Pathogenesis of prion diseases in animals is associated with the misfolding of the cellular prion protein PrPC to the infectious form, PrPSc. We hypothesized that an animal’s susceptibility to prions is correlated with the propensity of an animal’s PrPC to adopt a β-sheet, PrPSc-like, conformation. We have developed a method which uses circular dichroism (CD) to directly calculate the relative population of PrP molecules that adopt a β-sheet conformation or the ‘β-state’, as a function of denaturant concentration and pH. We find that the PrP from animals that are more susceptible to prion diseases, like hamsters and mice, adopt the β-state more readily than the PrP from rabbits. The X-ray crystal structure of rabbit PrP reveals a helix-capping motif that may lower the propensity to form the β-state. PrP in the β-state contains both monomeric and octameric β-structured species, and possesses cytotoxic properties.

This thesis is focussed on structural and functional studies of a novel glycerophosphodiesterase (GpdQ) from Enterobacter aerogenes. GpdQ is highly promiscuous and is the first known phosphatase which is capable of degrading all three classes of phosphate esters (mono-, di- and triesters). Remarkably, GpdQ is also able to hydrolyse stable aliphatic phosphate esters and has been shown to degrade the hydrolysis product of the nerve agent VX. For these reasons, GpdQ has been realised to have potential as a powerful bioremediator for the removal of organophosphate pesticides and nerve agents. GpdQ is a binuclear metallohydrolase in which one of the metal ions is very weakly bound. Chapter 1 introduces the catalytic mechanisms of binuclear metallohydrolases by examining two related phosphate ester-degrading enzymes. Since one of the main features of catalysis addressed in this thesis are the differential metal binding affinities of GpdQ, Chapter 1 also canvasses a range of other binuclear metallohydrolases with similar behaviour. Chapter 2 examines the structural and evolutionary relationship between GpdQ and a number of other related enzymes. Using genome database searches, the two most closely related enzymes are identified. In performing these searches, a novel, putative binuclear metallohydrolase from Homo sapiens is also discovered. This enzyme, Hsa_aTRACP, is most closely related to PAPs, however construction of a homology model indicates that the active site tyrosine residue of PAP is replaced by histidine. In this respect, it may represent an evolutionary link to Ser/Thr protein phosphatases and GpdQ. The biology and chemistry of this putative enzyme is discussed. PAPs are the only binuclear enzymes with an established heterovalent active site of the type Fe(III)-M(II) (where M=Fe, Zn or Mn) whereas the majority of enzymes in this family have homovalent metal centres, including GpdQ and Ser/Thr protein. This is brought about due to the nature of the coordination sphere imposed by the enzyme. The activity of GpdQ can be reconstituted in the presence of Co(II), Zn(II), Mn(II) and Cd(II). Chapter 3 examines the kinetic properties of a binuclear homovalent system by studying the kinetic properties of Cd(II)-substituted GpdQ and a corresponding model complex. This comparative study leads to the