This thesis consists of two parts and nine chapters. The first part (Part I) presents theoretical studies on non-radiative mode of excitation energy transfer (EET) in donor-acceptor (D-A) systems involving metal nanoparticles. Part I contains four chapters and describes EET in following different D-A systems: (i) dye and a spherical metal nanoparticle of different sizes, (ii) two spherical metal nanoparticles, and (iii) two prolate shaped metal nanoparticles at different relative orientations. Part II provides a detailed study on the origin of photochemical funneling of excitation energy in conjugated polymers like poly-[phenylenevinylene] (PPV) and consists of three chapters. The ninth chapter provides a concluding note. The thesis begins with a basic introduction on Forster resonance energy transfer(FRET), presented in chapter 1. This chapter provides a detail derivation of Forster’s rate expression for a non-radiative process of EET from a donor to an acceptor molecule and discusses the limitations of Forster theory. The chapter highlights the huge success of FRET technique in understanding biological processes assisted by changes in conformations of biopolymers under conditions where Frster theory is valid. The chapter also discusses practical limitations of FRET technique such as use of pre-averaged value of orientation factor and photobleaching of dye molecules. Part I starts with chapter 2 which explains the advantages of using metal nanoparticles over dye molecules in D-A systems. The chapter discusses recent experimental re-ports of excitation energy transfer to nanoparticles, now commonly referred to as nanoparticle surface energy transfer (NSET). Theories describing the process of EET from a dye molecule (dye molecule is assumed to be a point dipole) to a planar metallic surface are discussed. In the case of energy transfer from a donor dye molecule to a planar metallic surface, the distance dependence of the rate of EET is found to vary as 1/d4 where dis a distance from the center of a dye molecule to the metallic surface. This is unlike conven-tional FRET where rate of EET follows 1/R6 distance dependence with R as a distance between the centers of D and A. Also, a recent experimental study by Yun et al [J. Am. Chem. Soc. 127, 3115 (2005)] on energy transfer from a dye molecule to a spherical gold nanoparticle reports that the rate of EET follows 1/d4 distance dependence. The remaining chapters of this part focus on understanding this deviation from the Forster theory in different D-A systems. Chapter 3 describes quantized electro-hydrodynamic approach used to model the plasmonic excitations in metal nanoparticles. The optical absorption frequencies of nanoparticles computed here are subsequently used in chapters 4 and 5 for the calculation of the rate of EET. The chapter discusses the merits and de-merits of electro-hydrodynamic approach in comparison to other available techniques. The electro-hydrodynamic method of calculating the absorption frequencies provide a physically appealing, mathematically simple and numerically tractable approach to the problem and is also at the same time, semi-quantitatively reliable. The optical frequencies obtained as a function of size and aspect ratio of metal nanoparticles are found to be in good agreement with physical predictions. Chapter 4 studies the distance dependence of rate of EET for a D-A system similar to one studied by Yun et al [J. Am. Chem. Soc. 127, 3115 (2005)]. The chapter contains the relevant derivations of the quantities required for computing the interaction matrix elements. The dependence of the rate of EET on R is found surprisingly to be in agreement with Forster theory even at intermediate distances compared to the size of spherical nanoparticles (a). However, the dependence of rate of EET on d is found to vary as 1/dσwith σ=3 - 4 at intermediate distances which is in good agreement with the experimental results of Yun et al. At large values of d, the distance dependence of rate is found to vary as 1/d6 . The chapter discusses the physical basis behind these results. The theory predicts a non-trivial dependence of rate on the size of a nanoparticle which ultimately attains the asymptotic a3 size dependence. The rate of EET is also studied for different orientations of dye molecule. Chapter 5 studies surface plasmon mediated EET between two metal nanoparticles. The rate of EET between two prolate and spherical shaped silver nanoparticles is studied as a function of Rand d. d, in present chapter denotes surface-to-surface separation distance between two nanoparticles. In case of EET between two non-spherical nanoparticles, even at separations larger than the size of