To see the other types of publications on this topic, follow the link: Site Function.
Dissertations / Theses on the topic 'Site Function'
Create a spot-on reference in APA, MLA, Chicago, Harvard, and other styles
Consult the top 50 dissertations / theses for your research on the topic 'Site Function.'
Next to every source in the list of references, there is an 'Add to bibliography' button. Press on it, and we will generate automatically the bibliographic reference to the chosen work in the citation style you need: APA, MLA, Harvard, Chicago, Vancouver, etc.
You can also download the full text of the academic publication as pdf and read online its abstract whenever available in the metadata.
Browse dissertations / theses on a wide variety of disciplines and organise your bibliography correctly.
1
Pietruszewski, Samantha. "A formal and functional analysis on the ceramic rims of the Little Midden site (8BR1933) : an identification of site function." Honors in the Major Thesis, University of Central Florida, 2010. http://digital.library.ucf.edu/cdm/ref/collection/ETH/id/1479.
Full textAbstract:
This item is only available in print in the UCF Libraries. If this is your Honors Thesis, you can help us make it available online for use by researchers around the world by following the instructions on the distribution consent form at http://library.ucf.edu/Systems/DigitalInitiatives/DigitalCollections/InternetDistributionConsentAgreementForm.pdf You may also contact the project coordinator, Kerri Bottorff, at kerri.bottorff@ucf.edu for more information.Bachelors
Sciences
Anthropology
2
Dou, Chao. "Site-directed mutagenesis as probes for F₁-ATPase function /." Diss., Connect to a 24 p. preview or request complete full text in PDF format. Access restricted to UC campuses, 1997. http://wwwlib.umi.com/cr/ucsd/fullcit?p9812499.
Full text
3
Gold, Nicola Diane. "Computational approaches to similarity searching in a functional site database for protein function prediction." Thesis, University of Leeds, 2003. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.400259.
Full text
4
Jones, Brendan T. (Brendan Taber). "Inhibition of IFN-[gamma] promoter function by site-specific methylation." Thesis, Massachusetts Institute of Technology, 2006. http://hdl.handle.net/1721.1/34188.
Full textAbstract:
Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Biology, 2006.In title on t.p., "[gamma]" appears as the lower-case Greek letter, subscript.
Includes bibliographical references.
When they become activated, naive helper T cells are able to polarize into either THI cells or TH2 cells. Development of naive CD4+ T cells into TH1 cells is characterized by the expression of IFN-y and the silencing of IL-4, while development into TH2 cells is characterized by expression of IL-4 and silencing of IFN-y. Naive helper T cells are hypomethylated at the IFN-y proximal promoter and hypermethylated at the contiguous transcribed region. During THI polarization, the promoter remains hypomethylated, while the transcribed region becomes demethylated. During TH2 polarization, the promoter undergoes progressive de novo methylation while the transcribed region remains hypermethylated. Notably, TH2 de novo methylation occurs at different rates at different CpG positions, with methylation occurring fastest at the CpG located at the -53 position relative to the transcription start site. Methylation at this position inhibits c-Jun, ATF2 and CREB binding in vitro. Consistently, the same factors bind to the unmethylated promoter in a TH1 cell line, but not the methylated promoter in a TH2 cell line. Furthermore, methylation of the proximal promoter at the -53 position alone is sufficient to inhibit promoter activity in transient transfection assays.
(cont.) Thus, the rapid methylation of the -53 CpG at the onset of TH2 polarization helps to prevent IFN-y transcription by directly inhibiting transcription factor binding prior to the extensive methylation of the IFN-y promoter. There are three known mammalian methyltransferase genes: dnmtl, dnmt3a, and dnmt3b. Dnmt3b is not required for the methylation changes that occur at the IFN-y locus during helper T cell polarization. De novo methylation during TH2 polarization is reduced in dnmt3a deficient T cells. Furthermore, helper T cells deficient in the dnmt3a alternative transcript, dnmt3a2, undergo de novo methylation at the IFN-y promoter during TH 1 polarization, and IFN-y expression is inhibited in these T cells. Collectively, this suggests that dnmt3a is required for efficient de novo methylation of the IFN-y promoter during TH2 polarization, and that dnmt3a2 suppresses IFN-y methylation during TH 1 polarization.
by Brendan T. Jones.
Ph.D.
5
Franchini, Patrick Lorenzo Angelo. "Structure/Function in the CD site of parvalbumin : understanding calcium affinity using synthetic single site EF-hand peptides." Thesis, National Library of Canada = Bibliothèque nationale du Canada, 1999. http://www.collectionscanada.ca/obj/s4/f2/dsk1/tape7/PQDD_0020/NQ46344.pdf.
Full text
6
WHITAKER, JASON MATTHEW. "Household Archaeology at Operation 11, Medicinal Trail Site." University of Cincinnati / OhioLINK, 2007. http://rave.ohiolink.edu/etdc/view?acc_num=ucin1196213016.
Full text
7
Falanga, Alessia. "Compensatory relationship between exonic splicing enhancer, splice site and protein function." Thesis, Open University, 2012. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.579797.
Full textAbstract:
The process of pre-mRNA splicing involves the removal of intronic sequences from the pre-mRNA and it is directed by intronic cis acting elements know as the 5' and 3' splice sites that mark the boundaries of the exons. Over the two decades, however, it has become clear that exons encode for auxiliary splicing signals that either enhance or perturb their inclusion in the final mRNA product. It is possible that the evolution of mRNA sequences could be conditioned by the presence of these exonic cis-acting splicing regulatory elements and not mainly by the selection of optimal protein function. To explore this hypothesis, I have investigated how the need for ESE influences the gene evolution of a paralogous gene family, specifically the human Alkaline Phosphatases (ALPs). In this work, I have identified in correspondence to a weak 3'splice site, two ESE sequences in the placental ALP exon 4, and demonstrate that the ESE are necessary for the exon inclusion in the mRNA due to the weak 3 'splice sites. Furthermore, I show that they are absent in the corresponding exon of the non-tissue specific ALP transcript, specifically exon 5 that carries a strong 3' splice site. Most importantly, the localization of the ESEs correspond to an area that in the paralogous non-tissue specific ALP gene differs in amino , acid composition with respect, not only to the placental ALP where I mapped the ESEs but also to the other members of the family, where this area is well conserved. These amino acid changes may represent a possible evolutionary constraint on enzymatic activity, in keeping with this hypothesis, substituting the amino acids in the region of the ESE for those of the paralogous non-tissue specific ALP gene increases the enzymatic activity. Thus splicing-related constraints challenge the primacy of biochemical function in rates of protein evolution.
8
Caffrey, Michael Stephen. "Characterization of cytochrome c structure and function by site-directed mutagenesis." Diss., The University of Arizona, 1991. http://hdl.handle.net/10150/185346.