identification of a terminal hydroxide molecule as the likely reaction-initiating nucleophile in Cd(II)-GpdQ with a pKa of 9.4. In Chapter 4, a detailed study of the structural, kinetic and spectroscopic behaviour of Co(II)-substituted GpdQ is presented. This chapter specifically probes the formation of the binuclear active site, the role of the metal ions in catalysis, the identity of the nucleophile and the potential role of any first or second coordination sphere residues in the regulation of enzyme activity, proton donation and metal ion coordination. Based on these findings, a detailed reaction mechanism is proposed in which the substrate itself promotes the formation of the catalytically competent binuclear centre and phosphorolysis occurs following nucleophilic attack by a terminal hydroxide molecule. A potential role of Asn80 (a ligand of one of the metal ions) in regulating both substrate and metal binding, and the role of the bridging hydroxide molecule in the activation of the terminal nucleophile is proposed. Chapter 5 employs a combination of kinetic and spectroscopic techniques to probe the proposed catalytic mechanism of GpdQ in depth. The formation of the catalytically competent binuclear centre is observed in pre-steady state studies, an integral first step in the catalytic mechanism. The dissociation and rate constants associated with formation of the binuclear centre are quantified. The rate of substrate turnover in GpdQ is relatively modest but is enhanced by a structural rearrangement involving the flexible Asn80 ligand. This structural change fine-tunes the reaction mechanism, leading to optimal reactivity. The steady-state kinetic properties of a series of metal ion derivatives (Co(II), Cd(II) and Mn(II)) of GpdQ and their reactivity towards a number of substrates are also compared. These findings lead to the conclusion that the reaction mechanism of GpdQ is modulated by both substrate and metal ion. In this respect, GpdQ is adaptive to the environmental conditions to which it is exposed by employing a flexible mechanistic strategy to achieve catalysis. Chapter 6 correlates the electronic and geometric structure of the binuclear centre in GpdQ as a means to probe specific aspects of the mechanism. This study uses the wild type enzyme and a site-directed mutant (Asn80Asp) to examine the structure of the metal ions at two stages of catalysis. The role of the bridging hydroxide molecule in nucleophilic activation is specifically addressed by monitoring changes in the electronic exchange interaction and other structural parameters as a result of phosphate binding. Also, the coordination environment of the metal ions in both the free enzyme and the phosphate-bound enzyme of wild type and Asn80Asp GpdQ were assessed against the currently proposed structures. The findings in this chapter corroborate the proposed catalytic mechanism of GpdQ. In summary, this project led to a detailed understanding of the mechanism of GpdQ, and provided insight into how both the metal ion composition and the identity of the substrate may modulate this mechanism. The knowledge gained may lead to the design of catalytically more efficient derivatives (mutants) of GpdQ for application in bioremediation.