the nanoparticle, a significant deviation from 1/R6 dependence is obtained. However, 1/R6 distance dependence of EET rate is found to be robust for spherical nanoparticles over an entire range of separations. The deviation of rate from 1/R6 distance dependence becomes more pronounced with in-crease in the aspect ratio of the nanoparticle. The relative orientation of the nanoparticles is found to markedly influence the R-dependence of EET rate. Interestingly, the relative orientation of nanoparticles effect the d-distance dependence of the rate to a lesser extend in comparison to the R-dependence of the rate. Therefore, we predict that for non-spherical nanoparticles studying EET rate as a function of will provide more conclusive results. The chapter also discusses the size dependence of rate of EET for this particular D-A system. In Part II, excitation energy transfer (EET) in a conjugated polymer is studied. To start with, chapter 6 provides a brief introduction to photophysics of conjugated polymers. The chapter discusses the nature of photoexcitations in these systems and stresses on the influence of polymer’s morphology on the optical properties of conjugated polymers. Chapter 7 describes the theory used for modeling conjugated polymer chain. A polymer chain consists of number of spectroscopic units (chromophores) of varying lengths. The average length of chromophores in conjugated polymer depends on defect concentration. In the present study we treat an excitation generated on each chromophore within “particle-in-a-box” formalism but one that takes into account the electron-hole interactions. The transition dipole moments and the radiative rates are computed for different lengths of chromophores with parameters appropriate for PPV chain. These quantities are used in chapter 8 for calculating the absorption and emission spectra of conjugated polymer chains at different defect concentrations. The main aim of Chapter 8 is to understand the origin of photochemical funneling of excitation energy in conjugated polymers. PPV chain is modeled as a polymer with the length distribution of chromophores given either by a Gaussian or by a Poissonian distribution. We observe that the Poissonian distribution of length segments explains the optical spectra of PPV rather well than the Gaussian distribution. The Pauli’s master equation is employed to describe the excitation energy transfer among different chromophores. The rate of energy transfer is assumed to be given here, as a first approximation, by the well-known Forster expression. The observed excitation population dynamics confirm the photochemical funneling of excitation energy from shorter to longer chromophores of the polymer chain. The calculations show that even in steady state more than one type of chromophore contribute towards the emission spectrum. The observed difference between the calculated emission spectra at equilibrium and in steady state indicates the existence of local domains in a polymer chain within which the non-radiative excitation energy transfer from shorter to longer chromophores take place. These results are found to be in agreement with recent experimental reports. The concluding chapter 9 gives a brief summary of the outcome of the thesis and ends up with suggestion of a few future problems which in current scenario are of great interest.

Hyperexcitabilité est l'un des changements les plus importants observés dans de nombreuses maladies neuro-dégénératives telles que la sclérose latérale amyotrophique (SLA) et la maladie d'Alzheimer. De nombreuses recherches études se sont concentrées sur la réduction de l'hyperexcitabilité, soit en inactivant les canaux sodiques ce qui va réduire la génération de potentiels d'action, soit en prolongeant l'ouverture des canaux potassiques ce qui va qui ramener la membrane à son état de repos et réduire l’activité des neurones. Ainsi, pour cibler l'hyperexcitabilité, il faut tout d’abord comprendre les différents aspects de la fonction des canaux ioniques au niveau. Les objectifs des travaux présentés dans cette thèse consistent à déterminer le mécanisme d'inactivation dans les canaux potassiques Shaker. Les canaux Shaker Kv s'inactivent rapidement pour culminer le potentiel d'action et maintenir l'homéostasie des cellules excitables. L'inactivation de type N est causée par les 46 premiers acides aminés situés de l'extrémité N-terminale du canal, encore appelé, peptide d'inactivation (IP). De nombreuses études mutationnelles ont caractérisé l'inactivation de type N au niveau fonctionnel, cependant, la position de l'IP à l'état de repos et leur transition lors de l'inactivation est encore débattue. L'objectif de la première étude