Thesis (Ph. D.) -- University of Texas Southwestern Medical Center at Dallas, 2005. / Vita. Bibliography: 209-224.

Thesis (doctoral)--Lund University, 1998. / Thesis statement inserted. Includes bibliographical references.

Thesis (doctoral)--Lund University, 1998. / Thesis statement inserted. Includes bibliographical references.

O trabalho descrito nesta tese mostra a aplicação de um sistema de detecção condutométrica sem contato acoplado capacitivamente (C4D) para monitorar interações biomoleculares em microssistemas analíticos. Inicialmente, o desempenho analítico de microssistemas fabricados em vidro, poli(dimetilsiloxano) (PDMS) e poliéster-toner (PT) foi avaliado de modo a escolher o melhor material (em termos de facilidades de fabricação, custo e repetibilidade) para os ensaios biomoleculares. Dentre os materiais estudados, os dispositivos fabricados em PT mostraram-se mais adequados para testes rápidos, onde a repetibilidade analítica não é o parâmetro mais importante. Os dispositivos fabricados em PDMS e selados contra uma placa de vidro apresentaram os melhores resultados em termos de repetibilidade e o desempenho analítico foi similar aos dispositivos de vidro. Dessa maneira, os dispositivos fabricados em PDMS/vidro foram escolhidos para a demonstração dos objetivos da tese. Por outro lado, os dispositivos fabricados em PT foram explorados para estudar a configuração geométrica do sistema de C4D. A instrumentação para monitoramento dos ensaios de ligação foi composta basicamente de dois sistemas de C4D, um software escrito em LabVIEW e um sistema de bombeamento das soluções. De modo a encontrar a configuração ideal da cela de detecção, geometrias contendo três, quatro e cinco eletrodos foram avaliadas em dispositivos de PT. A configuração ótima foi composta de três eletrodos, espaçados simetricamente. Nesta geometria, um eletrodo é utilizado para aplicar o sinal senoidal de excitação e os outros dois são utilizados para capturar o sinal resultante. As dimensões dos eletrodos (largura e espaçamento entre eles) foram otimizados usando ferramentas quimométricas. O complexo avidina-biotina foi utilizado como modelo de ligação para mostrar a aplicabilidade do sistema proposto. Para os microssistemas biomoleculares, os eletrodos (com geometria otimizada) foram fabricados sobre a superfície de uma placa de vidro por fotolitografia, sputtering e lift-off. Os eletrodos de detecção foram isolados com uma camada de óxido de silício com espessura de 50 nm, depositada pelo processo de deposição química em fase de vapor assistida por plasma. A camada de SiO2 foi modificada quimicamente com solução de 3-amino-propil-trietóxi-silano em etanol. Para imobilização covalente de biotina, uma alíquota de 10 ?L de fotobiotina dissolvida em água (0,1 mg/mL) foi adicionada à superfície e exposta a radiação ultravioleta (365 nm, 10 mW/cm2) durante 15 min. A detecção foi realizada aplicando um sinal senoidal, a partir de um gerador de funções, ao eletrodo de excitação registrando o sinal resultante nos dois eletrodos receptores. Para minimizar a captura de ruído elétrico, os experimentos foram realizados em uma gaiola de Faraday. O controle e a aquisição de dados foi feito mediante um software escrito em LabVIEW monitorando os sensorgramas de condutividade em tempo real. Os canais microfluídicos foram fabricados em PDMS por litografia suave e selados irrevesivelmente contra a placa de vidro contendo os eletrodos isolados e modificados quimicamente. As soluções (tampão e amostra) foram manuseadas com auxílio de uma bomba peristáltica ou duas bombas seringas. Soluções contendo tampão e avidina foram introduzidas nos microcanais e as mudanças de conductividade foram monitoradas em função do tempo. As soluções contendo avidina permaneceram em contato com a superfície modificada até o sinal de condutividade atingir um patamar de equilíbrio. Depois disso, solução tampão foi introduzida no microcanal para remover os analitos adsorvidos à superfície. Duas válvulas solenóides foram utilizadas para permitir um controle automático da distribuição das soluções nos microcanais. O limite de detecção obtido para a interação entre avidina e biotina foi de 75 nmol L-1. / The study reported in this thesis shows the application of a capacitively coupled contactless conductivity detection (C4D) for monitoring biomolecular interactions on analytical microsystems. Initially, the analytical performance of the microsystems fabricated in glass, poly(dimethylsiloxane) (PDMS) and polyester-toner (PT) was investigated in order to choose the best material (in terms of fabrication facilities, costs and repeatability) for the biomolecular assays. Among all substrate materials studied, devices fabricated in PT showed suitability for quick experiments, in which the analytical repeatability is not the most important parameter. The devices fabricated in PDMS and sealed against a glass plate presented the best results in terms of repeatability and the analytical performance was similar to that one of glass devices. For this reason, PDMS/glass devices were chosen for showing the goals of this thesis. On the other hand, PT devices were employed to study the geometrical design of the C4D system. The instrumentation for monitoring binding assays was basically composed of two C4D systems, a software written in LabVIEW and a solution pumping system. In order to find the suitable detection cell configuration for this dual-C4D system, designs containing three, four and five electrodes were evaluated on PT devices. The optimal design was composed of three electrodes symmetrically spaced. In this configuration, one electrode is used for applying an excitation sinusoidal wave and the other two for picking up the resulting signal. The dimensions of the electrodes (width and gap) were optimized by chemometric tools. The avidin-biotin complex was used as a binding model for showing the feasibility of the proposed system. For the biomolecular microsystems, electrodes were fabricated on glass surface using photolithographic, sputtering and lift-off processes. Detection electrodes were insulated with a 50-nm silicon oxide layer deposited by plasmaenhanced chemical vapor deposition. The SiO2 layer was functionalized by immersing the cleaned surface in a 3-aminopropyltriethoxy-silane solution in ethanol for 3 h. For biotinylation of the amino-silane layer, 10 ?L of photobiotin dissolved in deionized water (0.1 mg/mL) was dropped on the modified glass surface and exposed to a 365 nm UV radiation at intensity of 10 mW/cm2 for 15 min. Detection was carried out by passing a sinusoidal excitation signal from the function signal generator to the first electrode and picking up the resulting signal at the two receiver electrodes. To reduce electrical noise pickup, all measurements were carried out in a Faraday cage. The data acquisition was obtained in a software written in LabVIEW and the conductivity sensorgrams were recorded in real-time. The microfluidic network was fabricated in PDMS by soft lithography and irreversibly sealed against the electrodes plate. Solutions were handled into microfluidic channels using a peristaltic pump or two syringe pumps. Buffer and avidin-containing solution was injected into the microchannels and conductivity changes were monitored over time. Avidin solutions were allowed to remain in contact with the surface until a stable conductivity had reached equilibrium. Avidin-free buffer solutions were then injected to rinse off non-specifically bound analytes. Two solenoid valves were used to allow an automatic dispensing of the sample/buffer solution into microchannels. The limit of detection found for avidin-biotin system was 75 nmol L-1.

