Characterising transcription factor binding sites (TFBS) is an important problem in bioinformatics, since predicting binding sites has many applications such as predicting gene regulation. ChIP-seq is a powerful in vivo method for generating genome-wide putative binding regions for transcription factors (TFs). CentriMo is an algorithm that measures central enrichment of a motif and has previously been used as motif enrichment analysis (MEA) tool. CentriMo uses the fact that ChIP-seq peak calling methods are likely to be biased towards the centre of the putative binding region, at least in cases where there is direct binding. CentriMo calculates a binomial p-value representing central enrichment, based on the central bias of the binding site with the highest likelihood ratio. In cases where binding is indirect or involves cofactors, a more complex distribution of preferred binding sites may occur but, in many cases, a low CentriMo p-value and low width of maximum enrichment (about 100bp) are strong evidence that the motif in question is the true binding motif. Several other MEA tools have been developed, but they do not consider motif central enrichment. The study investigates the claim made by Zhao and Stormo (2011) that they have identified a simpler method than that used to derive the UniPROBE motif database for creating motifs from protein binding microarray (PBM) data, which they call BEEML-PBM (Binding Energy Estimation by Maximum Likelihood-PBM). To accomplish this, CentriMo is employed on 13 motifs from both motif databases. The results indicate that there is no conclusive difference in the quality of motifs from the original PBM and BEEML-PBM approaches. CentriMo provides an understanding of the mechanisms by which TFs bind to DNA. Out of 13 TFs for which ChIP-seq data is used, BEEML-PBM reports five better motifs and twice it has not had any central enrichment when the best PBM motif does. PBM approach finds seven motifs with better central enrichment. On the other hand, across all variations, the number of examples where PBM is better is not high enough to conclude that it is overall the better approach. Some TFs bind directly to DNA, some indirect or in combination with other TFs. Some of the predicted mechanisms are supported by literature evidence. This study further revealed that the binding specificity of a TF is different in different cell types and development stages. A TF is up-regulated in a cell line where it performs its biological function. The discovery of cell line differences, which has not been done before in any CentriMo study, is interesting and provides reasons to study this further.

Please read the abstract in the section 00front of this document / Thesis (PhD (Microbiology))--University of Pretoria, 2005. / Microbiology and Plant Pathology / unrestricted

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

Pituitary hormones are known to alter sex steroid receptor levels in the liver, and possibly the actions of the steroids as well. Recently, two classes of estrogen binding proteins have been characterized in male rat hepatic cytosol: a high affinity, low capacity estrogen receptor, and a lower affinity, higher capacity sex steroid binding component (moderate affinity component). It is of interest that the moderate affinity component binds both androgens and estrogens. A high affinity, low capacity androgen receptor has not been convincingly demonstrated in rat hepatic cytosol. Therefore, we have investigated the relationship of the moderate affinity component to sex steroid modulation of hepatic aryl hydrocarbon hydroxylase (AHH) activity as a possible control mechanism. Because of the sexual dimorphism for hepatic drug and steroid metabolism known to occur in rat liver, we chose this model to study. We have shown that no sex difference exists for the binding of pH]-estradiol to the estrogen receptor from either immature or adult rats. However, the moderate affinity component does exhibit a sex difference. We did not detect binding to the moderate affinity component in adult female or immature rats of either sex. This site could normally only be measured in the adult male. These findings were consistent with the age and sex dependent elevation of male AHH activity. We have also observed that gonadectomy of the male reduced the levels of AHH activity and the capacity of the moderate affinity component in a testosterone reversible fashion. These results were obtained using either unlabeled estradiol or dihydrotestosterone (DHT) as competitors for [³H]-estradiol binding. Administration of mestranol reduced AHH activity and the capacity of the moderate affinity component in the male. The moderate affinity component was not detected in the pseudoherma-phroditic rat which resembled the female, rather than the male, with respect to control and induced AHH activity. Hypophysectomy of the female resulted in an increase in AHH activity and detection of the moderate affinity component. Hypophysectomy of the male reduced both the capacity of the moderate affinity component and AHH activity. Unlike the gonadectomized male, testosterone had no restorative effect on the levels of AHH activity or the capacity of the moderate affinity component in the hypophy-sectomized rat. Continuous infusion of rat growth hormone (rGH) reversed the effect of hypophysectomy on the increased AHH activity and capacity of the moderate affinity component in the female. Administration of rGH to the hypophysectomized male abolished the detection of the moderate affinity component and reduced AHH activity to control female levels. This suggested rGH may be the pituitary hormone involved in production of the female level of metabolism. The effects of prolactin were not as clear. Therefore, we have demonstrated the modulation of AHH activity by peripheral sex steroids, and the regulation of these parameters by rGH. We have shown, the capacity of the moderate affinity component to vary in a manner that paralleled changes in hepatic AHH activity in different physiological models. Changes in the estrogen receptor were not found to be consistent with changes in AHH activity in these models. We conclude that the moderate affinity component is comparable to the male hepatic cytosolic DHT-binding protein. Furthermore, this component is associated with sex steroid action on hepatic AHH activity in the male rat. Interestingly, we have also shown this component as well as the estrogen receptor, to bind polycyclic aromatic hydrocarbons. Both 3-methylcholanthrene and benzo[a]pyrene competed for [³H]-estradiol binding to the estrogen receptor and moderate affinity component. In addition, dioxin congeners demonstrated specificity for the estrogen receptor in the female. However, this was not observed for the estrogen receptor or moderate affinity component in the male. The significance of this is presently unclear. / Pharmaceutical Sciences, Faculty of / Graduate