consiste à évaluer le mouvement des IP pendant leur inactivation à l'aide de la fluorométrie en voltage imposé. En insérant un acide aminé non naturel, la 3-[(6-acétyl-2-naphtalényl) amino]-L-alanine (Anap), qui est sensible aux changements d'environnement, nous avons identifié séparément les mouvements de la boule et de la chaîne. Nos données suggèrent que l'inactivation de type N se produit dans un mouvement biphasique en libérant d'abord le IP, ce qui va bloquer le pore du côté cytoplasmique. Pour affiner davantage la position de repos des IP, nous avons utilisé le transfert d'énergie de résonance à base de lanthanide et le métal de transition FRET. Nous proposons que le IP se situe dans la fenêtre formée par le canal et le domaine T1, interagissant avec les résidus acides-aminés du domaine T1. Dans notre deuxième étude, nous avons montré que le ralentissement de l'inactivation de type N observé dans la première étude est causée par une expression élevée des canaux Shaker. En effet, l'extrémité C-terminale du canal interagit avec les protéines d'échafaudage associées à la membrane pour la formation d'amas. Nous avons aussi montré qu'en tronquant les quatre derniers résidus C-terminaux impliqués dans la formation des amas, nous empêchons également le ralentissement de la cinétique d'inactivation dans les canaux Shaker. Nous avons également démontré que l'inactivation lente de type N n'est pas affectée par l'accumulation des cations potassiques [K+] externe ou toute diaphonie entre les sous-unités voisines. Cette étude élucide non seulement la cause du ralentissement de l'inactivation, mais montre également que les canaux modifient leur comportement en fonction des conditions d'expression. Les résultats trouvés au niveau moléculaire ne peuvent donc pas toujours être extrapolés au niveau cellulaire. / Hyperexcitability of neurons is a major symptom observed in many degenerative diseases such as ALS and Alzheimer’s disease. A lot of research is focused on reducing hyperexcitability, either by inactivating sodium channels that will reduce the generation of action potentials, or by prolonging the opening of potassium channels which will help to bring the membrane back to resting state and thus, reduce firing frequency of neurons. At the molecular level, it is important to understand different aspects of ion channel function to target hyperexcitability. The aim of this thesis was to investigate in two projects the inactivation mechanism in Shaker potassium channels. Shaker Kv channels inactivate rapidly to culminate the action potential and maintain the homeostasis of excitable cells. The so-called N-type inactivation is caused by the first 46 amino acids of the N-terminus of the channel, known as the inactivation peptide (IP). Numerous mutational studies have characterized N-type inactivation functionally, however, the position of the IP in the resting state and its transition during inactivation is still debated. The aim of the first project was to track the movement of IP during inactivation using voltage clamp fluorometry. By inserting an unnatural amino acid, 3-[(6-acetyl-2-naphthalenyl) amino]-L-alanine (Anap), which is sensitive to changes in environment, we identified the movements of ball and chain separately. Our data suggests that N-type inactivation occurs in a biphasic movement by first releasing the IP, which then blocks the pore from the cytoplasmic side. To further narrow down the resting position of the inactivation peptide, we used Lanthanide-based Resonance Energy transfer and transition metal FRET. We propose that the inactivation peptide is located in the window formed by the channel and the T1 domain, interacting with the acidic residues of the T1 domain. In a follow-up study, we explored the reason underlying slow inactivation kinetics observed during the study of N-type inactivation in the first project. High expression of Shaker channels results in slowing of the N-type inactivation. The C-terminus of the channel interacts with membrane associated scaffold proteins for cluster formation. In this study, we have shown that by truncating the last four C-terminal residues involved in cluster formation, and hence preventing channel clustering, we also prevent slowing of the inactivation kinetics in Shaker channels. We also showed that slow N-type inactivation is not affected by accumulation of external [K+] or any crosstalk between the neighboring subunits. The second project not only elucidates the cause of the inactivation slow-down but illustrates that the channels alter their behavior dependent on the expression conditions. Results found on the molecular level can thus not always be extrapolated to the cellular level.

