalities in functionally convergent and divergent enzymes. The first part is a study on catalytic residue conformational variation as captured in snapshots in enzyme crystal structures. The task is to explore active site flexibility and assess its importance as …
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Delineating the Steps of BAX Pore Activation
… in our assays uncovered that this BAX functional suppression was due to bilayer structure alteration rather than a stereospecific protein-cholesterol interaction. Real-time observation of BAX-vesicle binding showed that cholesterol curbs membrane integration by the protein, thus …
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The Influence of HIV-1 Subtype C LTR Genotype on Latency Potential
… r=-0.27). The DNA distance in characterised functional sites from consensus did not correlate with latency potential (Spearman correlation test p=0.67, r=0.14). Our data suggest that HIV-1 LTRs have intrinsic properties which influence latency potential and the proportion of latently infected …
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Insights into transcriptional regulation from natural and induced variation in closely related species
… activity and roles of TF binding within wider functional contexts. The molecular variation is manifested as variation in the sequence context and/or in the binding activity of the TFs, and it may be naturally fixed by evolution among the different species, and/or induced variation among …
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