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Rozprawy doktorskie na temat „Protein binding”

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Autor: Grafiati

Data publikacji: 4 czerwca 2021

Data aktualizacji: 1 sierpnia 2024

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1

Jones, Marc. "Folate binding protein : partial characterisation of bovine milk folate binding protein, includings its ligand binding /". [St. Lucia, Qld], 2004. http://www.library.uq.edu.au/pdfserve.php?image=thesisabs/absthe18263.pdf.

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2

Zeng, Bin. "Functional characterization of acyl-CoA binding protein (ACBP) and oxysterol binding protein-related proteins (ORPS) from Cryptosporidium parvum". Thesis, [College Station, Tex. : Texas A&M University, 2006. http://hdl.handle.net/1969.1/ETD-TAMU-1211.

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3

Tse, Muk-hei. "Investigations on recombinant Arabidopsis acyl-coenzyme A binding protein 1". View the Table of Contents & Abstract, 2005. http://sunzi.lib.hku.hk/hkuto/record/B36427664.

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4

Crombie, Catriona Ann. "Histone hairpin binding protein, an RNA binding protein, essential for development". Thesis, University of Aberdeen, 2003. http://digitool.abdn.ac.uk/R?func=search-advanced-go&find_code1=WSN&request1=AAIU602058.

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Histones are proteins found in the nuclei of eukaryotic cells where they are complexed to DNA in chromatin. Rephcation-dependent histones are expressed only during S-phase. Regulation of expression of replication-dependent histone genes requires a highly conserved hairpin RNA element in the 3' untranslated region of histone mRNAs. Replication-dependent histone mRNAs are not polyadenylated; their 3' end is formed by an endonucleolytic cleavage event, 3' of a hairpin element, which is recognised by the Hairpin Binding Protein, HBP (also known as Stem-Loop Binding Protein, SLBP). This protein-RNA interaction is important for the endonucleolytic cleavage that generates the mature mRNA 3' end. The 3' hairpin, and presumably HBP, are also required for nucleocytoplasmic transport, translation and stability of histone mRNAs. It is therefore important to understand this interaction. The hairpin is highly conserved and I have demonstrated that residues in the hairpin loop are important for binding the HBP. This complimented structural studies that showed that the same residues are involved in stacking interactions in the RNA loop. In cell culture, expression of replication-dependent histone genes is S phase specific as is the expresion of HBP. Here I demonstrated that in Caenorhabditis elegans the HBP promoter is active in dividing cells during embryonic and postembryonic development. Depletion of HBP by RNAi leads to an embryonic lethal phenotype associated with defects in chromosome condensation. Postembryonic depletion of HBP results in defects in cell fate during late larval development, specifically in vulval development. A similar phenotype was obtained when histone H3 and H2A were depleted by RNAi suggesting that the phenotype of the hbp (RNAi) worms was due to a lack of histone proteins. I have confirmed this by showing that histone proteins are indeed reduced in hbp (RNAi) worms. I have also shown that depletion of HBP leads to a change in expression of a number of other proteins and specifically an up-regulation of a histone H3 like protein with an apparent molecular mass of 34 kDa. I have evidence that suggests that this protein is the centromer specific protein, CENP-A. As this protein was up-regulated when RNAi was used to deplete histones proteins, this suggests that there could be a compensatory mechanism that helps the animal to deal with the shortage of histone proteins.

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5

Prigge, Justin Robert. "Identification and characterization of novel protein-protein interactions with the basal transcription factor, TATA-binding protein". Diss., Montana State University, 2006. http://etd.lib.montana.edu/etd/2006/prigge/PriggeJ0506.pdf.

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6

Wei, Heng. "Split PH domain identification & redundancy analyses in the classification of PDZ domains /". View abstract or full-text, 2006. http://library.ust.hk/cgi/db/thesis.pl?BICH%202006%20WEI.

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7

Fang, Lin. "Mechanism of client protein binding by heat shock protein 90 /". view abstract or download file of text, 2006. http://proquest.umi.com/pqdweb?did=1251819301&sid=2&Fmt=2&clientId=11238&RQT=309&VName=PQD.

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Thesis (Ph. D.)--University of Oregon, 2006.
Typescript. Includes vita and abstract. Includes bibliographical references (leaves 115-121). Also available for download via the World Wide Web; free to University of Oregon users.

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8

Ranganathan, Anirudh. "Protein – Ligand Binding: Estimation of Binding Free Energies". Thesis, KTH, Skolan för kemivetenskap (CHE), 2012. http://urn.kb.se/resolve?urn=urn:nbn:se:kth:diva-147527.

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Accurate prediction of binding free energies of protein-ligand system has long been a focus area for theoretical and computational studies; with important implications in fields like pharmaceuticals, enzyme-redesign, etc. The aim of this project was to develop such a predictive model for calculating binding free energies of protein-ligand systems based on the LIE-SASA methods. Many models have been successfully fit to experimental data, but a general predictive model, not reliant on experimental values, would make LIE-SASA a more powerful and widely applicable method. The model was developed such that There is no significant increase in computational time No increase in complexity of system setup No increase in the number of empirical parameters. The method was tested on a small number of protein-ligand systems, selected with certain constraints. This was our training set, from which we obtain the complete expression for binding free energy. Expectedly, there was good agreement with experimental values for the training set On applying our model to a similar sized validation set, with the same selection constraints as for the training set, we achieved even better agreement with experimental results, with lower standard errors. Finally, the model was tested by applying it to a set of systems without such selection constraints, and again found good agreement with experimental values. In terms of accuracy, the model was comparable to a system specific empirical fit that was performed on this set. These encouraging results could be an indicator of generality.