The Escherichia coli twin-arginine translocation (Tat) system transports fully folded and assembled proteins across the inner membrane into the periplasmic space. The E. coli Tat machinery minimally consists of three integral membrane proteins: TatA, TatB and TatC. A popular model of Tat translocation is that cargo first interacts with a substrate binding complex composed of TatB and TatC and then is transported across the inner membrane through a channel comprised primarily of TatA. The most common method for observing the kinetics of Tat transport, a protease protection assay, lacks the ability to distinguish between individual transport sub-steps and is limited by the inability to observe translocation in real-time. Therefore, a real-time FRET based assay was developed to observe interactions between the cargo protein pre-SufI, and its initial binding site, the TatBC complex. The cargo was found to first associate with the TatBC complex, and then, in the presence of a membrane potential (∆psi), migrate away from the initial binding site after a 20-45 second delay. Since cargo migration away from the TatBC complex was not directly promoted by the presence of a ∆psi, the delay likely represents some preparatory step that results in a transport competent translocon. In addition, the Tat system has long been identified as a potential biotechnological tool for protein production. However, much is still unknown about which cargos are suitable for transport by the Tat system. To probe the Tat system’s ability to transport substrates of different sizes and shapes, 18 different cargos were generated using the natural Tat substrate pre-SufI as a base. Transport efficiencies for these cargos indicate that not only is the Tat machinery’s ability to transport substrates determined by the protein’s molecular weight, as well as by its dimensions. In total, these results suggest a dynamic translocon that undergoes functionally significant, ∆psi-dependent changes during translocation. Moreover, not every protein cargo can be directed through the Tat translocon by a Tat signal peptide, and this selectivity is not only related to the overall size of the protein, but also dependent on shape.

The use of microfluidic tools to develop two novel approaches to surface-based oligonucleotide hybridization assays has been explored. In one of these approaches, immobilized oligonucleotide probes on a glass surface of a microfluidic channel were able to quantitatively hybridize with oligonucleotide targets that were electrokinetically injected into the channel. Quantitative oligonucleotide analysis was achieved in seconds, with nM detection limits and a dynamic range of 3 orders of magnitude. Hybridization was detected by the use of fluorescently labeled target. The fluorescence intensity profile evolved as a gradient that could be related to concentration, and was a function of many factors including hybridization reaction rate, convective delivery speed, target concentration and target diffusion coefficient. It was possible to acquire kinetic information from the static fluorescence intensity profile to distinguish target concentration, and the length and base-pair mismatches of target sequences. Numerical simulations were conducted for the system, and fit well with the experimental data. In a second approach, a solid-phase nucleic acid assay was developed using immobilized Quantum Dot (QD) bioprobes. Hybridization was used to immobilize QDs that had been coated with oligonucleotides having two different sequences. The hybridization of one oligonucleotide sequence conjugated to a QD (a linker sequence) with a complementary sequence that was covalently attached to a glass substrate of a microfluidic channel was shown to be an immobilization strategy that offered flexibility in assay design, with intrinsic potential for quantitative replacement of the sensing chemistry by control of stringency. A second oligonucleotide sequence conjugated to the immobilized QDs provided for the selective detection of target nucleic acids. The microfluidic environment offered the ability to manipulate flow conditions for control of stringency and increasing the speed of analytical signal by introduction of convective delivery of target sequences to the immobilized QDs. This work introduces a stable and adaptable immobilization strategy that facilitates solid-phase QD-bioprobe assays in microfluidic platforms.

