Nanoplasmonics has opened up the gates for numerous innovations. Recent studies showed that metal nanoparticles, when introduced into the solar cells and organic light emitting diodes, would greatly enhance their efficiencies. Though these advances are promising, they require a tool for investigating the interactions occuring at the microscopic level to further optimize their performance. In that context, we are interested in understanding the energy transfer mechanism between molecules in the vicinity of metal nanoparticle. Time-resolved fluorescence intensity and anisotropy experiments on single and clusters of Silver-Silica core-shell nanoparticles coated with Rhodamine B(RB) dye molecules, (Ag-SiO2-RB) were performed. We witnessed the signature of the interaction between RB molecules and metal nanoclusters in the form of the enhanced fluorescence intensity decay rates. The fluorescence lifetime of RB in the vicinity of the nanoparticles was (600 +/- 100) ps, as compared to (2.4+/-0.3)ns in the absence of nanoparticle. While the anisotropy of RB molecules in the absence of nanoparticle has remained almost constant(0.075+/-0.029) over long times; anisotropy in the presence of particles showed wide range of values immediately after excitation. Surprisingly high anisotropy values, at about 10 ns after excitation, were observed with a mean of about (0.145+/-0.025). We interpret the high and low initial anisotropies of the clusters, relative to the case of RB alone, to be due to the interaction of dye molecules with collective plasmon modes of the clusters. / Thesis (Master, Physics, Engineering Physics and Astronomy) -- Queen's University, 2011-06-30 23:29:38.658

<p> This thesis focuses on the use of time-resolved fluorescence anisotropy (TRF A) for the analysis of peptide-silica and protein-silica interactions. Previous studies from our group have shown that strong ionic binding of the cationic probe rhodamine 6G (R6G) to the anionic surface of silica particles in water provides a convenient labeling procedure to study both particle growth kinetics and surface modification by time-resolved fluorescence anisotropy (TRF A). The decays for R6G dispersed in diluted Ludox silica sols usually fit to a sum of picosecond and nanosecond decay components, along with a significant residual anisotropy component. The first objective of my work was to assess the nature of the R6G:silica interaction to determine the origin of the nanosecond decay component, and ultimately validate the model used to fit the TRFA data and gain further insight into the physical meaning of the anisotropy decay parameters. Our results show the origin of the nanosecond decay component ( ¢2) is due to the presence of a subpopulation of small nanoparticles in the Ludox sol. </p> <p> With the correct physical model in place, we have been able use TRFA ofR6G in aqueous Ludox to monitor peptide adsorption onto the silica particles in situ. Steady-state anisotropy and TRF A of R6G in Ludox sols were measured to characterize the extent of the ionic binding of the probe to silica particles in the presence of varying levels of tripeptides of varying charge, including Lys-Trp-Lys (KWK), N-acetylated Lys-Trp-Lys (Ac-KWK), Glu-Trp-Glu (EWE) and N-acetylated Glu-Trp-Glu (Ac-EWE). R6G showed significant decreases in anisotropy in the presence of cationic peptides, consistent with the addition of cationic peptides blocking the adsorption of the dye to the silica surface. The study shows that the competitive binding method can be used to assess the binding of various biologically relevant compounds onto silica surfaces, and demonstrates the potential of TRF A for probing peptide: silica and protein: silica interactions. </p> <p> We have also extended the application of TRF A to monitor protein adsorption onto plain and modified silica particles using a recently reported cationic long-lifetime quinolinium dye, CG437, which strongly binds to anionic silica particles through electrostatic interactions. In this case, alterations in the rotational correlation time of Ludox particles resulting from increases in the diameter of the rotating body upon binding of protein to the silica surface were monitored. The study shows that TRFA analysis of long-lived cationic probes such as CG437 can provide an effective method to investigate interactions between proteins and modified silica surfaces, extending the utility of the TRF A method. </p> / Thesis / Master of Science (MSc)