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9

Gao, Wei, i 高威. "Characterization of protein interactors of Arabidopsis acyl-coenzymea-binding protein 2". Thesis, The University of Hong Kong (Pokfulam, Hong Kong), 2009. http://hub.hku.hk/bib/B43223837.

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10

Chung, Jo-Lan. "Identifying protein-protein binding sites and binding partners using sequence and structure information /". Diss., Connect to a 24 p. preview or request complete full text in PDF formate. Access restricted to UC campuses, 2007. http://wwwlib.umi.com/cr/ucsd/fullcit?p3244170.

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11

Leung, Ka-chun. "Binding studies on Arabidopsis Acyl-coenzyme A binding proteins ACBP3, ACBP4 and ACBP5". Click to view the E-thesis via HKUTO, 2004. http://sunzi.lib.hku.hk/hkuto/record/B34825484.

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12

Tse, Muk-hei, i 謝牧熙. "Investigations on recombinant Arabidopsis acyl-coenzyme A binding protein 1". Thesis, The University of Hong Kong (Pokfulam, Hong Kong), 2005. http://hub.hku.hk/bib/B36427664.

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13

Bennett, D. H. "Protein phosphatase type 1 binding proteins in Drosophila melanogaster". Thesis, University of Oxford, 2000. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.365689.

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14

Gao, Wei. "Characterization of protein interactors of Arabidopsis acyl-coenzyme a-binding protein 2". Click to view the E-thesis via HKUTO, 2009. http://sunzi.lib.hku.hk/hkuto/record/B43223837.

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15

Leung, Ka-chun, i 梁家俊. "Binding studies on Arabidopsis Acyl-coenzyme A binding proteins ACBP3,ACBP4 and ACBP5". Thesis, The University of Hong Kong (Pokfulam, Hong Kong), 2004. http://hub.hku.hk/bib/B34825484.

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16

Zhang, Zhiwen. "Towards peptide-binding peptides". Access restricted to users with UT Austin EID, 2001. http://wwwlib.umi.com/cr/utexas/fullcit?p3037037.

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17

Matereke, Lavious Tapiwa. "Analysis of predictive power of binding affinity of PBM-derived sequences". Thesis, Rhodes University, 2015. http://hdl.handle.net/10962/d1018666.

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A transcription factor (TF) is a protein that binds to specific DNA sequences as part of the initiation stage of transcription. Various methods of finding these transcription factor binding sites (TFBS) have been developed. In vivo technologies analyze DNA binding regions known to have bound to a TF in a living cell. Most widely used in vivo methods at the moment are chromatin immunoprecipitation followed by deep sequencing (ChIP-seq) and DNase I hypersensitive sites sequencing. In vitro methods derive TFBS based on experiments with TFs and DNA usually in artificial settings or computationally. An example is the Protein Binding Microarray which uses artificially constructed DNA sequences to determine the short sequences that are most likely to bind to a TF. The major drawback of this approach is that binding of TFs in vivo is also dependent on other factors such as chromatin accessibility and the presence of cofactors. Therefore TFBS derived from the PBM technique might not resemble the true DNA binding sequences. In this work, we use PBM data from the UniPROBE motif database, ChIP-seq data and DNase I hypersensitive sites data. Using the Spearman’s rank correlation and area under receiver operating characteristic curve, we compare the enrichment scores which the PBM approach assigns to its identified sequences and the frequency of these sequences in likely binding regions and the human genome as a whole. We also use central motif enrichment analysis (CentriMo) to compare the enrichment of UniPROBE motifs with in vivo derived motifs (from the JASPAR CORE database) in their respective TF ChIP-seq peak region. CentriMo is applied to 14 TF ChIP-seq peak regions from different cell lines. We aim to establish if there is a relationship between the occurrences of UniPROBE 8-mer patterns in likely binding regions and their enrichment score and how well the in vitro derived motifs match in vivo binding specificity. We did not come out with a particular trend showing failure of the PBM approach to predict in vivo binding specificity. Our results show Ets1, Hnf4a and Tcf3 show prediction failure by the PBM technique in terms of our Spearman’s rank correlation for ChIP-seq data and central motif enrichment analysis. However, the PBM technique also matched the in vivo binding specificities of FoxA2, Pou2f2 and Mafk. Failure of the PBM approach was found to be a result of variability in the TF’s binding specificity, the presence of cofactors, narrow binding specificity and the presence ubiquitous binding patterns.

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18

Brayer, Kathryn Jo. "The Protein Binding Potential of C2H2 Zinc Finger Domains". Diss., The University of Arizona, 2008. http://hdl.handle.net/10150/195146.

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Cys2-His2 (C2H2) zinc finger domains were originally identified as DNA binding domains, and uncharacterized domains are typically assumed to bind DNA. However, a growing body of evidence suggests an important and widespread role for these domains in protein binding. Over 100 C2H2 zinc finger-protein interactions have been described. This study uses common bioinformatics tools to identify sequence features that predict a DNA- or protein-binding function. Several issues, including uncertainties about the full functional capabilities of the zinc fingers, complicated these efforts. Therefore, an unbiased approach which directly examined the potential for zinc fingers to facilitate DNA or protein interactions was used to determine the full functional capabilities of the C2H2 domains in two model proteins, human OLF-1/EBF associated zinc finger (OAZ) protein and Zif268. OAZ contains 30 zinc fingers in six clusters, some of which have been previously indicated in DNA or protein interactions. Zif268 is a well-known DNA binding protein with three C2H2 domains. DNA binding was assessed using a target site selection (CAST) assay, and protein binding was assessed using a yeast two-hybrid assay. Results indicate that clusters known to bind DNA could facilitate specific protein interactions, but clusters known to bind protein did not facilitate specific DNA interactions, indicating that DNA binding is a more restricted function of zinc fingers than has previously been recognized. These results also suggest that the role of C2H2 zinc finger domains in protein interactions has probably been underestimated. The implication of these findings for the prediction of zinc finger function is discussed.