The plasma protein complement factor H (fH, 155 kDa) regulates the activity of the alternative pathway of complement activation. Factor H is monomeric, and its 20 CCP modules are arranged in a predominantly elongated conformation, joined by linking sequences that vary in length, with the longest linkers occurring in the central portion of the molecule. CCP modules 1 through 4 of fH host its capacity to act as a cofactor for fI-mediated proteolytic degradation of C3b and its ability to accelerate the decay of the C3 convertase, C3bBb, thereby regulating the so-called tick-over activation of the alternative pathway. Mutations in this part of fH might compromise its function and lead to underregulation of the alternative pathway. It is hypothesized that this can cause predisposition to diseases such as atypical haemolytic uraemic syndrome (aHUS) and age-related macular degeneration (AMD). In the current work, the known disease-associated mutations R53H and R78G were compared to wild-type in terms of fluid-phase cofactor assays, C3b-binding affinity and the ability to accelerate the decay of the convertase. In addition, the protective variant, I62, was also inspected because its protective role might be explained by an increased regulatory activity. The second, linked, aim of this project was to employ Forster resonance energy transfer (FRET) to study the link between conformation and function in fH. FRET is valuable for obtaining long-distance restraints up to a maximum of 100 °A and is therefore particularly useful for inferring domain orientations within multidomain proteins. This approach to measure long-range inter- and intramolecular distances is a convenient way to complement NMR-based structural investigations, which rely on short-range restraints. It is also a valuable complement to X-ray crystallography since it is a solution technique that can be conducted under physiological conditions. By using site-directed mutagenesis in the current work, free cysteines were introduced into CCP modules 1-4 at strategic points, which were then used for attachment of fluorescent tags. C3 possesses an internal thioester which can be labelled with a fluorophore upon activation to C3b. Intermolecular FRET measurements were thus undertaken to gain information about the interaction between the two proteins that is crucial for understanding functional activity. The CCP modules in the centre of fH may be responsible for introducing a bend into fH that brings the N-teminus close to the C-terminus (the latter is important for host versus non-host discrimination) joined by the longest linkers occurring in the whole molecule. This coincidence of two relatively small CCP modules, 12 and 13, with the highest number of eight amino acids between them, is hypothesised to reflect some unique architectural features. To explore the structural details of this portion of fH by FRET, single-labelled cysteine mutants were further modifed to provide a recognition site for transglutaminase (TGase), which can be enzymatically labeled with a second fluorophore. This stoichiometrically-labelled protein was used for intramolecular FRET studies.

Immobilisierung bzw. Mobilisierung und Transport von Schadstoffen in der Umwelt, besonders in den Kompartimenten Boden und Wasser, sind von fundamentaler Bedeutung für unser (Über)Leben auf der Erde. Einer der Hauptreaktionspartner für organische und anorganische Schadstoffe (Xenobiotika) in der Umwelt sind Huminstoffe (HS). HS sind Abbauprodukte pflanzlichen und tierischen Gewebes, die durch eine Kombination von chemischen und biologischen Ab- und Umbauprozessen entstehen. Bedingt durch ihre Genese stellen HS außerordentlich heterogene Stoffsysteme dar, die eine Palette von verschiedenartigen Wechselwirkungen mit Schadstoffen zeigen. Die Untersuchung der fundamentalen Wechselwirkungsmechanismen stellt ebenso wie deren quantitative Beschreibung höchste Anforderungen an die Untersuchungsmethoden. Zur qualitativen und quantitativen Charakterisierung der Wechselwirkungen zwischen HS und Xenobiotika werden demnach analytische Methoden benötigt, die bei der Untersuchung von extrem heterogenen Systemen aussagekräftige Daten zu liefern vermögen. Besonders spektroskopische Verfahren, wie z.B. lumineszenz-basierte Verfahren, besitzen neben der hervorragenden Selektivität und Sensitivität, auch eine Multidimensionalität (bei der Lumineszenz sind es die Beobachtungsgrößen Intensität IF, Anregungswellenlänge lex, Emissionswellenlänge lem und Fluoreszenzabklingzeit tF), die es gestattet, auch heterogene Systeme wie HS direkt zu untersuchen. Zur Charakterisierung können sowohl die intrinsischen Fluoreszenzeigenschaften der HS als auch die von speziell eingeführten Lumineszenzsonden verwendet werden. In beiden Fällen werden die zu Grunde liegenden fundamentalen Konzepte der Wechselwirkungen von HS mit Xenobiotika untersucht und charakterisiert.