Full textAbstract:
A dual Rhodobacter capsulatus/Rhodobacter sphaeroides genetic system has been used to study the structure and function of R. capsulatus cytochrome c₂. In the first part of this study, the processing, stability and in vivo, functionality of nine site-directed mutants have been examined. Mutations were designed to test various structural and functional properties of cytochrome c₂ such as redox potential (Y75C, Y75F and Y75S), surface charges (K12D, K14E, K32E and K14E/K32E), and protein conformation (P35A and W67Y). All R. capsulatus cytochrome c₂ mutants, except Y75C and Y75S, were overproduced in both R. capsulatus and R. sphaeroides suggesting that these mutations had no effects on heme attachment and protein stability. Furthermore, all R. capsulatus cytochrome c₂ mutants transcomplement for photosynthetic growth a cytochrome c₂ minus mutant of R. sphaeroides suggesting that these mutations function in vivo. Analysis of the spectroscopic, redox potential, kinetic and stability properties of mutants Y75C and Y75F suggested that R. capsulatus tyrosine 75 or its equivalent in other species plays an important role in formation of a hydrogen bonding network which results in maintaining redox potentials and stability of cytochromes c in general. It was found that the charge mutants exhibited small reductions in redox potentials that were consistent with the substitution of positively charged groups with negatively charged groups. Kinetic analyses of the charge mutant photooxidations by R. sphaeroides reaction centers suggested that the lysine groups surrounding the cytochrome c exposed heme edge are not critical to cytochrome c structure and function but play a role in optimal molecular orientation for electron transfer reactions. In addition, denaturation studies of the charge mutants indicated that lysine groups in the amino terminal alpha helix may be important to cytochrome c₂ stability. Analysis of the spectroscopic, redox potential, kinetic and stability properties of mutants P35A and W67Y suggested that proline 35 and tryptophan 67 of R. capsulatus cytochrome c₂ or their equivalents in other species are important to stability but not critical to the structure, redox potential, and function of cytochromes c in general.
9
Keiler, Kenneth Charles. "Substrate specificity, active-site residues, and function of the Tsp protease." Thesis, Massachusetts Institute of Technology, 1995. http://hdl.handle.net/1721.1/39746.
Full text
10
Gunnoo, Smita B. "Site-specific chemical modification of antibodies for the modulation of function." Thesis, University of Oxford, 2013. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.644879.
Full textAbstract:
Chemical modification of antibodies is critical for many research areas including therapeutic and biotechnological applications. In particular, strategies for site-specific chemical modification via non-natural amino acids forming homogenous immunoconjugates are of interest. The use of fully functional single-domain antibodies derived from naturally occurring heavy chain antibodies in Camelidae species is attractive due to their enhanced properties, which are discussed in this piece of work. In terms of chemical antibody modification, much of the existing research is focused on modification away from binding regions, thus minimising disturbance to antibody function. In this thesis however, modifications within the binding region of the single-domain antibody cAb-Lys3 are described in a site-specific fashion with the aim of modulating binding affinities. An efficient and high yielding method for the expression and purification of cAh-Lys3 is described, followed by the site-specific installation of dehydroalanine, an electrophilic non-natural amino acid, able to react with nucleophiles that are inert to reaction with other proteinogenic amino acids. Then, the use of dehydroalanine as a unique reaction handle is explored. Firstly, the addition of short alkyl chains to dehydroalanine within the binding region of cAb-Lys3 is described with the aim of increasing hydrophobic interactions when binding to antigen.
11
Clark, Angela Tracy. "Structure and function analysis of picornavirus internal ribosome entry site elements." Thesis, University of Leicester, 2003. http://hdl.handle.net/2381/29678.
Full textAbstract:
Picornaviruses have a single-stranded, positive-sense RNA genome. An internal ribosome entry site (IRES) situated within the 5' untranslated region of the genome mediates cap-independent translation of the picornavirus RNA. In an attempt to further understand the mechanism of IRES-mediated translation, it was decided to investigate the role of several nucleotides within the encephalomyocarditis virus IRES which are absolutely conserved among all cardiovirus and aphthovirus IRES elements and in close proximity to the binding site of the translation initiation factor, eIF4GI. Four nucleotides within the J domain were randomised to generate a pool of mutant IRES elements containing up to 256 different sequences. Analysis of this pool, using a cell selection system to isolate functional IRES elements, revealed that the four nucleotides were essential for IRES activity. Furthermore, it was shown that mutations at these nucleotides severely affected the binding of eIF4GI and eIF4A to the IRES. A clear correlation was seen between the activity of the mutant IRES element and its ability to bind eIF4GI/eIF4A. This strongly suggests that the binding of eIF4GI to the IRES is functionally relevant in vivo. It was also shown that the IRES elements from several different hepatitis C virus genotypes could be used within the cell selection system. This is particularly useful since the analysis of HCV within cells is currently restricted. Finally, the role of residue 20 within the swine vesicular disease virus 2A protease was investigated. This residue is known to affect translation of the picornavirus RNA and virus virulence. To analyse the role of residue 20 to the function of 2A, this residue was substituted for each of the 20 amino acids. This revealed that amino acids substitutions were reasonably well tolerated with the exception of proline.
12
Ciofalo, Andrew J. "Maya Use and Prevalence of the Atlatl: Projectile Point Classification Function Analysis from Chichen Itza, Tikal, and Caracol." Master's thesis, University of Central Florida, 2012. http://digital.library.ucf.edu/cdm/ref/collection/ETD/id/5167.
Full textAbstract:
Multiple scholars have briefly discussed the Maya use of the atlatl. Yet, there has never been a decisive encompassing discussion of prevalence and use of the atlatl in the Maya region with multiple lines of support from iconographic and artifactual analyses. This thesis explores the atlatl at Chichen Itza, Tikal, and Caracol Maya sites to prove that atlatl prevalence can be interpreted primarily based on projectile point "classification function" analysis with support from iconographic and artifactual remains. The classification functions are derived from creating mutually exclusive groups of dart points and arrow points by using discrete functional analysis. Discerning between dart and arrow points can be completed with a high degree of accuracy based on maximum shoulder width of lithic points in an assemblage. Because the atlatl and bow complexes have been primarily constructed of perishable materials, the best method to determine the prevalence of atlatl use is by identifying the launcher based on projectile point identification. Using a cross-site comparison of projectile point size, the Maya use and prevalence of the atlatl will be elucidated.ID: 031001285; System requirements: World Wide Web browser and PDF reader.; Mode of access: World Wide Web.; Title from PDF title page (viewed February 26, 2013).; Thesis (M.A.)--University of Central Florida, 2012.; Includes bibliographical references (p. 85-91).
M.A.
Masters
Anthropology
Sciences
Anthropology; Maya Studies
13
Nishijima, Yoshinori. "Effects of single-site and multi-site ventricular pacing on left and right ventricular mechanics and synchrony is there an optimal pacing sequence? /." Connect to resource, 2005. http://rave.ohiolink.edu/etdc/view?acc%5Fnum=osu1126717344.
Full text
14
Lau, Joey. "Implantation-Site Dependent Differences in Engraftment and Function of Transplanted Pancreatic Islets." Doctoral thesis, Uppsala : Acta Universitatis Upsaliensis : Universitetsbiblioteket [distributör], 2008. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-8418.
Full text
15
Harris, Mark Scott. "Project performance as a function of subsystem interdependence for multi-site projects." Thesis, Massachusetts Institute of Technology, 1987. http://hdl.handle.net/1721.1/14819.
Full text
16
Dupureur, Cynthia M. "Structure-function studies in the active site of bovine pancreatic phospholipase A2 /." The Ohio State University, 1992. http://rave.ohiolink.edu/etdc/view?acc_num=osu1487775034179833.
Full text
17
Sillos, Valeria Lucchetti de. "Qualidade de site de governo eletrônico: estudo de caso sobre a aplicação do QFD ao site da SH/CDHU." Universidade de São Paulo, 2009. http://www.teses.usp.br/teses/disponiveis/12/12139/tde-01072009-121639/.