Glycerol kinase (GK) from Escherichia coli is allosterically controlled by fructose 1,6-bisphosphate (FBP) and the glucose-specific phosphocarrier protein IIAGlc of the phosphotransferase system. These controls allow glucose to regulate glycerol utilization. Fluorescence spectroscopic and enzyme kinetic methods are applied to investigate these allosteric controls in this study. The linkage between FBP binding and GK tetramer assembly is solved by observation of homo-fluorescence energy transfer of the fluorophore Oregon Green (OG) attached specifically to an engineered surface cysteine in GK. FBP binds to tetramer GK with an affinity 4000-fold higher than to dimeric GK. A region named the coupling locus that plays essential roles in the allosteric signal transmission from the IIAGlc binding site to the active site was identified in GK. The relationship between the coupling locus sequence in Escherichia coli or Haemophilus influenzae GK variants and the local flexibility of the IIAGlc binding site is established by fluorescence anisotropy determinations of the OG attached to the engineered surface cysteine in each variant. The local flexibility of the IIAGlc binding site is influenced by the coupling locus sequence, and in turn affects the binding affinity for IIAGlc. Furthermore, the local dynamics of each residue in the IIAGlc binding site of GK is studied systematically by the fluorescence anisotropy measurements of OG individually attached to each position of the IIAGlc binding site. The fluorescence steady-state anisotropy measurement provides a valid estimation of the local flexibility and correlates well with the crystallographic B-factors. Steady-state kinetics of FBP inhibition shows that the data are best described by a model in which the partial inhibition and FBP binding stoichiometry are taken into account. Kinetic viscosity effects show that the product-release step is not the purely rate-limiting step in the GK-catalyzed reaction. Viscosity effects on FBP inhibition are also discussed.

Glycerol kinase (GK) from Escherichia coli is allosterically controlled by fructose 1,6-bisphosphate (FBP) and the glucose-specific phosphocarrier protein IIAGlc of the phosphotransferase system. These controls allow glucose to regulate glycerol utilization. Fluorescence spectroscopic and enzyme kinetic methods are applied to investigate these allosteric controls in this study. The linkage between FBP binding and GK tetramer assembly is solved by observation of homo-fluorescence energy transfer of the fluorophore Oregon Green (OG) attached specifically to an engineered surface cysteine in GK. FBP binds to tetramer GK with an affinity 4000-fold higher than to dimeric GK. A region named the coupling locus that plays essential roles in the allosteric signal transmission from the IIAGlc binding site to the active site was identified in GK. The relationship between the coupling locus sequence in Escherichia coli or Haemophilus influenzae GK variants and the local flexibility of the IIAGlc binding site is established by fluorescence anisotropy determinations of the OG attached to the engineered surface cysteine in each variant. The local flexibility of the IIAGlc binding site is influenced by the coupling locus sequence, and in turn affects the binding affinity for IIAGlc. Furthermore, the local dynamics of each residue in the IIAGlc binding site of GK is studied systematically by the fluorescence anisotropy measurements of OG individually attached to each position of the IIAGlc binding site. The fluorescence steady-state anisotropy measurement provides a valid estimation of the local flexibility and correlates well with the crystallographic B-factors. Steady-state kinetics of FBP inhibition shows that the data are best described by a model in which the partial inhibition and FBP binding stoichiometry are taken into account. Kinetic viscosity effects show that the product-release step is not the purely rate-limiting step in the GK-catalyzed reaction. Viscosity effects on FBP inhibition are also discussed.