<br> Für die intrinsische Fluoreszenz der HS konnte gezeigt werden, dass neben molekularen Strukturen besonders die Verknüpfung der Fluorophore im Gesamt-HS-Molekül von Bedeutung ist. Konformative Freiheit und die Nachbarschaft zu als Energieakzeptor fungierenden HS-eigenen Gruppen sind wichtige Komponenten für die Charakteristik der HS-Fluoreszenz. Die Löschung der intrinsischen Fluoreszenz durch Metallkomplexierung ist demnach auch das Resultat der veränderten konformativen Freiheit der HS durch die gebundenen Metallionen. Es zeigte sich, dass abhängig vom Metallion sowohl Löschung als auch Verstärkung der intrinsischen HS-Fluoreszenz beobachtet werden kann.<br> Als extrinsische Lumineszenzsonden mit wohl-charakterisierten photophysikalischen Eigenschaften wurden polyzyklische aromatische Kohlenwasserstoffe und Lanthanoid-Ionen eingesetzt. Durch Untersuchungen bei sehr niedrigen Temperaturen (10 K) konnte erstmals die Mikroumgebung von an HS gebundenen hydrophoben Xenobiotika untersucht werden. Im Vergleich mit Raumtemperaturexperimenten konnte gezeigt werden, dass hydrophobe Xenobiotika an HS-gebunden in einer Mikroumgebung, die in ihrer Polarität analog zu kurzkettigen Alkoholen ist, vorliegen. Für den Fall der Metallkomplexierung wurden Energietransferprozesse zwischen HS und Lanthanoidionen bzw. zwischen verschiedenen, gebundenen Lanthanoidionen untersucht. Basierend auf diesen Messungen können Aussagen über die beteiligten elektronischen Zustände der HS einerseits und Entfernungen von Metallbindungsstellen in HS selbst angeben werden. Es ist dabei zu beachten, dass die Experimente in Lösung bei realen Konzentrationen durchgeführt wurden. Aus Messung der Energietransferraten können direkte Aussagen über Konformationsänderungen bzw. Aggregationsprozesse von HS abgeleitet werden. / Transport and fate of xenobiotics in the environment, especially in water and soil, are of utmost importance for life on earth. A major reaction partner for xenobiotics in the environment are humic substances (HS). HS are degradation products of plant and animal tissue, which are formed in a combination of subsequent chemical and/or biochemical processes. Because of the complex history of their origin HS are extremely heterogeneous mixtures of different compounds. Consequently, they posses a great variety of interaction capabilities with various xenobiotics. The investigations of the fundamental interaction mechanisms between HS and xenobiotics make high demands on the analytical techniques used. Especially spectroscopic techniques are promising for the investigation of interaction mechanisms in complex systems. Luminescence spectroscopy has the great advantage of outstanding sensitivity and of multidimensionality, which in principle allows the investigation of HS under environmental relevant conditions. For the characterisation of interaction processes of HS with xenobiotics the intrinsic fluorescence of HS as well as the luminescence of extrinsic probes can be used.<br> The intrinsic HS fluorescence is determined by the molecular structure as well as the connection of the basic fluorophores. Conformational freedom as well as the presence of energy accepting groups in the neighbourhood of the fluorophores are highly important for the overall intrinsic HS fluorescence. The presence of metal ions can either quench or enhance the intrinsic HS fluorescence, which depends on the metal ion as well as on the origin of the HS investigated. While in most cases Al3+ ions enhance the intrinsic HS fluorescence, Ln3+ ions induce a fluorescence quenching.<br> Polycyclic aromatic hydrocarbons were used as extrinsic fluorescence probes in order to characterize the interaction of HS and hydrophobic organic xenobiotics. In investigations at ultra-low temperatures (10 K) it could be shown that pyrene is bound in a HS microenvironment with an polarity which resembles that of small alcohols (e.g., butanol).<br> In case of metal complexation, the lanthanide ions Eu3+ and Tb3+ were used as luminescence probes. Due to the outstanding luminescence properties of those ions, information about metal binding sites in HS were obtained. Based on the measurements of intramolecular and intermolecular energy transfer processes average distances of metal binding sites were deduced.