Full textAbstract:
O principal objetivo deste trabalho é avaliar a qualidade de um site de governo eletrônico. Para atingir essa meta, a pesquisa descreve a aplicação da ferramenta Quality Function Deployment, QFD, para melhoria da qualidade do site da Secretaria de Estado da Habitação de São Paulo, SH, e Companhia de Desenvolvimento Habitacional e Urbano, CDHU. CDHU é a empresa do governo do Estado de São Paulo responsável pela execução do plano de habitação de interesse social para o Estado. O QFD foi desenvolvido no Japão, na década de 60, para melhorar a qualidade de produtos industriais desde o projeto. Apesar disso, o foco deste estudo é sua aplicação para melhorar a qualidade do site, apresentando as adaptações necessárias ao modelo original e observando as possíveis limitações de sua aplicação para esse fim. Como ponto de partida para a pesquisa, foram realizadas entrevistas com os profissionais de informática da empresa, responsáveis pelo desenvolvimento e manutenção do site, com outros colaboradores que utilizam diariamente o site da companhia e com o ouvidor da CDHU. Essas entrevistas, juntamente com a revisão bibliográfica, formaram a base para a elaboração de um questionário para avaliar a percepção dos clientes da CDHU sobre o site. O questionário foi aplicado a mutuários da CDHU para captar a voz do cliente e construir a casa da qualidade, principal produto da aplicação do QFD. O QFD mostrou ser uma ferramenta útil para priorização das mudanças a serem feitas no site e para iniciar discussões sobre a necessidade de sistematizar rotinas de teste e de melhoria contínua do site, além da gestão do conteúdo. Este trabalho abrange os temas Qualidade da Informação e Governo Eletrônico e apresenta sugestões de melhoria para o site da SH/CDHU.The main purpose of this study is to evaluate the quality of an e-government website. To achieve that goal, this paper describes the advantages of using the Quality Function Deployment (QFD) tool to improve the quality of Secretaria de Estado da Habitação de São Paulo, SH, and Companhia de Desenvolvimento Habitacional e Urbano, CDHU, website. CDHU is a governmental company of São Paulo state which is responsible for developing urban plans focused on low revenues families. QFD was developed in Japan, in the 60s, to improve the quality of industrial products from the project. Even tough the focus of this study is the use of such managerial tool as a website quality inducer, presenting the necessary adjustments to original QFD model and pointing out some possible limitations of such application. First of all, interviews were conducted with technology information professionals from CDHU, who are in charge for the website development and maintenance; with CDHU workers who access company website daily; and with CDHU ombudsman. These interviews along with bibliography review allowed the development of a questionnaire to evaluate CDHU customers perception on its site quality and performance. The answers captured the voice of the customer and were used to build the house of quality, main deliver of QFD. QFD demonstrated to be powerful tool to help prioritizing desirable changes in the website and also to start PDCA discussions about the site content management. This study covers the Information Quality and E-Government subjects and it also presents improvement suggestions to SH/CDHU website as an answer to clients willing and recommendations.
18
Hill, Erik R. "Cocaine Binding Site from the Structure Function Analysis of the Neurotransmitter Reuptake Transporters." The Ohio State University, 2010. http://rave.ohiolink.edu/etdc/view?acc_num=osu1273590773.
Full text
19
Rusk, Rachel Aline. "Measuring bovine γδ T cell function at the site of Mycobacterium bovis infection." Thesis, Kansas State University, 2017. http://hdl.handle.net/2097/35801.
Full textAbstract:
Master of Science in Biomedical SciencesDepartment of Diagnostic Medicine/Pathobiology
Jodi L. McGill
The causative agent of tuberculosis (TB) in cattle is Mycobacterium bovis (M. bovis). γδ T cells are a unique subset of nonconventional T cells that play major roles in both the innate and adaptive arms of the immune system. Bovine γδ T cells have the capacity for multiple immune functions during infection with M. bovis. However, the alternative functions of γδ T cells as well as the responses of γδ T cells in vivo at the site of infection remain unclear. To identify novel functions for γδ T cells in response to M. bovis infections, RNA sequencing and transcriptomics analysis was completed on peripheral blood γδ T cells isolated from virulent M. bovis-infected cattle. Differentially expressed genes were confirmed with real-time PCR. In an attempt to model in vivo cell-to-cell interactions at the site of infection, γδ T cells were also isolated from naïve and M. bovis-infected calves and co-cultured with autologous, BCG-infected, monocyte-derived macrophages. γδ T cell chemokine and cytokine expression was analyzed via ELISA and real-time PCR. The characteristic lesions of bovine tuberculosis are well-organized pulmonary granulomas. To determine the relevance of the RNA-sequencing and in vitro co-culture results to in vivo infection, tissue samples from granulomatous lesions in the lungs and mediastinal lymph nodes of virulent M. bovis-infected cattle were collected 3 months after infection. mRNA transcripts for γδ T cells expression of-- IFN-γ, IL-17, IL-10, IL-22, and CCL2 were microscopically evaluated within the granulomas using an in situ hybridization system, RNAScope (Advanced Cell Diagnostics Inc.). Co-culture experiments and transcriptomics analysis revealed increased expression of chemokines and various cytokines by γδ T cells responding to M. bovis infection. The novel in situ hybridization assay revealed that cytokine expression by γδ T cells varied within the lesions, with significant levels of CCL2 and IFN-γ, and low expression of IL-10, IL-22, and IL-17 in situ at this time-point after infection. Co-culture experiments also revealed that γδ T cells from virulent M. bovis-infected cattle have the capacity to directly impact the viability of M. bovis in vitro. Our results suggest that γδ T cells accumulate within the granulomas, and influence host immunity to M. bovis by secretion of cytokines and chemokines, and direct cytotoxicity, in response to infected macrophages.
20
Zinn-Justin, Sophie. "Etude structurale du site toxique et de deux sites antigéniques d'une toxine curaremimétique." Châtenay-Malabry, Ecole centrale de Paris, 1993. http://www.theses.fr/1993ECAP0326.
Full textAbstract:
Le but de l'étude présentée dans ce document est de montrer l'apport de la détermination de la structure tridimensionnelle en solution de la toxine extraite du venin du naja nigricollis a la compréhension des mécanismes biologiques dans lesquels la toxine est impliquée. Cette étude comprend trois parties. Dans une première partie, la résolution de la structure tridimensionnelle de la toxine (61 acides amines, 4 ponts disulfure) est présentée. Le repliement de la toxine consiste en 3 boucles principales stabilisées par 3 ponts disulfure et 1 boucle c-terminale de plus petite taille stabilisée par un 4eme pont disulfure. Cette structure est très proche de celle d'une autre toxine de serpent, l'erabutoxine B, telle qu'elle a été déterminée par radiocristallographie. En revanche, aucune des molécules d'eau observées dans le cristal d'erabutoxine B n'a pu être mis en évidence par RMN sur la toxine. L'analyse des vitesses d'échange des protons amide de la toxine a plusieurs températures a permis d'aborder l'étude de la dynamique de la toxine. Dans une deuxième partie, les sites antigéniques correspondant a deux anticorps neutralisant l'activité toxique de la toxine ont été identifies. La comparaison de ces sites avec le site toxique a permis d'élucider les événements moléculaires associes au mécanisme de neutralisation. Dans une dernière partie, la connaissance de la structure du site toxique a permis de tenter de reconstruire ce site au sein d'une plateforme structurale stable et de petite taille
21
Cabas, Mijares Ashly Margot. "Improvements to the Assessment of Site-Specific Seismic Hazards." Diss., Virginia Tech, 2016. http://hdl.handle.net/10919/82352.