No description available.

NMR chemical shifts have an extremely high information content on the behaviour of macromolecules, owing to their non-trivial dependence on myriads of structural and environmental factors. Although such complex dependence creates an initial barrier for their use for the characterisation of the structures of protein and nucleic acids, recent developments in prediction methodologies and their successful implementation in resolving the structures of these molecules have clearly demonstrated that such barrier can be crossed. Furthermore, the significance of chemical shifts as useful observables in their own right has been substantially increased since the development of the NMR techniques to study low populated 'excited' states of biomolecules. This work is aimed at increasing our understanding of the multiple factors that affect chemical shifts in proteins and nucleic acids, and at developing high-quality chemical shift predictors for atom types that so far have largely escaped the attention in chemical shift restrained molecular dynamics simulations. A general approach is developed to optimise the models for structure-based chemical shift prediction, which is then used to construct CH3Shift and ArShift chemical shift predictors for the nuclei of protein side-chain methyl and aromatic moieties. These results have the potential of making a significant impact in structural biology, in particular when taking into account the advent of recent techniques for specific isotope labelling of protein side-chain atoms, which make large biomolecules accessible to NMR techniques. Through their incorporation as restraints in molecular dynamics simulations, the chemical shifts predicted by the approach described in this work create the opportunity of studying the structure and dynamics of proteins in a wide range of native and non-native states in order to characterise the mechanisms underlying the function and dysfunction of these molecules.

In the first part of this research, we constructed a Genome scale Metabolic Model (GEM) of Taxus cuspidata, a medicinal plant used to produce paclitaxel (Taxol®). The construction of the T. cuspidata GEM was predicated on recent acquisition of a transcriptome of T. cuspidata metabolism under methyl jasmonate (MJ) elicited conditions (when paclitaxel is produced) and unelicited conditions (when paclitaxel is not produced). Construction of the draft model, in which transcriptomic data from elicited and unelicited conditions were included, utilized tools including the ModelSEED developed by Argonne National Laboratory. Although a model was successfully created and gapfilled by ModelSEED using their software, we were not able to reproduce their results using COBRA, a widely accepted FBA software package. Further work needs to be done to figure out how to run ModelSEED models on commonly available software. In the second part of this research, we modeled the MJ elicited/defense response phenotype in Arabidopsis thaliana. Previously published models of A. thaliana were tested for suitability in modeling the MJ elicited phenotype using publicly available computation tools. MJ elicited and unelicited datasets were compared to ascertain differences in metabolism between these two phenotypes. The MJ elicited and unelicited datasets were significantly different in many respects, including the expression levels of many genes associated with secondary metabolism. However, it was found that the expression of genes related to growth and central metabolism were not generally significantly different for the MJ+ and MJ- datasets, the pathways associated with secondary metabolism were incomplete and could not be modeled, and FBA methods did not show the difference in growth that was expected. These results suggest that behavior associated with the MJ+ phenotype such as slow growth and secondary metabolite production may be controlled by factors not easily modeled with transcriptome data alone. Additional research was performed in the area of cryosectioning and immunostaining of fixed Taxus aggregates. Protocols developed for this work can be found in Appendix B.

