Thesis (Ph. D.)--University of Wyoming, 2006. / Title from PDF title page (viewed on Dec. 21, 2007). Includes bibliographical references.

Nuclear receptors are ligand activated transcription factors, where upon binding with small molecule ligands, these proteins are involved in the regulation of gene expression. To date there are approximately 48 human nuclear receptors known, involved in multiple biological and cellular processes, ranging from differentiation to maintenance of homeostasis. Due to their critical role in transcriptional regulation, these receptors are implicated in several diseases. Currently, 13% of prescribed drugs in the market are NR ligands for diseases such as cancer, diabetes and osteoporosis. In addition to drug discovery, the mechanism of function, mobility and trafficking of these receptors is poorly understood. Gaining insight into the relationship between the function and /or dysfunction of these receptors and their mobility will aid in a better understanding of the role of these receptors. The green fluorescent protein (GFP) has revolutionized molecular biology by providing the ability to monitor protein function and structure via fluorescence. The fluorescence contribution from this biological marker is the chromophore, formed from the polypeptide backbone of three amino acid residues, buried inside 11-stranded â-barrel protein. Synthesis of GFP derivatives of is based on the structure of the arylmethyleneimidazolidinone (AMI), creating a molecule that is only weakly fluorescent. Characterizing these AMI derivatives for other proteins can provide a powerful visualization tool for analysis of protein function and structure. This development could provide a very powerful method for protein analysis in vitro and in vivo. Development of such fluorescent ligands will prove beneficial for the nuclear receptors. In this work, libraries of AMIs derviatives were synthesized by manipulating various R groups around the core structure, and tested for their ability to serve as nuclear receptor ligands with the ability to fluoresce upon binding. The fluorogens are developed for steroidal and non-steroidal receptors, two general classes of nuclear receptors. Specific AMIs were designed and developed for steroid receptor estrogen receptor á (ERá). These ligands are showed to activate the receptor with an EC50 of value 3 ìM and the 10-fold activation with AMI 1 and AMI 2 in comparison to the 21-fold activation observed with natural ERá ligand, 17â-estradiol. These novel ligands were not able to display the fluorescence upon binding the receptor. However, fluorescence localized in nucleus was observed in case of another AMI derivative, AMI 10, which does not activate the receptor. Such ligands open new avenues for developing fluorescent probes for ERá that do not involve fluorescent conjugates attached to a known ERá ligand core. AMIs were also characterized for non-steroidal receptors,specifically the pregnane x receptor (PXR) and retinoic acid receptor á (RARá). To date, fluorogens which turn fluorescence upon binding and activate the receptor have not been developed for these receptors. With respect to PXR, several AMI derivatives were discovered to bind and activate this receptor with a fold-activation better than the known agonist, rifampicin. The best characterized AMI derivative, AMI 4, activates the receptor with an EC50 of value 6.3 ìM and the 154-fold activation in comparison to the 90-fold activation and an EC50 value of 1.3 ìM seen with rifamipicin. This ligand is not only able to activate PXR but also displays fluorescence upon binding to the receptor. The fluroscence pattern was observed around the nucleus. Besides AMI 4, 16 other AMI derivatives are identified that activate PXR with different activation profiles. Thus, a novel class of PXR ligands with fluorescence ability has been developed. The AMI derivatives able to bind and activate RAR, also displayed activation profiles that were comparable to the wild-type ligand, all trans retinoic acid. These ligands activated the receptor with an EC50 value of 220 nM with AMI 109 in comparison to an EC50 value of 0.8 nM with the natural ligand for RARá. When these ligands were tested for fluorescence in yeast, the yeast were able to fluoresce only in the presence of the receptor and the AMI derivative, indicating that these agonists also have the ability to fluoresce.

The human body is an intricate network of many highly regulated biochemical processes and cell adhesion is one of them. Cell adhesion is mediated by specific interactions between molecules on apposing cell surfaces and is critical to many physiological and pathological processes like inflammation and cancer metastasis. During inflammation, blood-borne circulating leukocytes regularly stick to and roll on the vessel walls, which consist in part, adhesive contacts mediated by the selectin family of adhesion receptors (P-, E- and L-selectin). This is the beginning of a multi-step cascade that ultimately leads to leukocyte recruitment in areas of injury or infection. In vivo, selectin-mediated interactions take place in a hydrodynamic milieu and hence, it becomes imperative to study these interactions under very similar conditions in vitro. The goal of this project was to characterize the kinetic and mechanical properties of selectin interactions with different physiologically relevant ligands and selectin-specific monoclonal antibodies (mAbs) under a mechanically stressful milieu, using atomic force microscopy (AFM). Elasticity studies revealed that bulk of the complex compliance came from the selectins, with the ligands or mAbs acting as relatively stiffer components in the stretch experiments. Furthermore, molecular elasticity was inversely related to selectin length with the Consensus Repeats (CRs) behaving as Hookean springs in series. Besides, monomeric vs. dimeric interactions could be clearly distinguished from the elasticity measurements. L-selectin dissociation studies with P-selectin Glycoprotein Ligand 1 (PSGL-1) and Endoglycan revealed that catch bonds operated at low forces while slip bonds were observed at higher forces. These results were consistent with previous P-selectin studies and suggested that catch bonds could contribute to the shear threshold for L-selectin-mediated rolling By contrast, only slip bonds were observed for L-selectin-antibody interactions, suggesting that catch bonds could be a common characteristic of selectin-ligand interactions. Force History studies revealed that off-rates of L-selectin-sPSGL-1 (or 2-GSP-6) interactions were not just dependent on applied force, as has been widely accepted but in fact, depended on the entire history of force application, thus providing a new paradigm for how force could regulate bio-molecular interactions. Characterizing selectin-ligand interactions at the molecular level, devoid of cellular contributions, is essential in understanding the role played by molecular properties in leukocyte adhesion kinetics. In this aspect, data obtained from this project will not only add to the existing body of knowledge but also provide new insights into mechanisms by which selectins initiate leukocyte adhesion in shear.

An in silico design algorithm has been developed to design binding ligands for protein targets of known three-dimensional structure. In this method, the binding energy of a candidate ligand is used to ascribe it a probability of binding. A sample of a virtual library of candidate ligands is then used to ascribe implicit weights to all the ligands in the library. These weights are used to obtain virtual sub-libraries which collectively carry a greater probability to bind to the target. This algorithm is presented along with validation studies on the different algorithmic components, demonstrating how optimization of the design method can be best achieved.

Thesis (M. S.)--Biomedical Engineering, Georgia Institute of Technology, 2006. / Committee Chair: Zhu, Cheng; Committee Member: Babensee, Julia; Committee Member: Dustin, Michael; Committee Member: Garcia, Andres; Committee Member: Jo, Hanjoong; Committee Member: van der Merwe, Anton. Part of the SMARTech Electronic Thesis and Dissertation Collection. Non-Latin script record

Thesis (Ph. D.)--University of Washington, 2002. / Vita. Includes bibliographical references (leaves 141-161).

Thesis (Ph. D.)--University of Oregon, 2002. / Typescript. Includes vita and abstract. Includes bibliographical references (leaves 159-167). Also available for download via the World Wide Web; free to University of Oregon users.

Thesis (Ph. D.)--University of Washington, 2003. / Vita. Includes bibliographical references (leaves 110-117).

Thesis (M. Sc.)--York University, 2001. Graduate Programme in Biology. / Typescript. Includes bibliographical references (leaves 106-118). Also available on the Internet. MODE OF ACCESS via web browser by entering the following URL: http://wwwlib.umi.com/cr/yorku/fullcit?pMQ66399.

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