Full textAbstract:
The understanding of the impact of site effects on ground motions is crucial for improving the assessment of seismic hazards. Site response analyses (SRA) can numerically accommodate the mechanics behind the wave propagation phenomena near the surface as well as the variability associated with the input motion and soil properties. As a result, SRA constitute a key component of the assessment of site-specific seismic hazards within the probabilistic seismic hazard analysis framework. This work focuses on limitations in SRA, namely, the definition of the elastic half-space (EHS) boundary condition, the selection of input ground motions so that they are compatible with the assumed EHS properties, and the proper consideration of near-surface attenuation effects. Input motions are commonly selected based on similarities between the shear wave velocity (Vs) at the recording station and the materials below the reference depth at the study site (among other aspects such as the intensity of the expected ground motion, distance to rupture, type of source, etc.). This traditional approach disregards the influence of the attenuation in the shallow crust and the degree to which it can alter the estimates of site response. A Vs-κ correction framework for input motions is proposed to render them compatible with the properties of the assumed EHS at the site. An ideal EHS must satisfy the conditions of linearity and homogeneity. It is usually defined at a horizon where no strong impedance contrast will be found below that depth (typically the top of bedrock). However, engineers face challenges when dealing with sites where this strong impedance contrast takes place far beyond the depth of typical Vs measurements. Case studies are presented to illustrate potential issues associated with the selection of the EHS boundary in SRA. Additionally, the relationship between damping values as considered in geotechnical laboratory-based models, and as implied by seismological attenuation parameters measured using ground motions recorded in the field is investigated to propose alternative damping models that can match more closely the attenuation of seismic waves in the field.Ph. D.
22
Dharmarajan, Lakshmi. "Structure-Function Studies on Two Phosphoenolpyruvate Carboxylases." Diss., Virginia Tech, 2010. http://hdl.handle.net/10919/77040.
Full textAbstract:
Phosphoenolpyruvate carboxykinase (PEPCK) and phosphoenolpyruvate carboxylase (Pepc) are two important CO₂-fixation enzymes which share a similar reaction mechanism. Both operate through a lid-gated active site and have a hypothesized enol-pyruvate intermediate in their catalytic pathway. While PEPCK is an important metabolic enzyme in animals and plays a broad role in cataplerosis, gluconeogenesis and glyceroneogenesis, Pepc reaction in plants catalyzes the first committed step in CO₂ fixation in CAM and C₄ plants via Rubisco. We are studying the structure-function aspects of both enzymes, with a goal of discovering new elements in these enzymes which can modulate catalysis. We have undertaken an interdisciplinary approach for this work and have shown that a combination of experimental and computational techniques can be complementary and can provide novel information.
We have determined that in human PEPCK, Tyr235 forms an anion-quadrupole interaction with the carboxylate of PEP and thus positions the latter with respect to the enzyme-bound Mn²+ for optimal phosphoryl transfer and catalysis. We have also identified Pro82 as a catalytically influential residue in this enzyme. Using molecular dynamics simulations we have noted that absence of ligands induces active-site lid opening in GTP-PEPCKS and we have made the first observation of the intermediary structures of the lid opening event, the dynamics of which is an important element that controls GTP-PEPCK catalysis.
We have determined the first three-dimensional crystal structure of an archaeal-type Pepc, i.e. C. perfringens PepcA. Our experimental data also provide information about the oligomerization of PepcAs and reveal that aspartate inhibits the C. perfringens enzyme competitively compared to the allosteric inhibition in Pepcs. Structure-based modeling has led to the identification of putative aspartate- and bicarbonate-binding residues in C. perfringens PepcA, of which Arg82, His11, Ser201, Arg390, Lys340, Arg342 and Arg344 probably play an important role.Ph. D.
23
Deshpande, Seemantini R. "Evaluation of PM2.5 Components and Source Apportionment at a Rural Site in the Ohio River Valley Region." Ohio University / OhioLINK, 2007. http://rave.ohiolink.edu/etdc/view?acc_num=ohiou1187123906.
Full text
24
Eriksson, Jesper. "Structure-Function Studies of Bacteriophage P2 Integrase and Cox protein." Doctoral thesis, Stockholm University, Department of Genetics, Microbiology and Toxicology, 2005. http://urn.kb.se/resolve?urn=urn:nbn:se:su:diva-683.
Full textAbstract:
Probably no group of organisms has been as important as bacteriophages when it comes to the understanding of fundamental biological processes like transcriptional control, DNA replication, site-specific recombination, e.t.c.
The work presented in this thesis is a contribution towards the complete understanding of these organisms. Two proteins, integrase, and Cox, which are important for the choice of the life mode of bacteriophage P2, are investigated. P2 is a temperate phage, i.e. it can either insert its DNA into the host chromosome (by site-specific recombination) and wait (lysogeny), or it can produce new progeny with the help of the host protein machinery and thereafter lyse the cell (lytic cycle). The integrase protein is necessary for the integration and excision of the phage genome. The Cox protein is involved as a directional factor in the site-specific recombination, where it stimulates excision and inhibits integration. It has been shown that the Cox protein also is important for the choice of the lytic cycle. The choice of life mode is regulated on a transcriptional level, where two mutually exclusive promoters direct whether the lytic cycle (Pe) or lysogeny (Pc) is chosen. The Cox pro-tein has been shown to repress the Pc promoter and thereby making tran-scription from the Pe promoter possible, leading to the lytic cycle. Further, the Cox protein can function as a transcriptional activator on the parasite phage, P4. P4 has gained the ability to adopt the P2 protein machinery to its own purposes.
In this work the importance of the native size for biologically active integrase and Cox proteins has been determined. Further, structure-function analyses of the two proteins have been performed with focus on the protein-protein interfaces. In addition it is shown that P2 Cox and the P2 relative Wphi Cox changes the DNA topology upon specific binding. From the obtained results a mechanism for P2 Cox-DNA interaction is discussed.
The results from this thesis can be used in the development of a gene delivery system based on the P2 site-specific recombination system.
25
Hayhurst, Graham Patrick. "Analysis of the structure-function relationships of cytochrome P450 2D6 by site-directed mutagenesis." Thesis, University of Sheffield, 1997. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.265573.
Full text
26
Lalies, Margaret D. M. "Neurochemical studies of α2-adrenoceptor and imidazoline-2 binding site function in rat brain." Thesis, University of Bristol, 1998. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.285816.
Full text
27
Tian, Meilin. "Structure-function studies of membrane proteins by site-specific incorporation of unnatural amino acids." Thesis, Paris 6, 2017. http://www.theses.fr/2017PA066166.