One of the most promising routes to renewable liquid fuels and chemicals is the fermentation of waste carbon by specialized microbes. Commercial development of gas fermentation technology is underway but many fundamental research problems must be addressed to further advance the technology towards economic competitiveness. This thesis addresses the important problem of developing integrated metabolic and transport models that predict gas fermentation performance in industrially relevant bubble column reactors. The computational models describe the conversion of CO-rich waste streams including synthesis gas to the platform chemical butyrate. The proposed modeling approach involves combining genome-scale reconstructions of bacterial species metabolism with transport equations that govern the relevant multiphase convective and diffusional processes within the spatially-varying system. I compared the combination of the acetogen Clostridium autoethanogenum for CO conversion to the intermediate acetate and three different gut bacteria (Clostridium hylemonae, Eubacterium rectale and Roseburia hominis) for conversion of acetate to butyrate. Trial-and-error optimization of the three co-culture designs was performed to assess their relative performance and guide future experimental studies.

<div>Protein N-terminal methyltransferases (NTMTs) are a family of enzymes that methylate the α-N-terminus of a variety of protein substrates. Both NTMT1 and NTMT2 recognize a unique N-terminal X-P-K/R motif (X represents any amino acid other than D/E) to install 1-3 methyl group(s) on the substrates. NTMT1 plays important roles in mitosis regulation, chromatin interactions, and DNA damage repair. Another member NTMT2 shares ~50% sequence similarity and the same substrate recognition motif although NTMT2 was initially characterized as a mono-methyltransferase. To understand the molecular mechanism of NTMT2, we obtained the first co-crystal structure of NTMT2 in complex with its peptide substrate. After an extensive investigation of substrate recognition and methylated products of NTMT1/2, we found out that NTMT2 can fully methylate G/P-PKRIA peptides despite a predominant mono-methyltransferase. Moreover, we identified a gatekeeper N89 in NTMT2 that controls the substrate entry and the product specificity of NTMT2.</div><div>To elucidate the biological functions of NTMT1/2-catalyzed N-terminal methylation, we applied two different strategies to discover cell-potent inhibitors. Guided by the co-crystal structures of NTMT1 in complex with previously reported inhibitors, we designed and synthesized a series of new peptidomimetic inhibitors. By introducing more hydrophobic groups, the most cell-potent peptidomimetic inhibitor GD562 (IC50 = 0.93 ± 0.04 µM) exhibited over 2-fold increased inhibition on cellular N-terminal methylation levels with an IC50 value of ~50 µM compared to previously reported peptidomimetic inhibitor DC541. Meanwhile, we also discovered the first potent small molecule inhibitor Genz-682452 (IC50 = 0.5 ± 0.04 µM) after screening ~58,000 compounds. Subsequent structural modifications led to the discovery of GD433 (IC50 = 27 ± 0.5 nM) with a 20-fold increased potency compared to the initial hit Genz-682452. Inhibition mechanism indicated both inhibitors bind to peptide-binding pocket and co-crystal structures of both Genz-682452 and GD433 with NTMT1 confirmed their binding modes. Furthermore, GD433 shows over 7-fold selectivity over other major 40 protein methyltransferases and DNA methyltransferase and exhibits improved selectivity for NTMT1 over glucosylceramide synthase (GCS). GD433 significantly decreases the cellular N-terminal methylation level of NTMT1 substrates RCC1 and SET at 10 nM in both HEK293 and HCT116 cells, providing a valuable probe for cell-based studies in the future.<br></div><p><br></p>

Surface plasmon resonance (SPR) biosensors represent one of the most advanced sensing technologies for real-time studies of biomolecular interactions. In this thesis, methods for functionalization of SPR substrates were optimized and studied via spectroscopic methods. Effects related to the SPR sensor microfluidic interface on the measured biomolecular interactions were analyzed, and furthermore, means to decrease mass-transport limitations were proposed. Several SPR-based assays regarding the detection of nucleic acids were developed, which allow for the detection of physiologically relevant concentrations of nucleic acids as well as point mutations in a nucleic acid sequence. Assays for the determination of the enzymatic activity of HIV integrase and ribonuclease H were developed. These assays can be employed for the design and synthesis of molecules that function either as antiviral drugs or as gene-regulating agents.