The studies in this thesis are mainly focused on the effects that the chaperonin mechanisms have on a bound target protein. Earlier studies have shown that the bacterial chaperonin GroEL plays an active role in unfolding a target protein during the initial binding. Here, the effects of the eukaryotic chaperonin TRiC’s mechanical action on a bound target protein were studied by fluorescence resonance energy transfer (FRET) measurements by attaching the fluorophore fluorescein to specific positions in the structure of the target protein, β-actin. Actin is an abundant eukaryotic protein and is dependent on TRiC to reach its native state. It was found that at the initial binding to TRiC, the actin structure is stretched, particularly across the nucleotide-binding site. This finding led to the conclusion that the binding-induced unfolding mechanism is conserved through evolution. Further studies indicated that in a subsequent step of the chaperonin cycle, the actin molecule collapses. This collapse leads to rearrangements of the structure at the nucleotide-binding cleft, which is also narrowed as a consequence. As a comparison to the productive folding of actin in the TRiC chaperonin system, FRET studies were also performed on actin interacting with GroEL. This is a non-productive interaction in terms of guiding actin to its native state. The study presents data indicating that the nucleotide-binding cleft in actin is not rearranged by GroEL in the same way as it is rearranged during the TRiC interaction. Thus, it could be concluded that although the general unfolding mechanism is conserved through the evolution of the chaperonins, an additional and specific binding to distinct parts of the actin molecule has evolved in TRiC. This specific binding leads to a directed unfolding and rearrangement of the nucleotide-binding cleft, which is vital for actin to reach its native state. The differences in the chemical properties of the actin-GroEL and the actin-TRiC complexes were also determined by measurements of fluorescein anisotropies and AEDANS emission shifts for probes attached to positions spread throughout the actin structure. The evolutionary aspects of the chaperonin mechanisms and the target protein binding were further investigated in another study. In this study, the prokaryotic homologue to actin, MreB, was shown to bind to both TRiC and GroEL. MreB was also shown to bind to the co-chaperonin GroES. In a separate study, the interaction between actin and the chaperone prefoldin was investigated. In vivo prefoldin interacts with non-native actin and transfers it to TRiC for subsequent and proper folding. In this homo-FRET study, it was shown that actin binds to prefoldin in a stretched conformation, similar to the initial binding of actin to TRiC. / On the day of the defence date the satus of article I was: In press.

In this thesis, I describe experiments that were designed to provide a better understanding of polymer diffusion during latex film formation. This step leads to the improvement of film mechanical properties. Polymer diffusion in these films was monitored by fluorescence resonance energy transfer. Current paint formulations contain Volatile Organic Compounds (VOCs) as plasticizers to facilitate polymer diffusion. The drawback of this technology is the release of VOCs to the atmosphere. VOCs are deleterious to the environment and contribute to smog and ground level ozone formation. The propensity of water, an indispensible part of any latex dispersion, to promote polymer diffusion was studied. Copolymers of poly (butyl acrylate-co-methyl methacrylate) and poly(ethylhexyl acrylate-co-tertiary butyl methacrylate) with similar glass transition temperatures but different hydrophobicity were compared. Polymer diffusion was monitored for films aged at different relative humidities. Water absorbed by the hydrophobic copolymer film was less efficient in promoting polymer diffusion than in the hydrophilic polymer. Only the fraction of water which is molecularly dissolved in the film participate actively in plasticization. Although water has low solubility in most latex polymers, molecularly dissolved water is more efficient than many traditional plasticizers. The possibility of modifying film formation behavior of acrylic dispersions with oligomers was studied by synthesizing hybrid polymer particles consisting of a high molecular weigh (high-M) polymer and an oligomer with the same composition. Oligomers with lower molecular weight are more efficient as diffusion promoters and have less deleterious effect on high-M polymer viscosity. A different set of hybrid particles were prepared in which the oligomer contained methacrylic acid units. The composition of the oligomer was tuned to be miscible with the high-M polymer when the acid groups were protonated but to phase separate when the acid groups were deprotonated. At basic pH, these particles adopt a core-shell morphology, with a shell rich in neutralized oligomers. After film formation, the oligomer shell retarded polymer diffusion. This retardation is expected to expand the time window during which the paint surface can be altered without leaving brush marks (open time). Short open time is a pressing problem in current technology.