Full textAbstract:
Les protéines membranaires comme les récepteurs, les canaux ioniques et les transporteurs possèdent des rôles cruciaux dans les processus biologiques tels que la signalisation physiologique et les fonctions cellulaires. La description dynamique et fonctionnelle des structures protéiques est fondamentale pour comprendre la plupart des processus concernant les macromolécules biologiques. L'incorporation, dans des protéines, d'acides aminés non naturels (Uaas) possédant des propriétés physiques ou chimiques spécifiques fournit un puissant outil pour définir la structure et la dynamique de protéines complexes. Ces sondes permettent le suivi et la détection en temps réel de la conformation des récepteurs et des complexes de signalisation. Les approches d'expansion du code génétique ont permis l'incorporation d'Uaas servant de sondes dans des protéines avec une précision moléculaire. L'expansion héréditaire du code génétique peut permettre d'étudier la biologie des protéines de manière systémique.Avec cette stratégie, des Uaas capables de photopontage ont été utilisés pour étudier la relation structure/fonction des Protéines G Couplées aux Récepteurs (GPCR), telles que l'identification de la liaison du ligand ou des interactions protéine-protéine, en détectant les changements dynamiques avec les Uaas spectroscopiques et l'étiquetage bioorthogonal. Sur la base d'applications relativement bien établies d'Uaa dans les GPCR, ici, les analyses fonctionnelles sont combinées à l'incorporation génétique d'un Uaa photosensible spécifique au site, p-azido-L-phénylalanine (AzF) dans d'autres protéines membranaires, pour détecter la protéine, les changements conformationnels et les interactions protéiques. Contrairement à d’autres molécules photosensibles qui permettent aux protéines de répondre à la lumière, l'insertion des Uaas directement dans la chaine d’acides aminés offre des possibilités uniques pour le photo-contrôle de la protéine. Les aspects dynamiques de l'allostérie sont plus difficiles à visualiser que les modèles structuraux statiques. Une stratégie photochimique est présentée pour caractériser la dynamique des mécanismes allostériques des récepteurs NMDA neuronaux (NMDAR). Ces récepteurs appartiennent à la famille des canaux ioniques activés par le glutamate et portent la transmission synaptique excitatrice rapide associée à l'apprentissage et à la mémoire. En combinant le balayage AzF et un test fonctionnel résistant à la lumière, nous avons pu apporter des éléments permettant de mieux comprendre la dynamique des interfaces NTD (N-Terminal Domain des NMDAR) ainsi qu’un nouveau mécanisme de régulation allostérique, améliorant notre compréhension de la base structurale du mécanisme d’activation et de modulation des récepteurs NMDA.Outre l'incorporation de l’Uaa photopontant AzF dans les récepteurs neuronaux pour détecter l'effet fonctionnel, AzF a été appliqué pour piéger des interactions faibles et transitoires entre protéines dans un transporteur d'acides aminés LAT3, impliqué dans le cancer de la prostate. Les techniques de dépistage ont été établies en appliquant un photo-cross-linker positionné dans la protéine pour examiner les interactions entre LAT3 et les interacteurs inconnus et fournir des indices d'identification des partenaires de liaison.Dans l'ensemble, ce travail dévoile de nouvelles informations sur la modulation allostérique de l'activité du récepteur NMDA et sur les interactions protéines-protéines.. Les résultats pourraient fournir de nouvelles informations structurales et fonctionnelles et guider le dépistage de composés thérapeutiques pour des maladies associées au dysfonctionnement de ces protéines membranairesMembrane proteins including receptors, channels and transporters play crucial roles in biological processes such as physiological signaling and cellular functions. Description of dynamic structures and functions of proteins is fundamental to understand most processes involving biological macromolecules. The incorporation of unnatural amino acids (Uaas) containing distinct physical or chemical properties into proteins provides a powerful tool to define the challenging protein structure and dynamics. These probes allow monitoring and real-time detection of receptor conformational changes and signaling complexes. The genetic code expansion approaches have enabled the incorporation of Uaas serving as probes into proteins with molecular precision. Heritable expansion of the genetic code may allow protein biology to be investigated in a system-wide manner.With this strategy, photocrosslinking Uaas have been used to study GPCR structure/function relationship, such as identifying GPCR-ligand binding or protein-protein interactions, detecting dynamic changes with spectroscopic Uaas and bioorthogonal labeling. Based on relatively well-established applications of Uaa in GPCRs, here, functional assays are combined with the site-specific genetic incorporation of a photo-sensitive Uaa, p-azido-L-phenylalanine (AzF) into other membrane proteins, to probe protein conformational changes and protein interactions. Unlike photo-sensitive ligands that enable proteins in response to light, the site-specific insertion of light-sensitive Uaas facilitates directly light-sensitive proteins. Dynamic aspects of allostery are more challenging to visualize than static structural models. A photochemical strategy was presented to characterize dynamic allostery of neuronal NMDA receptors (NMDARs), which belong to the ionotropic glutamate receptor channel family and mediate the fast excitatory synaptic transmission associated with learning and memory. By combining AzF scanning and a robust light-induced functional assay the dynamics of NMDAR N-terminal domain (NTD) interfaces and novel allosteric regulation mechanism were uncovered, improving our understanding of the structural basis of NMDAR gating and modulation mechanism.Besides incorporation of photo-cross-linker AzF into neuronal receptors to detect the functional effect, AzF was used to trap transient and weak protein-protein interactions in an amino acid transporter LAT3, which is critical in prostate cancer. Screening technique was established by applying genetically encoded photo-cross-linker to examine interactions between LAT3 and unknown interactors and provide clues to identify the binding partners.Overall, the work reveals new informations about the allosteric modulation of channel activity and proteins interactions. These light-sensitive proteins facilitated by site-specific insertion of light-sensitive Uaas enable profiling diversity of proteins. The results will provide novel structural and functional information and may guide screening of therapeutic compounds for diseases associated with malfunctioning of these membrane proteins
28
Tjernström, Linnéa. "Function of soil-based on-site wastewater treatment systems - Biological and chemical treatment capacity." Thesis, KTH, Mark- och vattenteknik (flyttat 20130630), 2017. http://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-210716.
Full textAbstract:
On-site wastewater treatment systems are among the main Swedish anthropogenic sources of nutrients causing euthropication of the Baltic Sea. Among on-site systems in Sweden almost half have septic tank treatment followed by a soil-based system, in which the wastewater is treated through soil filtration. In this study a soil based technique for on-site wastewater treatment is studied where wastewater is filtered through a sand filter. Composite samples of influent and effluent at two sand filters in the area of Stockholm are sampled to determine their chemical and biological function and to compare their treatment capacity to requirements. Parameters within the scope of the study are tot-P, NH4-N, DOC, pH, turbidity and dissolved oxygen. Biological function was considered to be good in both systems as nitrification was high and the effluent had sufficient levels of dissolved oxygen suggesting aerobic conditions. Prevailing aerobic conditions in the sand filters would also indicate good reduction of organic substances which is the case for DOC as it was reduced by above 85 % for one site and almost 70 % for the other site. The overall high reduction of organic micropollutants in the systems, reported in another study, also suggests that biological function when it comes to reduction of organic substances is good. On the other hand, chemical function, with respect to reduction of phosphorus, was not sufficient as none of the systems fulfilled the requirements from HaV for normal or high protection level. In the systems tot-P was reduced by 42 and 54 % respectively. A drawback with the method approach used in the study is that the obtained reduction results only can represent the actual situation if variations in incoming and outgoing flow, variations in influent concentrations and magnitude of dilution of effluent compared to daily wastewater load are small. As these are unknown in this case it adds uncertainty to the results.Decentraliserade system för rening av avloppsvatten är bland de huvudsakliga svenska antropogena källorna till näringsämnen som bidrar till övergödning av Östersjön. Bland decentraliserade system i Sverige är nästan hälften system med slamavskiljare följt av ett markbaserat system i vilket avloppsvattnet renas genom infiltration i jord. I denna studie studeras en markbaserad teknik i vilken avloppsvattnet filtreras genom sand, en så kallad markbädd. En fältundersökning gjordes där samlingsprov av ingående och utgående avloppsvatten togs på två markbäddar i Stockholmsområdet för att bestämma deras biologiska och kemiska reningsfunktion samt att jämföra avskiljningen av fosfor i systemen med rekommendationer från HaV. Parametrar som inkluderats i studien är totalfosfor, ammonium-kväve, löst organiskt kol, pH, turbiditet och löst syre. Biologisk funktion ansågs bra i båda markbäddarna eftersom nitrifikationen var hög och utgående vatten hade tillräckliga halter av löst syre vilket implicerar att markbäddarna var väl syresatta. Rådande syrerika förhållanden i markbäddarna antyder också att organiskt material bryts ned avsevärt, vilket är fallet för löst kol som reducerades med mer än 85 % i en av markbäddarna och med nästan 70 % i den andra. Den höga reduktionen av organiska mikroföroreningar som påvisats i markbäddarna i en annan studie tyder också på att biologisk funktion med avseende på avsklijning av organiska substanser är bra. Kemisk funktion, med avseende på avskiljning av totalfosfor, var inte tillräcklig då ingen av markbäddarna levde upp till reduktionskraven från HaV för normal eller hög skyddsnivå. Totalfosfor avskiljdes med 42 respektive 54 % i markbäddarna. En nackdel med metoden som användes i studien är att de resultat som fåtts för avkiljning av de olika parametrarna endast kan representera den verkliga situationen om variationer i in- och utgående flöde samt variationer i ingående vattenkoncentrationer är små och om utspädningseffekten av utgående vatten är försumbar.