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19

Lubeseder-Martellato, Clara. "The guanylate binding protein-1". Diss., lmu, 2003. http://nbn-resolving.de/urn:nbn:de:bvb:19-11959.

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20

Wang, Xue. "Predicting Protein Calcium Binding Sites". Digital Archive @ GSU, 2009. http://digitalarchive.gsu.edu/cs_diss/46.

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Calcium is one of the closely relevant metal ions that involves in enormous physicochemical activities in human body, including cell division and apoptosis, muscle contraction, neurotransmitter release, enzyme activation, and blood-clotting. Calcium fulfills its functions through the binding to different classes of calcium-binding proteins. To facilitate our understanding of the roles of calcium in biological systems, and to design novel metal-binding proteins with tailored binding capabilities, it is important to develop computation algorithms to predict calcium-binding sites in different classes of proteins. In literature, calcium-binding sites may be represented by either a spacial point, or the set of residues chelating calcium ion. A thorough statistical analysis of known calcium-binding proteins deposited in Protein Data Bank gives reference values of various parameters characterizing geometric and chemical features in calcium-binding sites including distances, angles, dihedral angles, the Hull property, coordination numbers, ligand types and formal charges. It also reveals clear differences between the well-known EF-hand calcium-binding motif and other calcium-binding motifs. Utilizing the above multiple geometric and chemical parameters in well-formed calcium binding sites, we developed MUG (MUltiple Geometries) program. MUG can re-identify the coordinates of the documented calcium ion and the set of ligand residues. Three previously published data sets were tested. They are comprised of, respectively, 19, 44 and 54 holo protein structures with 48, 92 and 91 documented calcium-binding sites. Defining a "correct hit" as a point within 3.5 angstrom to the documented calcium location, MUG has a sensitivity around 90% and selectivity around 80%. The set of ligand residues (calcium-binding pockets) were identified for 43, 66 and 63 documented calcium ion in these three data set respectively. In order to achieve true prediction, our program was then enhanced to predict calcium-binding pockets in apo (calcium-free) proteins. Our new program MUGSR accounts for the conformational changes involved in calcium-binding pockets before and after the binding of calcium ions. It is able to capture calcium binding pockets that may undergo local conformational changes or side chain torsional rotations, which is validated by referring back to the corresponding holo protein structure sharing more than 98% sequence similarity with the apo protein.

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21

Smith, Nigel. "Plasma protein binding of noradrenaline". Thesis, University of Nottingham, 1990. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.252951.

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22

Matlin, Arianne Jane. "Regulation of α-actinin alternative splicing by polypyrimidine tract binding protein and CUG binding proteins". Thesis, University of Cambridge, 2005. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.614724.

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23

Prichard, Lisa. "The role of the IQ motif, a protein kinase C and calmodulin regulatory domain, in neuroplasticity, RNA processing, and RNA metabolism /". Thesis, Connect to this title online; UW restricted, 1998. http://hdl.handle.net/1773/6302.

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24

Martin, Andrew. "Glycosylated green fluorescent protein for carbohydrate binding protein analysis". Thesis, University of Manchester, 2015. https://www.research.manchester.ac.uk/portal/en/theses/glycosylated-green-fluorescent-protein-for-carbohydrate-binding-protein-analysis(9ddae46e-b4d7-4c08-8240-94b9b804ac68).html.

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The interactions of glycoconjugates with carbohydrate binding proteins are responsible for a wide range of recognition events in vivo; including immune response, cell adhesion and signal transduction. Glycoconjugates have already found many medicinal uses as therapeutic and diagnostic agents, but their full potential is yet to be realised. Access to a variety of homogeneously glycosylated glycoproteins is essential for the study of these important carbohydrate binding events. This requires the chemical synthesis and attachment of biologically relevant glycans to unglycosylated protein scaffolds in a site selective manner. Here we describe the use of a range of glycosyl iodoacetamides to glycosylate proteins selectively via their cysteine residues. We have chosen the green fluorescent protein mutant GFPuv for use as a protein scaffold due its known tolerance of two cysteine mutations (E6C and I229C) and the previous successful derivatisation of these cysteines with iodoacetamides.1 The inherent fluorescence of GFPuv also makes it a useful candidate for fluorescence based binding assays or cell labelling studies.16 active, mutants of GFPuv were created using a mixture of site directed mutagenesis and DNA shuffling (including one mutant containing six reactive cysteine residues). This was achieved by producing random combinations of two synthetic variants of GFPuv, one of which contained 33 surface cysteines. 94 bacterial colonies expressing active GFPuv were then sequenced and the new chimeric genes analysed. Four monosaccharides and one trisaccharide (N-glycan core mimic) suitable for the chemical glycosylation via cysteines were synthesised and successfully used to create a selection of homogeneous neoglycoproteins. These neoglycoproteins were demonstrated to interact differently with different lectins (including ConA, GNL and Jacalin) in a qualitative fluorescence based assay. Interactions were shown to vary with glycan structure, position of glycosylation sites and the number of glycosylation sites.