E2A-PBX1 is expressed as a consequence of a recurring chromosomal translocation seen in 5% of acute lymphoblastic leukemia cases. We recently reported that substitution of a leucine residue (L20A) within the N-terminal transcriptional activation domain (AD1) of E2A-PBX1 markedly impairs binding to the KIX domain of CBP/p300 and, importantly, leukemia induction in a mouse bone marrow transplantation model. Since both the protein-protein interaction and consequent leukemogenesis rely on a focal contact point and might therefore be susceptible to antagonism by small molecules, we devised a cell-free assay based on fluorescence anisotropy (FA) to detect binding of a fluorescently labeled peptide derived from AD1 of E2A-PBX1 (FITC-E2A) with recombinantly expressed KIX domain. The optimized FA assay reveals a dissociation constant of 2 µM for the wild-type interaction and correctly detects disruption of the complex by naphthol AS-E phosphate, a compound previously shown to antagonize KIX binding. The optimized FA assay was used to screen the Prestwick, Spectrum and Chembridge libraries containing 12400 compounds in total. Of the initial 43 positive hits from the libraries, 10 caused a reproducible decrease in FA. Since intrinsic small molecule fluorescence can produce false positive results in the FA-based screen, intrinsically fluorescent compounds were excluded from further analysis unless they could be shown to bind to KIX. Two hits, L1 and C2, were intrinsically fluorescent but demonstrated KIX interactions and one hit, P9, was not intrinsically fluorescent. These three compounds were tested for their ability to inhibit binding of a larger portion of E2A (residues 1 to 483) to full length CBP in a pull down assay with only compound P9 demonstrating efficacy. Further characterization of P9 by NMR showed no binding to KIX, however evaluation by FA showed binding to FITC-E2A with a 20 µM affinity. A cell-based cytotoxicity assay demonstrated that compound P9 was slightly more toxic on leukemic cells that express E2A-PBX1, compared to leukemic cells lacking E2A-PBX1 expression. Mammalian two-hybrid analysis did not provide details of the effects of P9 on the E2A:KIX interaction. We expect the identification of a novel compound, P9, capable of disrupting the oncogenic E2A-PBX1:CBP interaction, to guide the development of effective, less toxic leukemia drugs and provide new tools for elucidating the molecular mechanisms of leukemia induction by E2A-PBX1. / Thesis (Master, Pathology & Molecular Medicine) -- Queen's University, 2009-08-31 11:13:19.517

The ubiquitin proteasome system targets proteins to the proteasome where they are degraded. Substrate recognition and processing prior to degradation take place at the 19S regulatory particle of the proteasome. A polyubiquitin chain, linked through isopeptide bonds formed between the C-terminal G76 and K48, is the signal responsible for delivery to the proteasome. Because chains linked via any of the seven lysine residues of ubiquitin exist in vivo and encode signals unrelated to protein degradation it is crucial for cells to avoid crosstalk between these different pathways. Several ubiquitin receptors related to proteasomal degradation have been identified but the selectivity between the different ubiquitin chains has not been assessed quantitatively while avoiding artefacts attributed to GST-dimerisation. By employing isothermal titration calorimetry, analytical ultracentrifugation and nuclear magnetic resonance, discrimination between K48- and K63-linked diubiquitin was established for the S. pombe proteasomal receptor Rpn10 and the shuttle protein Rhp23. The same methods allowed us to propose a discriminatory model for Rpn10. The crystal structures of the 19S regulatory particle subunits Rpn101-193 and Rpn121-224 have been determined and possible protein-protein interaction sites were identified by surface conservation and electrostatics analysis. Rpn12 surface residues were identified that had a negative effect on Rpn10-binding. This interaction was studied by surface plasmon resonance, fluorescence anisotropy and nuclear magnetic resonance. These experiments revealed a binding site on Rpn10 that is exclusively occupied by either ubiquitin or Rpn12 and for the first time demonstrated the interaction of a ubiquitin interacting motif with a protein other than ubiquitin.

O estudo de agregados anfifílicos é de extrema importância devido à sua mimetização de membranas celulares, que são essenciais para a vida da célula. Sabe-se que os fosfolipídios não possuem estruturas moleculares bem definidas nas membranas, porém exercem um papel essencial na manutenção da sua integridade. Fosfolipídios zwitteriônicos são um dos principais componentes estruturais das membranas celulares, e um modelo simplificado destas membranas são as bicamadas que estes fosfolipídios podem formar em meio aquoso. A principal característica destas bicamadas lipídicas é a auto-organização dos lipídios, fazendo-se necessário o estudo de processos naturais e espontâneos, como suas propriedades estruturais e dinâmicas. A espectroscopia de fluorescência tem sido utilizada no estudo de diversos processos e sistemas de interesse biológico, principalmente