29
Carter, Rolinda Louise Raphaelle. "Effects of direct active-site anticoagulants on the fibrinolytic function of coagulation factor Xa." Thesis, University of British Columbia, 2017. http://hdl.handle.net/2429/63386.
Full textAbstract:
Treatment of occlusive clots (thrombi) is important for proper health yet systemic bleeding remains a major complication of thrombolytic therapy. Thus, the utility of agents such as alteplase, the current thrombolytic approved to rapidly lyse thrombi, is limited. As an alternative, our laboratory has found that cleavage products of clotting factor Xa (FXa) can enhance the generation of localized plasmin, the enzyme that degrades and solubilizes clots. This function is stabilized by blocking or chemically modifying the active site of FXa such that FXaβ, the first resulting fragment, persists.
In recent years, direct oral anticoagulants (DOACs) have been approved for the treatment and prevention of venous thromboembolism and stroke in patients with atrial fibrillation. Two agents in this class of drugs, rivaroxaban and apixaban, are direct inhibitors of FXa. This dissertation addresses the effect these two DOACs have on fibrinolysis and FXa fragmentation due to their ability to block the active site of FXa. Results presented in Chapter 3 demonstrate that in normal pooled plasma, rivaroxaban and apixaban enhance clot lysis in a FX- and dose-dependent manner. Downstream effects caused by a potential reduction in thrombin generation were not the basis for the enhancement. Instead, FXaβ persisted in plasma. In purified protein experiments, FXaβ, generated in the presence of rivaroxaban and apixaban, enhanced plasmin generation by binding plasminogen.
Results in chapter 4 showed persistence of FXaβ in rivaroxaban-treated patient samples but not in samples from non-anticoagulated patients and those treated with a thrombin-specific DOAC. A strong correlation between increasing FXaβ amounts and faster fibrinolysis time was shown in rivaroxaban-treated patients with atrial fibrillation, the approved indication in which thrombosis is the least provoked. Fibrinolysis was not, however, dose-dependently enhanced. There was also no statistical difference in fibrinolysis times between rivaroxaban-treated and non-anticoagulated atrial fibrillation patients; an observation attributed to the involvement of potential confounders. Findings in this dissertation may have implications in the use of FXa-specific DOACs as thrombolytic adjuncts and as the anticoagulants of choice in preventing post-thrombotic syndrome, a common long-term morbidity in patients with deep vein thrombosis that may result from delayed or impaired clot dissolution.Medicine, Faculty of
Pathology and Laboratory Medicine, Department of
Graduate
30
Croitoru, Victor. "Study on the Function of Translation Initiation Factor IF1." Doctoral thesis, Stockholm : Department of Genetics, Microbiology and Toxicology, Stockholm University, 2006. http://urn.kb.se/resolve?urn=urn:nbn:se:su:diva-1032.
Full text
31
Woods, Aaron R. "Distribution, Function, And Value Of Parowan Valley Projectile Points." Diss., CLICK HERE for online access, 2009. http://contentdm.lib.byu.edu/ETD/image/etd2905.pdf.
Full text
32
Nickels, Karen. "Food function and status analysis of faunal remains from the Maya site of Pusilhá, Belize /." Diss., Connect to a 24 p. preview or request complete full text in PDF format. Access restricted to UC campuses, 2008. http://wwwlib.umi.com/cr/ucsd/fullcit?p1453677.
Full textAbstract:
Thesis (M.A.)--University of California, San Diego, 2008.Title from first page of PDF file (viewed July 28, 2008). Available via ProQuest Digital Dissertations. Includes bibliographical references (p. 40-44).
33
Huwiler, Simona G. [Verfasser], and Matthias [Akademischer Betreuer] Boll. "Structure and function of the tungsten-containing active site of class II benzoyl-CoA reductases." Freiburg : Universität, 2015. http://d-nb.info/1140735284/34.
Full text
34
Loizzi, Marianna. "Investigation of the function of delta-cadinene synthase with aza-analogues and site directed mutagenesis." Thesis, Cardiff University, 2017. http://orca.cf.ac.uk/110674/.
Full textAbstract:
Terpenes are one of the most structurally varied families of natural products with extraordinary chemical properties that have been exploited for numerous applications. Sesquiterpene synthases are a family of metal-dependent enzymes that catalyse the cyclisation of farnesyl diphosphate (FDP) into a myriad of complex C15-isoprenoid hydrocarbons, the sesquiterpenes. δ-Cadinene synthase (DCS) from Gossypium arboreum (cotton tree) catalyses the formation of δ-cadinene (DCN), a bicyclic intermediate in the biosynthesis of important phytoalexins such us gossypol. Two mechanistic proposals have been made for the formation of δ-cadinene: a 1,10-ring closure mechanism leading to the key intermediate germacradienyl cation, or a 1,6-ring closure leading to theaalpha-bisabolyl carbocation. Previous investigation with fluorinated FDP analogues were in partial agreement with both scenarios and hence it was not possible to distinguish unambiguously between the two possible cyclisation reactions. To investigate the catalytic mechanism of DCS, enantiopure samples of the azaanalogues of alpha-bisabolyl cation and germacradienyl cation were needed. These compounds are designed as stable structural and electrostatic mimics of the putative short-lived carbocationic intermediates generated by terpene synthases, and hence often act as potent reversible competitive inhibitors (low Ki) of these enzymes. Here, the enantioselective total synthesis of R- and S- aza-analogues of the alpha-bisabolyl cation are described as well as the partial racemic synthesis of azagermacradienyl cation. Both enantiomers of aza-bisabolyl cation were goodmimics of α-bisabolene. They were competitive inhibitors of DCS, providing evidence for a 1,6-cyclisation closure. The second part of the project involved the investigation of the role of tryptophan 279 for the desolvation of the active site of DCS and therefore for the formation of DCN. Seven mutants of W279 were created. The data obtained showed that W279 is essential to prevent water from entering the active site and form the hydroxylate terpenoid germacradien-4-ol (GD4ol). Mutagenesis studies yielded a mutant, W279A, capable of making GD4ol as the sole product.
35
Kusano, Masayuki. "Studies on Expression of Recombinant Thermolysin and Engineering of Its Function by Site-directed Mutagenesis." Kyoto University, 2010. http://hdl.handle.net/2433/120457.
Full textAbstract:
Kyoto University (京都大学)0048
新制・課程博士
博士(農学)
甲第15413号
農博第1798号
新制||農||978(附属図書館)
学位論文||H22||N4512(農学部図書室)
27891
京都大学大学院農学研究科食品生物科学専攻
(主査)教授 井上 國世, 教授 安達 修二, 教授 河田 照雄
学位規則第4条第1項該当
36
Sheikh, Qaiser Iftikhar. "Exploring the structure and function of bacterial cytosine specific DNA methyltransferases using site-directed mutagenesis." Thesis, University of Sheffield, 2001. http://etheses.whiterose.ac.uk/10258/.