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25

Bramble, Sharyl Elizabeth. "Guanine nucleotide binding properties and attempted immunopurification of ras protein from dictyostelium discoideum". Thesis, University of British Columbia, 1987. http://hdl.handle.net/2429/26172.

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One purpose of this study was to determine whether the ras protein from Dictyostelium discoideum (p23) binds guanine nucleotides like the ras proteins from mammals (p21) and yeast. The other purpose of this investigation was to purify or enrich for p23ras from D. discoideum by immunoaffinity chromatography. A number of different approaches were used to determine guanine nucleotide binding by p23RAS . A simple filter binding assay, binding to Western blots, and photoaffinity labeling all failed to demonstrate specific binding with lysates of D. discoideum cells. In contrast p21RAS from transformed NIH-3T3 cell lysate was successfully photoaffinity labeled in the presence of ³²P-α-guanosine 5¹-triphosphate (GTP) suggesting that the technique had been performed correctly. It was concluded that either p23RAS has a very low affinity for guanine nucleotides such that GTP binding was not detectable in these experiments or that the ras protein from D. discoideum simply does not bind guanine nucleotides. The purification of p23RAS from D. discoideum cells was attempted in order to provide a purified protein preparation for guanine nucleotide binding and for reconstitution studies. An anti-ras monoclonal antibody (Y13-259) was used as the ligand for the immunoaffinity chromatography. This approach was not successful in that the ras protein could not be enriched relative to other proteins because the immunoaffinity columns did not bind p23RAS.
Science, Faculty of
Microbiology and Immunology, Department of
Graduate

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26

Crane, Jennine Marie. "Characterization of two modes of interaction between the chaperone SecB and its binding partners". Free to MU Campus, others may purchase, 2004. http://wwwlib.umi.com/cr/mo/fullcit?p3144410.

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27

Parissiadis, Anne. "La C4B-Binding protein : structure, biologie, intérêt de son dosage en pathologie". Université Louis Pasteur (Strasbourg) (1971-2008), 1990. http://www.theses.fr/1990STR1M060.

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28

Terasmaa, Anton. "Dopamine D2 receptor G protein coupling and its regulation /". Stockholm, 2003. http://diss.kib.ki.se/2004/91-7349-788-6/.

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29

Collins, Malcolm Robert. "Characterisation of the human α2(I) procollagen promoter-binding proteins". Doctoral thesis, University of Cape Town, 1993. http://hdl.handle.net/11427/27139.

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In an attempt to elucidate the transcriptional mechanisms that regulate the expression of the human α2(I) procollagen gene, cis-acting DNA-elements within the proximal promoter were identified and their corresponding trans-acting factors characterised. The fibroblast cell lines used in this study had previously been transformed with either simian virus 40 (SVWI-38) or by γ-radiation (CT-1). The SVWI-38 fibroblasts do not produce any α2(I) collagen chains, whereas the CT-1 cell line produces normal type I collagen. Previous studies suggested that trans-acting factor(s) may be responsible for the inactivation of the α2(I) procollagen gene in SVWI-38 fibroblasts (Parker et. al. (1989) J. Biol. Chem 264, 7147-7152; Parker et. al. (1992) Nucleic Acids Res. 20, 5825-5830). In this study, the SVWI-38 proximal promoter (-350 to +54) was sequenced and shown to be normal, thereby ruling out any possibility that mutations within this region was responsible for inactivation of the gene.

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30

McClelland, David Andrew. "The refolding of riboflavin binding protein". Thesis, University of Stirling, 1996. http://hdl.handle.net/1893/3408.

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Hen egg riboflavin binding protein (RfBP) acts as a source of riboflavin to the developing embryo. It is the most abundant vitamin binding protein in the egg white. Mutations giving rise to a lack of RfBP lead to embryo death at approximately 13 days. RfBP binds riboflavin tightly in a 1:1 ratio. On formation of this complex, the fluorescence of riboflavin is completely quenched; this quenching is thought to be due to the stacking of aromatic groups within the hydrophobic binding pocket. This quenching provides a convenient assay for the integrity of the riboflavin-binding site of the protein. RfBP consists of a single polypeptide chain of 219 amino acids of molecular mass 29.2 kDa. RfBP undergoes a number of post-translational modifications, namely: the formation of nine disulphide bonds, extensive glycosylation on Asn 36 and Asn 147, and the phosphorylation of eight serine side chains from between Ser 186 and Ser 197. The unfolding and refolding of RfBP was studied by denaturing in 6M guanidium chloride, followed by dilution in buffer, to start refolding. The processes were followed by both steady-state and stopped-flow circular dichroism and fluorescence spectroscopy. RfBP was found to readily unfold and refold, provided the disulphide bonds were intact. The regain of secondary structure was found to be too rapid to measure by the methods available (<12msec). The regain of tertiary structure was found to consist of 4 main phases, and a large proportion (80%) of the tertiary structure formed within 2 msec. The regain of riboflavin binding ability was complete at the end of the second phase, a reaction with a half-life of around 30 msec. In the presence and absence of riboflavin, the kinetics for the first 3 stages of tertiary structure changes seemed to be identical. In the presence of riboflavin, however, seemed to impede the completion of the final, very slow stage, with the refolding reaction only going to 95% completion. The dephosphorylation of the protein seemed to have no affect on this process. When the 9 disulphide bonds are reduced however, RfBP is unable to spontaneously reoxidise to a native-like state in the presence of an oxidised/reduced glutathione redox system. However, the addition of protein disulphide isomerase to the system increases significantly the yield of successfully reoxidised RfBP to about 50%. Attempts to prepare deglycosylated RfBP by chemical methods were unsuccessful since the treatment led to fragmentation of the polypeptide chain.