This thesis is focussed on structural and functional studies of a novel glycerophosphodiesterase (GpdQ) from Enterobacter aerogenes. GpdQ is highly promiscuous and is the first known phosphatase which is capable of degrading all three classes of phosphate esters (mono-, di- and triesters). Remarkably, GpdQ is also able to hydrolyse stable aliphatic phosphate esters and has been shown to degrade the hydrolysis product of the nerve agent VX. For these reasons, GpdQ has been realised to have potential as a powerful bioremediator for the removal of organophosphate pesticides and nerve agents. GpdQ is a binuclear metallohydrolase in which one of the metal ions is very weakly bound. Chapter 1 introduces the catalytic mechanisms of binuclear metallohydrolases by examining two related phosphate ester-degrading enzymes. Since one of the main features of catalysis addressed in this thesis are the differential metal binding affinities of GpdQ, Chapter 1 also canvasses a range of other binuclear metallohydrolases with similar behaviour. Chapter 2 examines the structural and evolutionary relationship between GpdQ and a number of other related enzymes. Using genome database searches, the two most closely related enzymes are identified. In performing these searches, a novel, putative binuclear metallohydrolase from Homo sapiens is also discovered. This enzyme, Hsa_aTRACP, is most closely related to PAPs, however construction of a homology model indicates that the active site tyrosine residue of PAP is replaced by histidine. In this respect, it may represent an evolutionary link to Ser/Thr protein phosphatases and GpdQ. The biology and chemistry of this putative enzyme is discussed. PAPs are the only binuclear enzymes with an established heterovalent active site of the type Fe(III)-M(II) (where M=Fe, Zn or Mn) whereas the majority of enzymes in this family have homovalent metal centres, including GpdQ and Ser/Thr protein. This is brought about due to the nature of the coordination sphere imposed by the enzyme. The activity of GpdQ can be reconstituted in the presence of Co(II), Zn(II), Mn(II) and Cd(II). Chapter 3 examines the kinetic properties of a binuclear homovalent system by studying the kinetic properties of Cd(II)-substituted GpdQ and a corresponding model complex. This comparative study leads to the identification of a terminal hydroxide molecule as the likely reaction-initiating nucleophile in Cd(II)-GpdQ with a pKa of 9.4. In Chapter 4, a detailed study of the structural, kinetic and spectroscopic behaviour of Co(II)-substituted GpdQ is presented. This chapter specifically probes the formation of the binuclear active site, the role of the metal ions in catalysis, the identity of the nucleophile and the potential role of any first or second coordination sphere residues in the regulation of enzyme activity, proton donation and metal ion coordination. Based on these findings, a detailed reaction mechanism is proposed in which the substrate itself promotes the formation of the catalytically competent binuclear centre and phosphorolysis occurs following nucleophilic attack by a terminal hydroxide molecule. A potential role of Asn80 (a ligand of one of the metal ions) in regulating both substrate and metal binding, and the role of the bridging hydroxide molecule in the activation of the terminal nucleophile is proposed. Chapter 5 employs a combination of kinetic and spectroscopic techniques to probe the proposed catalytic mechanism of GpdQ in depth. The formation of the catalytically competent binuclear centre is observed in pre-steady state studies, an integral first step in the catalytic mechanism. The dissociation and rate constants associated with formation of the binuclear centre are quantified. The rate of substrate turnover in GpdQ is relatively modest but is enhanced by a structural rearrangement involving the flexible Asn80 ligand. This structural change fine-tunes the reaction mechanism, leading to optimal reactivity. The steady-state kinetic properties of a series of metal ion derivatives (Co(II), Cd(II) and Mn(II)) of GpdQ and their reactivity towards a number of substrates are also compared. These findings lead to the conclusion that the reaction mechanism of GpdQ is modulated by both substrate and metal ion. In this respect, GpdQ is adaptive to the environmental conditions to which it is exposed by employing a flexible mechanistic strategy to achieve catalysis. Chapter 6 correlates the electronic and geometric structure of the binuclear centre in GpdQ as a means to probe specific aspects of the mechanism. This study uses the wild type enzyme and a site-directed mutant (Asn80Asp) to examine the structure of the metal ions at two stages of catalysis. The role of the bridging hydroxide molecule in nucleophilic activation is specifically addressed by monitoring changes in the electronic exchange interaction and other structural parameters as a result of phosphate binding. Also, the coordination environment of the metal ions in both the free enzyme and the phosphate-bound enzyme of wild type and Asn80Asp GpdQ were assessed against the currently proposed structures. The findings in this chapter corroborate the proposed catalytic mechanism of GpdQ. In summary, this project led to a detailed understanding of the mechanism of GpdQ, and provided insight into how both the metal ion composition and the identity of the substrate may modulate this mechanism. The knowledge gained may lead to the design of catalytically more efficient derivatives (mutants) of GpdQ for application in bioremediation.