Full textAbstract:
Point mutations were engineered into the sequence of the multispecific DNA methyltransferase (Mtase) M. SPRI in motif IX, in order to mimic the corresponding motif IX of mono-specific Mtase. A similar approach was adopted to modify the sequence of the monospecific enzyme M. HhaI in motifs IX and X based on the available structure and as a consequence the enzyme regained methylation potential. It was thought that these changes might be sufficient to enable functional exchange of the target recognition domains (TRDs) between a mono- and a multispecific enzyme. However, insertion of various segments of TRD region from M. SPRI into the M. HhaI was not successful (Chapter 4). To establish whether mono- and multispecific Mtases are incompatible in terms of sequence exchanges, a systematic "swapping" of motifs was carried out (Chapter 5). These experiments suggested that there are some enzyme-specific structural interactions between different subunits within each class of Mtases. In second half of this thesis a bacterial two-hybrid system based on the reversible assembly of an engineered form of M. SPRI was developed (Chapter 6). However the Mtase protein does not assemble into an active species until a DNA segment encoding a leucine zipper motif is fused to each of the two halves. Co-transformation of E. coli with the plasmids expressing the C-terminal and N-terminal domains respectively resulted in the abolition of colonies on double antibiotic plates, when an mcr strain was used as host. High performance liquid chromatography was used to estimate the extent of modification of plasmids indirectly. The extent of methylation at specific sequences within a plasmid molecule was readily detected by the corresponding differential susceptibility to digestion by specific restriction enzymes. Using this approach it proved possible to detect different levels of activity produced by wild type and mutant recombinant DNA Methyltransferases with sensitivity and in a semi quantitative manner. In order to analyse the biochemical properties of Mtase, I have developed an in vitro translation-modification assay. Binary studies with the mutants (from Chapter 3 and 5) showed that there were no detectable sequence-specific recognition differences between these enzymes. Taken together, these results suggest that motif IX plays a role in general stabilisation of the enzyme core structure and has a less significant role in DNA recognition.
37
Rudberg, Peter C. "Leukotriene A4 hydrolase : studies of structure-function relationships by site-directed mutagenesis and X-ray crystallography /." Stockholm, 2004. http://diss.kib.ki.se/2004/91-7140-038-9/.
Full text
38
Bogyo, Matthew Steven 1971. "Peptide vinyl sulfones : inhibitors and active site probes for the study of proteasome function in vivo." Thesis, Massachusetts Institute of Technology, 1997. http://hdl.handle.net/1721.1/28184.
Full text
39
Li, Yishan. "Structure-function studies of phospholipase A(2): a site-directed mutagenesis and nuclear magnetic resonance study /." The Ohio State University, 1994. http://rave.ohiolink.edu/etdc/view?acc_num=osu1487857546387323.
Full text
40
Agarwal, Anshu. "Structure - function studies of the active site residues of recombinant high potential iron protein (Chromatium vinosum) /." The Ohio State University, 1996. http://rave.ohiolink.edu/etdc/view?acc_num=osu1487935573770586.
Full text
41
Da, Chenxiao. "The Development and Applications of the HINT Scoring Function: Exploring Colchicine-Site Anticancer Agents and Tautomerism." VCU Scholars Compass, 2013. http://scholarscompass.vcu.edu/etd/3002.
Full textAbstract:
The overall aim of this work was to apply HINT, an empirical scoring function based on the understanding of hydrophobicity, to analyze and predict the binding affinities and biological activities of colchicine-site anticancer agents. The second, concurrent aim was to improve the scoring function by incorporating tautomerism within the modeling process. Our belief is that proper evaluation of tautomeric forms for small molecules will improve performance of virtual screening. The novel pyrrole-based compounds targeting the colchicine site were docked into the receptor using HINT as a rescoring function. Two distinct binding modes dictated by the size and shape of a subpocket were predicted to differentiate the highly active compounds from the weak ones. Of the residues predicted to participate in binding for the active binding mode, Cys241β was revealed to form a weak but critical hydrogen bond with the ligand. A larger collection of colchicine-site agents, biologically tested in the same laboratory including our pyrrole-based compounds were subject to 3D quantitative structure-activity relationship (QSAR) study. Using results on docking the pyrrole compounds as a guide, relative binding poses and QSAR models were built to facilitate ligand design and optimization. A new 3D modeling approach was introduced to visually highlight the unique features of highly active compounds and the commonality of all compounds in the dataset using HINT maps and successfully tested on the colchicine-site agents. These results will provide valuable guidance in the future design and development of new colchicine-site agents. To incorporate tautomerism within HINT, we proposed and developed two workflow approaches: a general search tool using a simple and intuitive algorithm analyzing hydrogen shift patterns to identify and enumerate tautomeric structures, and a database that contains commonly observed tautomeric structures. The first approach was designed for small-scale docking studies and the second approach was designed for large-scale virtual screening. The tautomer module in HINT will give more accurate modeling results when the compound encountered is able to tautomerize.
42
Forouzan, Firoozeh. "Small Finds From Chogha Gavaneh Site in the Islamabad Plain, Central Zagros Mountains, Iran." Digital Archive @ GSU, 2010. http://digitalarchive.gsu.edu/anthro_theses/46.
Full textAbstract:
This study examines small finds from the site of Chogha Gavaneh, Iran, including zoomorphic clay figurines, geometric-shaped objects, and sling bullets in order to deter-mine if they served an economic function during the Early Chalcolithic period (ca. 5000-4000 B.C.E.). A total of 104 animal figurines, sling bullets, and geometric-shaped objects have been found at Chogha Gavaneh. This research challenges previous archaeological interpretations of animal figurines that have interpreted them as being magical or lucky objects for hunting and religious rituals, or for use as game pieces, educational objects, or toys. Through the use of XRF (x-ray fluorescence spectrometry) analysis and the chaine opératoire approach, I suggest, contrary to the conventional wisdom, that some of these clay objects might represent another kind of social practice and may have had an economic function.
43
Sherratt, Allison R. "Beyond the Active Site of the Bacterial Rhomboid Protease: Novel Interactions at the Membrane to Modulate Function." Thesis, Université d'Ottawa / University of Ottawa, 2012. http://hdl.handle.net/10393/22664.
Full textAbstract:
Rhomboids are unique membrane proteins that use a serine protease hydrolysis mechanism to cleave a transmembrane substrate within the lipid bilayer. This remarkable proteolytic activity is achieved by a core domain comprised of 6 transmembrane segments that form a hydrophilic cavity submerged in the membrane. In addition to this core domain, many rhomboids also possess aqueous domains of varying sizes at the N- and/or C-terminus, the sequences of which tend to be rhomboid-type specific. The functional role of these extramembranous domains is generally not well understood, although it is thought that they may be involved in regulation of rhomboid activity and specificity. While extramembranous domains may be important for rhomboid activity, they are absent in all x-ray crystal structures available. For this reason, we have focused on uncovering the structural and functional relationship between the rhomboid cytoplasmic domain and its catalytic transmembrane core.
To investigate the structure and function of the bacterial rhomboid cytoplasmic domain, full-length rhomboids from Escherichia coli and Pseudomonas aeruginosa were studied using solution nuclear magnetic resonance (NMR) spectroscopy, mutation and activity assays. The P. aeruginosa rhomboid was purified in a range of membrane-mimetic media, evaluated for its functional status in vitro and investigated for its NMR spectroscopic properties. Results from this study suggested that an activity-modulating interaction might occur between the catalytic core transmembrane domain and the cytoplasmic domain. Further investigation of this hypothesis with the E. coli rhomboid revealed that protease activity relies on a short but critical sequence N-terminal to the first transmembrane segment. This sequence was found to have a direct impact on the rhomboid active site, and should be included in future structural studies of this catalytic domain.