The field of metabolic engineering focuses on using molecular biology tools to genetically modify the metabolic pathways of cells for the production of chemical compounds. The field of directed evolution can alter the native abilities of proteins by taking inspiration from natural evolution. Both fields bring novel solutions to current problems in energy, the environment, and medicine. However, there is still no general higher throughput screening method for both of these fields. In this dissertation, we apply our designed fluorescence polarization assay to fill this need in the fields of metabolic engineering and directed evolution. Chapter 0 gives background information related to metabolic engineering, directed evolution, tetracyclines, the Tetracycline Repressor protein (TetR), TAN-1612, and fluorescence polarization. Chapter 1 describes our development of a quantitive, sensitive, and fast fluorescence polarization assay which uses the TetR protein to detect the binding of the small molecule tetracycline TAN-1612. Chapter 2 demonstrates that the binding affinity of the TetR protein for TAN-1612 can be improved using directed evolution and by incorporating our assay to screen TetR mutants. Finally, in Chapter 3 we apply our fluorescence polarization assay to the screening of yeast strains biosynthesizing TAN-1612, without the need of time and labor intensive extraction and purification steps.

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.

Indiana University-Purdue University Indianapolis (IUPUI) / Molecular recognition plays an important role in biological systems. The purpose of this study was to get a better understanding of the process by incorporating computational tools.Molecular Mechanics-Generalized Born Surface Area (MM-GBSA) method and Molecular Mechanics-Poisson Boltzmann Surface Area (MM-PBSA) method, the end-point free energy calculations provide the binding free energy the can be used to rank-order protein–ligand structures in virtual screening for compound or target identification. Free energy calculations were performed on a diverse set of 11 proteins bound to 14 small molecules was carried out for. A direct comparison was taken between the calculated free energy and the experimental isothermal titration calorimetry (ITC) data. Four and three systems in MM-GBSA and MM-PBSA calculations, respectively, reproduced the ITC free energy within 1 kcal•mol–1. MM-GBSA exhibited better rank-ordering with a Spearman ρ of 0.68 compared to 0.40 for MM-PBSA with dielectric constant (ε = 1). The rank-ordering performance of MM-PBSA improved with increasing ε (ρ = 0.91 for ε = 10), but the contributions of electrostatics became significantly lower at larger ε level, suggesting that the only nonpolar and entropy components contribute to the improved results. Our previously developed scoring function, Support Vector Regression Knowledge-Based (SVRKB), resulted in excellent rank-ordering (ρ = 0.81) when applied into MD simulations. Filtering MD snapshots by prescoring protein–ligand complexes with a machine learning-based approach (SVMSP) resulted in a significant improvement in the MM-PBSA results (ε = 1) from ρ = 0.40 to ρ = 0.81. Finally, the nonpolar components in the free energy calculations showed strong correlation to the ITC free energy while the electrostatic components did not; the computed entropies did not correlate with the ITC entropy. Explicit-solvent molecular dynamics (MD) simulations offer an opportunity to sample multiple conformational states of a protein-ligand system in molecular recognition. SVMSP is a target-specific rescoring method that combines machine learning with statistical potentials. We evaluate the performance of SVMSP in its ability to enrich chemical libraries docked to MD structures. Seven proteins from the Directory of Useful Decoys (DUD) were involved in the study. We followed an innovative approach by training SVMSP scoring models using MD structures (SVMSPMD). The resulting models remarkably improved enrichment in two cases. We also explored approaches for a prior identification of MD snapshots with high enrichment power from an MD simulation in the absence of active compounds. SVMSP rescoring of protein–compound MD structures was applied for the search of small-molecule inhibitors of the mitochondrial enzyme aldehyde dehydrogenase 2 (ALDH2). Rank-ordering of a commercial library of 50,000 compounds docked to MD optimized structures of ALDH2 led to five small-molecule inhibitors. Four compounds had IC50s below 5 μM. These compounds serve as leads for the design and synthesis of more potent and selective ALDH2 inhibitors.

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.

No description available.

Objectives: Traditional guided tissue regeneration procedures use particulate bone graft materials and occlusive membranes with the primary aim of reconstitution of the supporting periodontal tissues. Currently, the Food and Drug Administration has cleared only four treatment modalities for true periodontal regeneration. These materials are autogenous bone, demineralized freeze dried bone allograft, LANAP (Millennium Dental Technologies INC, Cerritos, CA) and Emdogain (Institut Straumann AG, Basel, Switzerland). The biologically inactive nature of many commercially available bone graft materials provides an opportunity for the addition of certain biologic materials to enhance the healing response. The development of an adequate carrier for biologic agents is a crucial step in the creation of a bioactive graft material. This experiment uses Emdogain (Institut Straumann AG, Basel, Switzerland) to study the specific characteristics of protein binding and release on three different commonl / Oral Biology