por medidas de anisotropia de fluorescência, que fornece informações sobre a dinâmica rotacional das sondas fluorescentes inseridas nos sistemas de interesse, refletindo efeitos combinados de flexibilidade, fluidez e interações estáticas com moléculas circundantes. Neste trabalho examinamos as propriedades estruturais e dinâmicas de membranas modelo fosfolipídicas formadas de 1,2-dipalmitoil-sn-glicero-3-fosfocolina (DPPC) por técnicas relacionadas à espectroscopia de fluorescência, principalmente por medidas de anisotropia do estado estacionário e resolvida no tempo, das sondas fluorescentes 1,6-diphenil-1,3,5-hexatrieno (DPH), 7-nitrobenz-2-oxa-1,3-diazol-il (NBD) ligado em diferentes regiões das moléculas fosfolipídicas e também da sonda lipofílica 2-amino-N-hexadecil-benzamida (Ahba). As medidas foram realizadas tanto acima como abaixo da temperatura de transição de fase das bicamadas fosfolipídicas de DPPC, na fase gel e líquido-cristalina, devido à diferença da organização lateral das cadeias de hidrocarboneto nestas duas fases. Medidas de espalhamento dinâmico de luz foram realizadas para confirmar a formação das vesículas unilamelares pelo processo de extrusão da suspensão lipídica contendo vesículas multilamelares, e a técnica de calorimetria diferencial de varredura foi empregada para verificar se baixa concentração das sondas fluorescentes nas vesículas afetam seu empacotamento lipídico. Pelos resultados obtidos, constatamos que os comportamentos das três sondas fluorescentes diferem em ambas as fases das bicamadas fosfolipídicas, revelando suas propriedades estruturais e dinâmicas, principalmente pelas diferentes localizações dos fluoróforos. Verificamos que, devido à afinidade pela região hidrofóbica, o movimento do DPH é restrito ao movimento \"wobbling\", limitado pelas cadeias alifáticas. Para o NBD em lipídios marcados, o movimento do análogo fluorescente como um todo depende da localização do fluoróforo e de sua conformação em ambas as fases das bicamadas lipídicas. Devido à localização do grupo fluorescente da sonda Ahba na interface das bicamadas lipídicas, verificamos que seu movimento rotacional aumenta à medida que a bicamada torna-se mais fluida, mostrando uma dependência deste movimento com a microviscosidade destas bicamadas. / The study of amphiphilic aggregates is extremely important due to their cell membrane mimic, which are essential for the life of the cell. It is known that phospholipids do not have molecular structure well defined in membranes, but play an essential role in maintaining of their integrity. Zwitterionic phospholipids are one of the main components of cell membranes, and a simplified model for the membranes are the bilayers they can form in aqueous medium. The main characteristic of lipid bilayers is the self-organization of lipids, making it necessary to study natural and spontaneous process, as their structural and dynamical properties. The fluorescence spectroscopy has been used to study many processes and systems of biological interest, especially by measurement of fluorescence anisotropy, which gives information about the rotational dynamics of the fluorescent probe inserted in the systems of interest, reflecting the combined effects of flexibility, fluidity and static interactions with surrounding molecules. In this work we examined the structural and dynamic properties of phospholipid model membranes formed of 1,2-dipalmitoyl-sn-glycero-3-phosphocoline DPPC by techniques related to fluorescence spectroscopy, mainly by measurements of steady-state and time resolved anisotropy of the probes 1,6-diphenyl-1,3,5-hexatriene (DPH), 7-nitrobenz-2-oxa-1,3-diazol-yl (NBD) attached to different regions of phospholipid molecules and also the lipophilic probe 2-amino-N-hexadecyl-benzamide (Ahba). The measurements were perfomed above and below of the phase transition temperature of the phospholipid bilayers of DPPC, gel and liquid-crystalline phase, due to the difference in the lateral organization of hydrocarbon chains in these two phases. Measures of dynamic light scattering (DLS) was performed to confirm the formation of the unilamellar vesicles by extrusion of lipid suspension containing multilamellar vesicles, and the technique of differential scanning calorimetry (DSC) was used to verify if the low concentration of fluorescent probes in lipid vesicles affect its packing. From the results, we found that the behavior of the three different fluorescent probes differ in both phases of phospholipid bilayers, revealing their structural and dynamic properties, mainly because to specific locations of the fluorophores. We verify that, due to the affinity for the hydrophobic region, the motion of the DPH is restricted to the \"wobbling\" motion, limited by hydrocarbon chains. For the NBD labeled in lipids, the motion of the fluorescent analogues as a whole depends on the location of the fluorophore and on the lipid conformation in both phases of lipid bilayers. Because of the location of the fluorescent group of the probe Ahba in the interface of lipid bilayers, we found that its rotational motion increases as the bilayers becomes more fluid, showing a dependency of the motion with the microviscosity of these bilayers.