The structure of the cytoplasmic domain from the E. coli rhomboid was also determined by solution NMR. We found that it forms slowly-exchanging dimers through an exchange of secondary structure elements between subunits, commonly known as three-dimensional domain swapping. Beyond this rare example of domain swapping in a membrane protein extramembranous domain, we found that the rate of exchange between monomeric and dimeric states could be accelerated by transient interactions with large detergent micelles with a phosphocholine headgroup, but not by exposure to other weakly denaturing conditions. This novel example of micelle-catalyzed domain swapping interactions raises the possibility that domain swapping interactions might be induced by similar interactions in vivo. Overall, the results of this thesis have identified detergent conditions that preserve the highest level of activity for bacterial rhomboids, defined the minimal functional unit beyond what had been identified in available x-ray crystal structures, and characterized a novel micelle-catalyzed domain-swapping interaction by the cytoplasmic domain.
44
Kim, Nak-Kyoon. "Metal dependent structure, dynamics, and function in RNA measured by site-directed spin labeling and EPR spectroscopy." Diss., Texas A&M University, 2005. http://hdl.handle.net/1969.1/4900.
Full textAbstract:
The structure and function of RNA molecules are dependent on RNA-metal ion interactions in both diffusive and direct ways. Structural information for RNA has been obtained using various biophysical and biochemical methods. In this study, using site-directed spin labeling (SDSL) and EPR spectroscopy, distances in RNA duplexes, TAR RNA, and the hammerhead ribozyme have been measured to investigate RNA structures. Kinetic measurements have been performed in the extended hammerhead ribozyme to correlate the catalytic function with metal dependent ribozyme folding. As a basic model system for distance measurements, inter-spin distances in RNA duplexes with spin labels at various positions are measured using SDSL with continuous EPR and a Fourier deconvolution method. Divalent metal-ion dependent TAR RNA folding from bent to extended conformers is monitored by measuring inter-spin distances near the bulge region. In order to investigate a proposed loop-loop interaction in the extended hammerhead ribozyme which significantly enhances the ribozyme activity, distance measurements, dynamics studies, and kinetics measurements have been performed. We have introduced PELDOR long-distance measurements in order to investigate metal dependent folding of the hammerhead ribozyme. The dynamics of the spin labels attached to the hammerhead ribozyme with increasing mono- and divalent metal ion concentrations are monitored using CW EPR spectroscopy at room temperature. EPR data show that a loop-loop interaction occurs near the U1.6 nucleotide, and that in 0.1 M NaCl the docking occurs at submillimolar Mg2+ concentrations ([Mg2+]1/2, docking = ~ 0.7 mM). Kinetics measurements show that the hammerhead ribozyme requires high concentration of Mg2+ for the maximum cleavage activity ([Mg2+]1/2, cleavage = ~ 90 mM).
45
Johansson, Anna Karin. "Linking structure and function of the asialoglycoprotein receptor H1-CRD using site-directed mutagenesis and isotope labeling /." [S.l.] : [s.n.], 2007. http://edoc.unibas.ch/diss/DissB_8736.
Full text
46
Shi, Zhengtao. "Structure-function studies of adenylate kinase by site-specific incorporation of both natural and unnatural amino acids /." The Ohio State University, 1994. http://rave.ohiolink.edu/etdc/view?acc_num=osu1487854314871531.
Full text
47
Jung, Giman. "The Charge-Relay System in Enzyme Catalysis : Construction and Function of Active Site Residues in Carboxypeptidase Y." Kyoto University, 1999. http://hdl.handle.net/2433/181885.
Full textAbstract:
Kyoto University (京都大学)0048
新制・課程博士
博士(農学)
甲第7876号
農博第1034号
新制||農||776(附属図書館)
学位論文||H11||N3239(農学部図書室)
UT51-99-G470
京都大学大学院農学研究科農芸化学専攻
(主査)教授 林 力丸, 教授 佐藤 文彦, 教授 江崎 信芳
学位規則第4条第1項該当
48
Birchfield, Aaron. "Preparation of a Flavonol Specific Glucosyltransferase found in Grapefruit and Site-Directed Mutants for Protein Crystallization." Digital Commons @ East Tennessee State University, 2019. https://dc.etsu.edu/etd/3523.
Full textAbstract:
This research was designed to determine the conditions necessary to remove c-myc and 6x-His tags from a flavonol specific glucosyltransferase found in grapefruit (CP3GT) using thrombin in preparation for crystallization. X-ray crystallography of CP3GT crystals may elucidate structural features that account for flavonol specificity in some glucosyltransferase enzymes. A thrombin cleavage site was inserted into WT CP3GT and one mutant. Recombinant CP3GT was expressed in yeast and purified. Optimal conditions for thrombin digestion were explored. Digestion with 100U of thrombin for 2 hours at 4o C was optimal for removing tags from CP3GT. Storage at 4o C for 2 hours resulted in approximately 70% retention of activity. The effect of thrombin treatment on CP3GT activity was tested. Purified CP3GT protein with and without tags was tested for activity with the flavonol quercetin. Data showed no significant difference in overall activity between tagged and native protein.
49
Kang, You-Na. "Studies on the Structure and Function of Soybean β-Amylase by Mutations at Active Site and Surface Residues." Kyoto University, 2004. http://hdl.handle.net/2433/147767.
Full textAbstract:
Kyoto University (京都大学)0048
新制・課程博士
博士(農学)
甲第10918号
農博第1424号
新制||農||892(附属図書館)
学位論文||H16||N3929(農学部図書室)
UT51-2004-G765
京都大学大学院農学研究科農学専攻
(主査)教授 内海 成, 教授 廣瀬 正明, 助教授 三上 文三
学位規則第4条第1項該当
50
Harris, Jocelyn Ellen. "Studies of upper limb function in indivduals with subacute stroke : a multi-site single blind randomized controlled trial." Thesis, University of British Columbia, 2009. http://hdl.handle.net/2429/7387.
Full textAbstract:
Introduction
Approximately 70% of individuals with stroke have upper limb impairment. Inability to use the upper limb can lead to difficulties in activities of daily living. Increased time spent in therapy improves outcome of the upper limb post stroke however, length of stay in rehabilitation has decreased. Innovative ways of increasing therapy intensity need to be explored.
Purpose
1) To undertake a meta-analysis to determine the treatment effect of upper limb strengthening on strength, function and activities of daily living.
2) To determine the effectiveness of a four week self-administered in-patient homework exercise program (GRASP) on upper limb function and depressive symptoms in individuals in the sub-acute stage of stroke recovery.
3) To determine modifiable predictors of upper limb function in individuals in the sub-acute stage of stroke recovery.
Methods
Design: Chapter 2 is a meta-analysis of upper limb strength training in individuals with stroke. Electronic databases were searched from 1950-September 2008. 14 articles were reviewed.
Chapter 3-5 involved a four week multi-site single blind randomized controlled trial of a self-administered upper limb exercise program (GRASP) compared to control. Subjects: 103 individuals with stroke were recruited from four rehabilitation units.
Results
Chapter 2: The meta-analysis showed strength training is effective in increasing paretic upper limb strength and function but not performance in activities of daily living. Chapters 3-5: The GRASP program improved upper limb function significantly more than the control group (p<0.001) and reported less depressive symptoms (p<0.001). Baseline Fugl-Meyer, change in grip strength, treatment intensity and family involvement were significant predictors of upper limb function (R²=0.507 to 0.597, p<0.001).
Conclusions
Strength training is a viable method to improve upper limb function in individuals with stroke. The randomized controlled trial showed that a self-administered homework exercise program for the upper limb is an effective method for 1) improving upper limb function and 2) decreasing depressive symptoms among individuals with sub-acute stroke. The trial provided evidence that modifiable variables are significant determinants of upper limb function among individuals with stroke. Further studies to evaluate the GRASP protocol within other conditions and treatment settings are warranted.Medicine, Faculty of
Graduate