All biological processes are fundamentally inter-molecular interactions. In order to understand, and hence control, biomolecular structure and function, methods are required that probe biological systems at the molecular level, ideally with those molecules being in their native environment. The research summarized herein has at its core the development and application of ultra violet (UV)-visible spectrophotometric techniquies for this prupose, in particular circular dichrosim (CD) and linear dichrosim (LD) but also absorbance, fluorescence and resonance light scattering. The spectroscopy is complemented by fundamental theoretical work on molecular structure and reactivity that forms the basis for designing molecules to bind to biomolecules for a particular structural or functional effect. A brief summary of the contributions of the listed publications to our understanding of 'Molecular aspects of biololecule structure and function' is given below under five headings: Circular dichroism theory Molecular geometry and reactivity Small molecule-macromolecule interactions: spectroscopic probes of inter-molecular geometries Molecular design for nucleic acid structure and control Spectroscopic probes of biomolecule structure: instrumentation and application In general terms these correspond to successive phases of the research programme, however, all areas have been present since the first publications in 1983 and can be traced weaving through all subsequent activity.

Thesis (Ph.D. in Molecular Biology) -- University of Colorado Denver, 2008. / Typescript. Includes bibliographical references (leaves 155-167). Free to UCD affiliates. Online version available via ProQuest Digital Dissertations;

Recently, there has been increasing focus toward the development of small molecules designed to target a specific sequences of double stranded DNA for therapeutic purposes1. Minor groove binding compounds have been shown to be capable of selectivity target GC sites in AT tract DNA2. In this research, binding selectivity was investigated using absorption, fluorescence and circular dichroic properties of selected DB minor groove binders in the presence of two unique DNA sequences. Further insight was gained by comparing the electrostatic potential maps and optimized structures of the compounds of interest. Using the results presented, potential selective minor groove binders can be selected for further investigation and kinetic studies.

Nanomatériaux de silice peuvent être facilement fabriqués, façonné et fonctionnalisés comme plates-formes pour le greffage des nanoparticules pour des applications biomédicales et optiques. Ici, nous utilisons une méthodologie basée sur un modèle de préparer une collection variée de hélicoïdale nanoparticules d'or (PNB) superstructures ayant impartialité contrôlable et mesures structurelles en utilisant PNB que les blocs de construction, et les nanohelices de silice que le modèle. Le matériaux présentent synthétisé bien définir Agencement chiral de PNB suivant l'hélicité de nanohelices de silice, montrant des signaux plasmoniques de dichorism circulaire (CD). D'autres observations ont prouvé ce plasmon CD vient de l'arrangement chiral de PNB et cet effet est très taille, l'échelle et dépend du pH. Nous nous attendons à ce que cette stratégie d'assemblage va découvrir une meilleure vue sur les métamatériaux et de susciter la vue vers "bottom-up" des approches en nanosciences. / Silica nanomaterials can be easily fabricated, fashioned and functionalized as platforms for grafting of nanoparticles for biomedical and optical applications. Herein, we utilize a template-based methodology to prepare a diverse collection of helical gold nanoparticle (GNPs) superstructures having controllable handedness and structural metrics by using GNPs as the building blocks, and the silica nanohelices as the template. The synthesized materials exhibit well-defined chiral arrangement of GNPs following the helicity of silica nanohelices, showing plasmonic circular dichorism (CD) signals. Further observations proved this plasmon CD comes from the chiral arrangement of GNPs and this effect is highly size, scale and pH dependent. We expect that this assembly strategy will discover a better view towards metamaterials and spark the view towards “bottom-up” approaches in nanoscience.

abstract: The photosynthetic reaction center is a type of pigment-protein complex found widely in photosynthetic bacteria, algae and higher plants. Its function is to convert the energy of sunlight into a chemical form that can be used to support other life processes. The high efficiency and structural simplicity make the bacterial reaction center a paradigm for studying electron transfer in biomolecules. This thesis starts with a comparison of the primary electron transfer process in the reaction centers from the Rhodobacter shperoides bacterium and those from its thermophilic homolog, Chloroflexus aurantiacus. Different temperature dependences in the primary electron transfer were found in these two type of reaction centers. Analyses of the structural differences between these two proteins suggested that the excess surface charged amino acids as well as a larger solvent exposure area in the Chloroflexus aurantiacus reaction center could explain the different temperature depenence. The conclusion from this work is that the electrostatic interaction potentially has a major effect on the electron transfer. Inspired by these results, a single point mutant was designed for Rhodobacter shperoides reaction centers by placing an ionizable amino acid in the protein interior to perturb the dielectrics. The ionizable group in the mutation site largely deprotonated in the ground state judging from the cofactor absorption spectra as a function of pH. By contrast, a fast charge recombination assoicated with protein dielectric relaxation was observed in this mutant, suggesting the possibility that dynamic protonation/deprotonation may be taking place during the electron transfer. The fast protein dielectric relaxation occuring in this mutant complicates the electron transfer pathway and reduces the yield of electron transfer to QA. Considering the importance of the protein dielectric environment, efforts have been made in quantifying variations of the internal field during charge separation. An analysis protocol based on the Stark effect of reaction center cofactor spectra during charge separation has been developed to characterize the charge-separated radical field acting on probe chromophores. The field change, monitored by the dynamic Stark shift, correlates with, but is not identical to, the electron transfer kinetics. The dynamic Stark shift results have lead to a dynamic model for the time-dependent dielectric that is complementary to the static dielectric asymmetry observed in past steady state experiments. Taken together, the work in this thesis emphasizes the importance of protein electrostatics and its dielectric response to electron transfer. / Dissertation/Thesis / Ph.D. Physics 2012