none

Doctor of Philosophy / Biochemistry and Molecular Biophysics / Phillip E. Klebba / The goal of the research included in this dissertation is to provide a more complete model of the role of TonB, an energy transducing protein that resides in the inner membrane and is an essential component of the iron transport of Escherichia coli under iron-starved conditions. Using fluorescent hybrid proteins, the anisotropy of TonB in the cytoplasmic membrane (CM) of Escherichia coli was determined. With the aim of understanding the bioenergetics of outer membrane (OM) iron transport, the dependence of TonB motion on the electrochemical gradient and the effect of CM proteins ExbB and ExbD on this phenomenon was monitored and analyzed. The native E. coli siderophore, enterobactin chelates Fe⁺³ in the environment and ferric enterobactin (FeEnt) enters the cell by energy- and TonB-dependent uptake through FepA, its OM transporter. The TonB-ExbBD complex in the CM is hypothesized to transfer energy to OM transporters such as FepA. We observed the polarization of GFPTonB hybrid proteins and used metabolic inhibitors (CCCP, azide and dinitrophenol) and chromosomal deletions of exbBD to study these questions. The results showed higher anisotropy (R) values for GFP-TonB in energy-depleted cells, and lower R-values in bacteria lacking ExbBD. Metabolic inhibitors did not change the anisotropy of GFP-TonB in ΔexbBD cells. These findings suggest that TonB undergoes constant, energized motion in the bacterial CM, and that ExbBD mediates its coupling to the electrochemical gradient. By spectroscopic analyses of extrinsic fluorophore labeled site-directed Cys residues in 7 surface loops of Escherichia coli FepA, binding and transport of ferric enterobactin (FeEnt) was characterized. Changes in fluorescence emissions reflected conformational motion of loops that altered the environment of the fluorophore, and we observed these dynamics as quenching phenomena during FeEnt binding and transport in living cells or outer membrane vesicles. Cys residues in each of the 7 surface loops (L2, L3, L4, L5, L7 L8, and L11) behaved individually and characteristically with regard to both fluorophore maleimide reactivity and conformational motion. Fluorescence measurements of FeEnt transport, by either microscopic or spectroscopic methodologies, demonstrated that ligand uptake occurs uniformly throughout the cell envelope, and susceptibility of FeEnt uptake to the proton ionophore m-chlorophenyl hydrazone (CCCP) at concentrations as low as 5 uM. The latter result recapitulates the sensitivity of inner membrane major facilitator transporters to CCCP (Kaback, 1974), providing further evidence of the electrochemical gradient as a driving force for TonB-dependent metal transport.

O estudo de agregados anfifílicos é de extrema importância devido à sua mimetização de membranas celulares, que são essenciais para a vida da célula. Sabe-se que os fosfolipídios não possuem estruturas moleculares bem definidas nas membranas, porém exercem um papel essencial na manutenção da sua integridade. Fosfolipídios zwitteriônicos são um dos principais componentes estruturais das membranas celulares, e um modelo simplificado destas membranas são as bicamadas que estes fosfolipídios podem formar em meio aquoso. A principal característica destas bicamadas lipídicas é a auto-organização dos lipídios, fazendo-se necessário o estudo de processos naturais e espontâneos, como suas propriedades estruturais e dinâmicas. A espectroscopia de fluorescência tem sido utilizada no estudo de diversos processos e sistemas de interesse biológico, principalmente por medidas de anisotropia de fluorescência, que fornece informações sobre a dinâmica rotacional das sondas fluorescentes inseridas nos sistemas de interesse, refletindo efeitos combinados de flexibilidade, fluidez e interações estáticas com moléculas circundantes. Neste trabalho examinamos as propriedades estruturais e dinâmicas de membranas modelo fosfolipídicas formadas de 1,2-dipalmitoil-sn-glicero-3-fosfocolina (DPPC) por técnicas relacionadas à espectroscopia de fluorescência, principalmente por medidas de anisotropia do estado estacionário e resolvida no tempo, das sondas fluorescentes 1,6-diphenil-1,3,5-hexatrieno (DPH), 7-nitrobenz-2-oxa-1,3-diazol-il (NBD) ligado em diferentes regiões das moléculas fosfolipídicas e também da sonda lipofílica 2-amino-N-hexadecil-benzamida (Ahba). As