In this thesis, I describe experiments that were designed to provide a better understanding of polymer diffusion during latex film formation. This step leads to the improvement of film mechanical properties. Polymer diffusion in these films was monitored by fluorescence resonance energy transfer. Current paint formulations contain Volatile Organic Compounds (VOCs) as plasticizers to facilitate polymer diffusion. The drawback of this technology is the release of VOCs to the atmosphere. VOCs are deleterious to the environment and contribute to smog and ground level ozone formation. The propensity of water, an indispensible part of any latex dispersion, to promote polymer diffusion was studied. Copolymers of poly (butyl acrylate-co-methyl methacrylate) and poly(ethylhexyl acrylate-co-tertiary butyl methacrylate) with similar glass transition temperatures but different hydrophobicity were compared. Polymer diffusion was monitored for films aged at different relative humidities. Water absorbed by the hydrophobic copolymer film was less efficient in promoting polymer diffusion than in the hydrophilic polymer. Only the fraction of water which is molecularly dissolved in the film participate actively in plasticization. Although water has low solubility in most latex polymers, molecularly dissolved water is more efficient than many traditional plasticizers. The possibility of modifying film formation behavior of acrylic dispersions with oligomers was studied by synthesizing hybrid polymer particles consisting of a high molecular weigh (high-M) polymer and an oligomer with the same composition. Oligomers with lower molecular weight are more efficient as diffusion promoters and have less deleterious effect on high-M polymer viscosity. A different set of hybrid particles were prepared in which the oligomer contained methacrylic acid units. The composition of the oligomer was tuned to be miscible with the high-M polymer when the acid groups were protonated but to phase separate when the acid groups were deprotonated. At basic pH, these particles adopt a core-shell morphology, with a shell rich in neutralized oligomers. After film formation, the oligomer shell retarded polymer diffusion. This retardation is expected to expand the time window during which the paint surface can be altered without leaving brush marks (open time). Short open time is a pressing problem in current technology.

Single-molecule spectroscopy has provided a means to uncover pathways and heterogeneities that were previously hidden beneath the ensemble average. Such heterogeneity, however, is often obscured by the artifacts of experimental noise and the occurrence of undesired processes within the experimental medium. This has subsequently caused in the need for new analytical methodologies. It is particularly important that objectivity be maintained in the development of new analytical methodology so that bias is not introduced and the results improperly characterized. The research presented herein identifies two such sources of experimental uncertainty, and constructs objective approaches to reduce their effects in the experimental results. The first, photoblinking, arises from the occupation of dark electronic states within the probe molecule, resulting in experimental data that is distorted by its contribution. A method based in Bayesian inference is developed, and is found to nearly eliminate photoblinks from the experimental data while minimally affecting the remaining data and maintaining objectivity. The second source of uncertainty is electronic shot-noise, which arises as a result of Poissonian photon collection. A method based in wavelet decomposition is constructed and applied to simulated and experimental data. It is iii found that, while making only one assumption, that photon collection is indeed a Poisson process, up to 75% of the shot-noise contribution may be removed from the experimental signal by the wavelet-based procedure. Lastly, in an effort to connect model-based approaches such as molecular dynamics simulation to model-free approaches that rely solely on the experimental data, a coarse-grained molecular model of a molecular ionic fluorophore diffusing within an electrostatically charged polymer brush is constructed and characterized. It is found that, while the characteristics of the coarse-grained simulation compare well with atomistic simulations, the model is lacking in its representation of the electrostatically-driven behavior of the experimental system.