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31

Bisset, Louise Clair. "Fluorescence of a DNA-binding protein". Thesis, University of Newcastle Upon Tyne, 1996. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.320129.

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32

Holding, Jeremy David. "Cisplatin : protein binding and biological activity". Thesis, University of Liverpool, 1989. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.257185.

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33

Sheridan, Mary T. "Studies of fatty acid binding protein". Thesis, University of Southampton, 1989. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.235759.

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34

Weiser, Armin. "Amino acid substitutions in protein binding". Doctoral thesis, Humboldt-Universität zu Berlin, Mathematisch-Naturwissenschaftliche Fakultät I, 2009. http://dx.doi.org/10.18452/15962.

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Die Modifizierung von Proteinsequenzen unter anderem durch den Austausch von Aminosäuren ist ein zentraler Aspekt in evolutionären Prozessen. Solche Prozesse ereignen sich nicht nur innerhalb großer Zeiträume und resultieren in der Vielfalt des Lebens, das uns umgibt, sondern sind auch täglich beobachtbar. Diese mikroevolutionären Prozesse bilden eine Grundlage zur Immunabwehr höherer Wirbeltiere und werden durch das humorale Immunsystem organisiert. Im Zuge einer Immunantwort werden Antikörper wiederholt der Diversifizierung durch somatische Hypermutation unterworfen. Ziele dieser Arbeit waren, neue Kenntnisse über die Mikroevolution von Antikörpern während der Immunantwort zu gewinnen und die Beziehung zwischen Aminosäureaustauschen und Affinitätsänderungen zu verstehen. Zu diesem Zweck wurde zunächst gezeigt, dass die SPOT Synthese eine präzise Methode ist, um Signalintensitäten drei verschiedenen Bindungsaffinitätsklassen zuzuordnen. Antikörper-Peptid Bindungsdaten, die aus SPOT Synthese Experimenten generiert wurden, bildeten die Grundlage zur Konstruktion der Substitutionsmatrix AFFI - der ersten Substitutionsmatrix, die ausschließlich auf Bindungsaffinitätsdaten beruht. Diese bildete die Grundlage für die Gewinnung eines reduzierten Aminosäuresatzes. Durch einen theoretischen Ansatz konnte gezeigt werden, dass der reduzierte Aminosäuresatz eine optimale Basis für die Epitopsuche darstellt. Für den Prozess der somatischen Hypermutation und Selektion wurde ein neuer Ansatz präsentiert, um für die Affinitätsreifung relevante Mutationen zu identifizieren. Die Analyse zeigte, dass das Spektrum der selektierten Mutationen viel umfangreicher ist als bisher angenommen wurde. Die Tatsache, dass auch einige stille Mutationen stark bevorzugt werden, deutet darauf hin, dass entweder die intrinsische Mutabilität stark unterschätzt wurde oder, dass Selektion nicht nur auf Affinitätsreifung von Antikörpern basiert sondern auch auf ihrer Expressionsrate.
A central task of the evolutionary process is the alteration of amino acid sequences, such as the substitution of one amino acid by another. Not only do these amino acid changes occur gradually over large time scales and result in the variety of life surrounding us, but they also happen daily within an organism. Such alterations take place rapidly for the purposes of defense, which in higher vertebrates, is managed by the humoral immune system. For an effective immune response, antibodies are subjected to a micro-evolutionary process that includes multiple rounds of diversification by somatic hypermutation resulting in increased binding affinity to a particular pathogen. The goal of this work was to provide insights into the microevolution of antibodies during the immune response, including the relationship between amino acid substitutions and binding affinity changes. A preliminary step in this work was to determine the accuracy of the SPOT synthesis technique, which could be shown to be an accurate method for assigning measured signal intensities to three different binding affinity classes. A substitution matrix based on data produced with these binding experiments was constructed and named AFFI. AFFI is the first substitution matrix that is based solely on binding affinity. A theoretical approach has additionally revealed that an AFFI-derived reduced set of amino acids constitutes an optimal basis for epitope searching. For the process of somatic hypermutation and selection, a novel approach to identify mutations relevant to affinity maturation was presented. The analysis revealed that the spectrum of mutations favored by the selection process is much broader than previously thought. The fact that particular silent mutations are strongly favored indicates either that intrinsic mutability has been grossly underestimated, or that selection acts not only on antibody affinity but also on their expression rates.

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35

Jones, Tiffany Celeste. "Syndecan-4 binds insulin-like growth factor binding protein-4". Birmingham, Ala. : University of Alabama at Birmingham, 2009. https://www.mhsl.uab.edu/dt/2010r/jones.pdf.

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Xie, Tian. "Scintillation proximity assay (SPA) measuring p53 DNA binding and total p53 level in human thyroid cancer cell line ARO". Diss., Online access via UMI:, 2007.

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Lucas, Olivier. "Molecular and systemic functions of the vertebrate-specific TATA-binding protein N terminus". Diss., Montana State University, 2009. http://etd.lib.montana.edu/etd/2009/lucas/LucasO0509.pdf.

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De, Lange W. J. (Willem Jacobus). "An investigation of myosin binding protein C mutations in South Africa and a search for ligands binding to myosin binding protein C". Thesis, Stellenbosch : University of Stellenbosch, 2004. http://hdl.handle.net/10019.1/16032.