medidas foram realizadas tanto acima como abaixo da temperatura de transição de fase das bicamadas fosfolipídicas de DPPC, na fase gel e líquido-cristalina, devido à diferença da organização lateral das cadeias de hidrocarboneto nestas duas fases. Medidas de espalhamento dinâmico de luz foram realizadas para confirmar a formação das vesículas unilamelares pelo processo de extrusão da suspensão lipídica contendo vesículas multilamelares, e a técnica de calorimetria diferencial de varredura foi empregada para verificar se baixa concentração das sondas fluorescentes nas vesículas afetam seu empacotamento lipídico. Pelos resultados obtidos, constatamos que os comportamentos das três sondas fluorescentes diferem em ambas as fases das bicamadas fosfolipídicas, revelando suas propriedades estruturais e dinâmicas, principalmente pelas diferentes localizações dos fluoróforos. Verificamos que, devido à afinidade pela região hidrofóbica, o movimento do DPH é restrito ao movimento \"wobbling\", limitado pelas cadeias alifáticas. Para o NBD em lipídios marcados, o movimento do análogo fluorescente como um todo depende da localização do fluoróforo e de sua conformação em ambas as fases das bicamadas lipídicas. Devido à localização do grupo fluorescente da sonda Ahba na interface das bicamadas lipídicas, verificamos que seu movimento rotacional aumenta à medida que a bicamada torna-se mais fluida, mostrando uma dependência deste movimento com a microviscosidade destas bicamadas. / The study of amphiphilic aggregates is extremely important due to their cell membrane mimic, which are essential for the life of the cell. It is known that phospholipids do not have molecular structure well defined in membranes, but play an essential role in maintaining of their integrity. Zwitterionic phospholipids are one of the main components of cell membranes, and a simplified model for the membranes are the bilayers they can form in aqueous medium. The main characteristic of lipid bilayers is the self-organization of lipids, making it necessary to study natural and spontaneous process, as their structural and dynamical properties. The fluorescence spectroscopy has been used to study many processes and systems of biological interest, especially by measurement of fluorescence anisotropy, which gives information about the rotational dynamics of the fluorescent probe inserted in the systems of interest, reflecting the combined effects of flexibility, fluidity and static interactions with surrounding molecules. In this work we examined the structural and dynamic properties of phospholipid model membranes formed of 1,2-dipalmitoyl-sn-glycero-3-phosphocoline DPPC by techniques related to fluorescence spectroscopy, mainly by measurements of steady-state and time resolved anisotropy of the probes 1,6-diphenyl-1,3,5-hexatriene (DPH), 7-nitrobenz-2-oxa-1,3-diazol-yl (NBD) attached to different regions of phospholipid molecules and also the lipophilic probe 2-amino-N-hexadecyl-benzamide (Ahba). The measurements were perfomed above and below of the phase transition temperature of the phospholipid bilayers of DPPC, gel and liquid-crystalline phase, due to the difference in the lateral organization of hydrocarbon chains in these two phases. Measures of dynamic light scattering (DLS) was performed to confirm the formation of the unilamellar vesicles by extrusion of lipid suspension containing multilamellar vesicles, and the technique of differential scanning calorimetry (DSC) was used to verify if the low concentration of fluorescent probes in lipid vesicles affect its packing. From the results, we found that the behavior of the three different fluorescent probes differ in both phases of phospholipid bilayers, revealing their structural and dynamic properties, mainly because to specific locations of the fluorophores. We verify that, due to the affinity for the hydrophobic region, the motion of the DPH is restricted to the \"wobbling\" motion, limited by hydrocarbon chains. For the NBD labeled in lipids, the motion of the fluorescent analogues as a whole depends on the location of the fluorophore and on the lipid conformation in both phases of lipid bilayers. Because of the location of the fluorescent group of the probe Ahba in the interface of lipid bilayers, we found that its rotational motion increases as the bilayers becomes more fluid, showing a dependency of the motion with the microviscosity of these bilayers.