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Thesis (PhD)--University of Stellenbosch, 2004.
426 Leaves printed single pages, preliminary pages i-xxiv and i-xxvii and 399 numberd pages. Includes bibliography. List of figures, List of tables, List of abbreviations.
ENGLISH ABSTRACT: Hypertrophic cardiomyopathy (HCM) is an autosomal dominantly inherited primary cardiac disease. The primary features of HCM are left ventricular hypertrophy, myocardial disarray, fibrosis and an increased risk of sudden cardiac death. To date, more than 264 HCM-causing mutations, occurring in thirteen genes, have been identified. As the vast majority of HCM-causing mutations occur in components of the cardiac sarcomere, HCM has been considered a disease of the cardiac sarcomere. Functional analyses of HCM-causing mutations in sarcomeric protein-encoding genes revealed that HCM-causing mutations have a vast array of effects on contractile function. The discovery of HCMcausing mutations in the gamma two subunit of adenosine monophosphate activated protein kinase highlighted the fact that mutations in non-sarcomeric proteins can also cause HCM and supports a hypothesis that HCM-causing mutations may result in energy wastage leading to energy depletion. Mutations in the cardiac myosin binding protein C (cMyBPC) gene (MYBPC3) are the second most prevalent cause of HCM. cMyBPC is a modular protein that forms an integral part of the sarcomeric thick filament, where it acts as a regulator of thick filament structure and cardiac contractility. Although cMyBPC has been studied extensively, the mechanisms through which it fulfill these functions have remained elusive, largely due to a lack of a comprehensive understanding of its interactions with other sarcomeric components and its quaternary structure. The aims of the present study were, firstly, to screen MYBPC3 for HCM-causing mutations in a panel of HCM-affected individuals and, secondly, to identify the ligands of domains of cMyBPC in which HCM-causing mutations were found.A panel of deoxyribonucleic acid (DNA) samples obtained from unrelated HCM-affected individuals was screened for HCM-causing mutations in MYBPC3, using polymerase chain reaction (PCR)- based single-strand conformation polymorphism method, as well as restriction enzyme digestion, DNA sequencing and reverse transcription PCR techniques. In order to identify the ligands of domains in which HCM-causing mutations were found, yeast two-hybrid (Y2H) candidate-ligandand library-assays were performed. Three novel and two previously described putative HCM-causing mutations were identified in MYBPC3. Data generated in this and other studies, however, suggest that two of these “mutations” are likely to be either polymorphisms, or disease-modifying factors, rather than main-locus HCMcausing mutations. Recent findings showed a specific interaction between domains C5 and C8 of cMyBPC. This finding identified domains C6 or C10 as candidate ligands of domain C7. Y2H-assays revealed a specific C7:C10 interaction. Additional Y2H assays also identified C-zone titin as a ligand of domain C7 and domain C10 as a ligand of domain C3. Several other Y2H assays, however, yielded no known sarcomeric ligands of the N-terminal region of cMyBPC. Identification of the ligands of specific domains of cMyBPC led to the development of detailed models of cMyBPC quaternary structure when cMyBPC is both unphosphorylated and fully phosphorylated. The integration of these models into an existing model of thick filament quaternary structure allows new insights into the functioning of cMyBPC as a regulator of both thick filament structure and cardiac contractility, as well as the pathophysiology of cMyBPC-associated HCM.
AFRIKAANSE OPSOMMING: Hipertrofiese kardiomiopatie (HKM) is ‘n outsosomaal dominante primêre hartsiekte. Die primêre kenmerke van HKM is linker ventrikulêre hipertrofie, miokardiale wanorde, fibrose en ‘n verhoogde risiko van skielike dood. Tot dusver is 260 HKM-veroorsakende mutasies in 13 gene geïdentifiseer. Aangesien die oorgrote meerderheid van HKM-veroorsakende mutasies in komponente van die kardiale sarkomeer voorkom, is HKM as ‘n siekte van die kardiale sarkomeer beskryf. Funksionele analise van HKM-veroorsakende mutasies in sarkomeriese protein-koderende gene het aan die lig gebring dat hierdie mutasies ‘n wye spektrum van gevolge op kontraktiele funksie het. Die ontdekking van HKM-veroorsakende mutasies in die gamma-twee subeenheid van adenosien monofosfaat-geaktiveerde proteïen kinase het die feit dat mutasies nie-sarkomeriese proteïene ook HKM kan veroorsaak onderstreep en ondersteun ‘n hipotese dat HKM-veroorsakende mutasies energievermorsing en energie uitputting tot gevolg het. Mutasies in die kardiale miosien-bindingsproteïen C (kMiBPC) geen (MYBPC3) is die tweede mees algemene oorsaak van HKM. kMiBPC is ‘n modulêre protein wat ‘n integrale deel van die sarkomeriese dik filament vorm, waar dit die struktuur van die dik filament en kardiale kontraktiliteit reguleer. Nieteenstaande die feit dat kMiBPC intensief bestudeer is, word die meganismes hoe hierdie funksies vervul word swak verstaan, grotendeels weens die afwesigheid van ‘n in diepte begrip van sy interaksies met ander komponente van die sarkomeer asook sy kwaternêre struktuur. Die doelstellings van hierdie studie was, eerstens, om MYBPC3 vir HKM-veroorsakende mutasies in ‘n paneel van HKM-geaffekteerde individue te deursoek en tweedens, om die ligande van domeine van kMiBPC waarin HKM-veroorsakende mutasies gevind is te identifiseer.‘n Paneel van deoksiribonukleïensuur (DNS) monsters verkry van onverwante HKM-geaffekteerde individue is deursoek vir HKM-veroorsakende mutasies in MYBPC3, deur middel van die polimerase ketting-reaksie (PKR)-gebasseerde enkelstrand konformasie polimorfisme metode, sowel as restriksie ensiem vertering, DNS volgordebepaling en terugtranskripsie PKR tegnieke. Die ligande van domeine van kMiBPC waarin HKM-veroorsakende mutasies gevind is, is geïdentifiseer deur middel van gis twee-hibried (G2H) kandidaat-ligand en biblioteek-siftings eksperimente. Drie onbeskryfde en twee voorheen beskryfde vermeende HKM-veroorsakende mutasies in MYPBC3 is geïdentifiseer. Data gegenereer in hierdie en ander studies dui daarop dat twee van hierdie “mutasies” eerder polimorfismes, of siekte-modifiserende faktore, as hoof-lokus HKMveroorsakende mutasies is. Onlangse bevindings het ‘n spesifieke interaksie tussend die C5 en C8 domeine van kMiBPC getoon. Hierdie bevindings het óf domein C6, óf C10, as kandidaat-ligande van domein C7 geïdentifiseer. G2H eksperimente het ‘n spesifieke interaksie tussen domains C7 en C10 getoon. Addisionele G2H eksperimente het ook C-zone titin as ‘n ligand van domein C7 sowel as domein C10 as ‘n ligand van domein C3 geïdentifiseer. Verdere G2H eksperimente het egter geen sarkomeriese ligande van die N-terminale gedeelte van kMiBPC geïdentifiseer nie. Die identifikasie van ligande van spesifieke domeins van kMiBPC het gelei tot die ontwikkelling van ‘n gedetaileerde model van kMiBPC kwaternêre struktuur wanneer kMiBPC beide ongefosforileerd en ten volle gefosforileerd is. Die intergrasie van hierdie modelle in bestaande modelle van dik filament kwaternêre struktuur werp nuwe lig op die funksionering van kMiBPC as ‘n reguleerder van beide dik filament struktuur en kardiale kontraktiliteit, sowel as die patofisiologie van kMiBPCgeassosieerde HKM.

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39

Portman, Katherine Louise. "Characterising the binding interactions and thermodynamics of odour binding protein 3". Thesis, University of Nottingham, 2012. http://eprints.nottingham.ac.uk/13704/.

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Odour Binding Proteins (OBPs) are found in the olfactory system of a range of species. Whilst invertebrate OBP function is well understood, the exact function of these proteins in the vertebrate nasal mucus is not fully understood. Multiple subtypes of rat OBPs have been identified and found to share less than 30% sequence identity. Studies have suggested each rat OBP binds to particular sets of odours, which may afford them a particularly important role within the olfactory system, pre-sorting odours. This study focuses on OBP3, closely examining the binding interaction of this protein with a range of odours. This has been done using Isothermal Titration Calorimetry which revealed that the binding of the highest affinity ligands, the heterocyclic compounds, is enthalpically driven. A defined odour series, the gamma-lactones showed that despite increasing ligand size and hydrophobicity, the free energy of binding of these ligands is maintained. Interactions with both 2-isobutylthiazole and the gamma-lactones were examinedusing NMR spectroscopy, which required the NMR assignment of OBP3 to be determined. In addition a homology model of OBP3 was created in order to structurally map the per-residue changes of OBP3 upon binding. It has been found that OBP3 is able to subtly adjust in order to accommodate each of these ligands. Protein engineering of the OBP3 binding pocket has been used to highlight the importance of its size and hydrophobicity. The importance of a tyrosine residue that appears to cover the opening to the binding pocket and is conserved across both the aBPs and the lipocalins family they are part of, has been demonstrated. Mutagenesis has also revealed the importance of a number of key residues for the binding of 2-isobutylthiazole. The ability to rationally improve the affinity of OBP3 for a particular odour has also been demonstrated.

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40

Goddard, C. "DNA and chromatin binding by the methyl-CpG-binding protein, MeCP2". Thesis, University of Cambridge, 2003. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.599452.

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In eukaryotes, methylation at CpG dinucleotides causes transcriptional repression. MeCP2 is a good candidate for a transducer of this methylation signal as it is capable of binding to methylated DNA and can repress transcription in vitro. This thesis describes experiments to further investigate the DNA and chromatin binding properties of MeCP2. Chapter 2 describes the subcloning, overexpression and purification of recombinant rat MeCP2 and also the purification of native MeCP2 from rat brain. The similarity in purification protocols indicates that the recombinant protein is a good model for the native protein. Chapter 3 describes in vitro assays for DNA and chromatin binding. The DNA binding assays confirm that MeCP2 binds to both methylated and unmethylated DNA but has a preference for methylated DNA. The chromatin binding assays show that MeCP2 binds chromatin of all lengths in vitro and most evidence indicates that it is capable of displacing histone H1. Crosslinking experiments showed that MeCP2 crosslinks to core histones and maybe also to itself. The electrophoretic mobility shift assay and also the arrangement of endogenous MeCP2 in native chromatin indicate that MeCP2 may exhibit co-operativity. The crosslinking data suggested that co-operativity may be mediated by protein-protein interactions but this was shown not to be the case by gel filtration. Another possibility was that MeCP2 arrays could be protected by higher order folding. Analytical ultracentrifugation and electron microscopic analysis show that MeCP2 does not induce higher order folding itself. It may be that other factors cause folding of inactive chromatin and protect MeCP2 arrays. The in vitro data indicates that MeCP2 acts non-specifically. In the work described in Chapter 4, a chromatin immunoprecipitation (ChIP) assay was used to investigate whether MeCP2 displays specificity in vivo. It was found that MeCP2 binds NSE, Mash2, H19 and HPRT, but not GAPDH in both female rat brain and female rat liver nuclei, and to ADH in female rat brain but not female rat liver nuclei.

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41

Sealey, Amy Lynn. "Loss of the murine TATA-binding protein N terminus leads to placental labyrinth defects but not maternal adaptive immune responses". Thesis, Montana State University, 2007. http://etd.lib.montana.edu/etd/2007/sealey/SealeyA0507.pdf.

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42

Bolotin, Eugene Leonidovich. "Investigation of transcription factor binding sequences and target genes using protein binding microarrays". Diss., [Riverside, Calif.] : University of California, Riverside, 2010. http://proquest.umi.com/pqdweb?index=0&did=2019822801&SrchMode=2&sid=3&Fmt=2&VInst=PROD&VType=PQD&RQT=309&VName=PQD&TS=1274203752&clientId=48051.

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Thesis (Ph. D.)--University of California, Riverside, 2010.
Includes abstract. Available via ProQuest Digital Dissertations. Title from first page of PDF file (viewed May 18, 2010). Includes bibliographical references. Also issued in print.

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43

Taubner, Lara Marie. "Structural investigations of the cancer-associated laminin binding protein and Nos L a novel copper binding protein /". Diss., Montana State University, 2005. http://etd.lib.montana.edu/etd/2005/taubner/TaubnerL1205.pdf.

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44

Tan, Yaw Sing. "Protein-protein interactions : binding site detection using molecular dynamics simulations". Thesis, University of Cambridge, 2014. https://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.708425.

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45

Guelev, Vladimir Metodiev. "Peptide-based polyintercalators as sequence-specific DNA binding agents /". Full text (PDF) from UMI/Dissertation Abstracts International, 2001. http://wwwlib.umi.com/cr/utexas/fullcit?p3008346.

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46

Philips, Brian John. "Protein interactions with the catechol estrogens 4-hydroxyestrone and 4-hydroxyestradiol in mouse tissue lysate : binding and metabolism studies /". free to MU campus, to others for purchase, 2001. http://wwwlib.umi.com/cr/mo/fullcit?p3036851.

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Jones, Lisa Michelle. "Using Protein Design to Understand the Role of Electrostatic Interactions on Calcium Binding Affinity and Molecular Recognition". Digital Archive @ GSU, 2008. http://digitalarchive.gsu.edu/chemistry_diss/16.

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Calcium regulates many biological processes through interaction with proteins with different conformational, dynamic, and metal binding properties. Previous studies have shown that the electrostatic environment plays a key role in calcium binding affinity. In this research, we aim to dissect the contribution of the electrostatic environment to calcium binding affinity using protein design. Many natural calcium binding proteins undergo large conformational changes upon calcium binding which hampers the study of these proteins. In addition, cooperativity between multiple calcium binding sites makes it difficult to study site-specific binding affinity. The design of a single calcium binding site into a host system eliminates the difficulties that occur in the study of calcium binding affinity. Using a computer algorithm we have rationally designed several calcium binding sites with a pentagonal bipyramidal geometry in the non-calcium dependent cell adhesion protein CD2 (CD2-D1) to better investigate the key factors that affect calcium binding affinity. The first generation proteins are all in varying electrostatic environments. The conformational and metal binding properties of each of these designed proteins were analyzed. The second generation designed protein, CD2.6D79, was designed based on criteria learned from the first generation proteins. This protein contains a novel calcium binding site with ligands all from the â-strands of the non-calcium dependent cell adhesion protein CD2. The resulting protein maintains native secondary and tertiary packing and folding properties. In addition to its selectivity for calcium over other mono and divalent metal ions, it displays strong metal binding affinities for calcium and its analogues terbium and lanthanum. Furthermore, our designed protein binds CD48, the ligand binding partner of CD2, with an affinity three-fold stronger than CD2. The electrostatic potential of the calcium binding site was modified through mutation to facilitate the study of the effect of electrostatic interactions on calcium binding affinity. Several charge distribution mutants display varying metal binding affinities based on their charge, distance to the calcium binding site, and protein stability. This study will provide insight into the key site factors that control calcium binding affinity and calcium dependent biological function.

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Johansson, Kenth. "Structural studies of four nucleotide binding proteins : aldehyde dehydrogenase, NADP-malate dehydrogenase and two deoxynucleoside kinases /". Uppsala : Swedish University of Agricultural Sciences, 2000. http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&doc_number=009416200&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA.

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Davies, Holly Gibs. "MSY4, a sequence-specific RNA binding protein expressed during mouse spermatogenesis /". Thesis, Connect to this title online; UW restricted, 2000. http://hdl.handle.net/1773/10307.

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Zhou, Li. "Binding study of nickel complex to protein by equilibrium dialysis". Scholarly Commons, 1998. https://scholarlycommons.pacific.edu/uop_etds/517.

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A pyridine-containing Schiff base complex, 2, 12-dimethyl-3,7, 11 ,17- tetraazabicyclo( 11.3 .1 )-heptadeca-1 ( 17),2, 11 ,13, 15-pentaene, was chosen as the complex in this study based on previous studies that showed it to be the most active complex among a series of square planar nickel complexes in promoting DNA oxidation. This complex was synthesized and its structure was proven by electrospray mass spectroscopy, H-NMR, and elemental analysis. The H-NMR data also demonstrated that this complex has two vacant coordination sites in the distorted octahedral form in aqueous solution. Histone and bovine serum albumin which are typical proteins in eukaryote animals were chosen as the target materials when I studied whether this nickel complex could bind to proteins in the body. Nickel complex was labeled with Ni63 during the dialysis, and counted by a liquid scintillation counter.

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