The canonical Wnt pathway is a vitally important signalling pathway that plays an important role in cell proliferation, differentiation and fate decisions in embryonic development and in the maintenance of adult tissues. The twelve Armadillo (ARM) repeat-containing protein beta-catenin acts as the signal transducer in this pathway and is continuously degraded in the cytosol by the beta-catenin destruction complex (BDC). Upon receiving the Wnt signal the BDC is inactivated, allowing beta-catenin to accumulate in the cytosol and be transported to the nucleus where it binds to the TCF/LEF family of transcription factors, inducing the expression of cell cycle promotor genes. In this Thesis I describe investigations into the roles of leucine-rich repeat kinase 2 (LRRK2) and the transcription factor TCF7L2 within this signalling pathway. LRRK2 is a large multi-domain protein with strong links to Parkinson’s disease and suggested to play a role in inactivating the BDC in response to the Wnt signal. A recent paper proposed that the previously uncharacterised regions of LRRK2 contain a series of tandem repeat sub-domains. I began an investigation into these sub-domains but I was unable to produce soluble protein constructs despite the use of a range of common techniques, and so I was forced to conclude this project early. The main body of this thesis focuses on the interaction between the intrinsically disordered TCF7L2 and the repeat protein beta-catenin, a very long interface of approximately 4800 Å2 that spans from the third to the eleventh ARM repeat of beta-catenin and residues 12 to 50 of TCF7L2, as determined by X-ray crystal structures. First, a fluorescence reporter system for the binding interaction was developed and used to determine the kinetic rate constants for the association and dissociation of the wild-type construct using stopped-flow fluorescence spectroscopy and time-dependent fluorescence spectroscopy. It was found that association of TCF7L2 and beta-catenin was rapid (7.3 ± 0.1 x107 M-1s-1) with only a single phase was observed, whereas dissociation was biphasic and slow (5.7 ± 0.4 x10-4 s-1, 15.2 ± 2.8 x10-4 s-1). Using either of these two dissociation rate constants the calculated Kd value obtained is much lower than the values previously reported in the literature (8 ± 1 / 20 ± 2 pM compared with 16 nM). This reporter system was then used to investigate the striking variability between three crystal structures previously obtained for the TCF7L2-beta-catenin complex, in which different regions of TCF7L2 show different elements of secondary structure. Mutational analysis revealed that the interface residues on TCF7L2 identified in these structures make little or no contribution to the overall binding affinity, pointing to a transient nature of these contact in solution and suggesting that the observed differences between the structures are due to differences in crystal packing. Further experiments into the effect of osmolarity on the binding equilibrium and kinetics supported this conclusion and suggest a change in the association/dissociation mechanism as a function of ionic strength. Lastly, further mutational analysis of TCF7L2 revealed two regions that contribute particularly strongly to the binding kinetics, suggesting that TCF7L2-beta-catenin assembly proceeds via a two-site avidity mechanism. Some of the most destabilising variants display two additional dissociation phases, indicating the presence of an alternative dissociation pathway that is inaccessible to the wild-type. In summary, the results presented here provide insights into the kinetics of molecular recognition of a long intrinsically disordered region with an extended repeat protein surface, a process shown to involve multiple routes with multiple steps in each.

Made available in DSpace on 2015-07-22T20:50:43Z (GMT). No. of bitstreams: 0 Previous issue date: 2008-03-26. Added 1 bitstream(s) on 2015-08-11T03:25:45Z : No. of bitstreams: 1 Publico-10806.pdf: 1743333 bytes, checksum: 379793d92e9d86096d10c579b33c757e (MD5) / A hormônio protéico produzido pelo gene-ob e denominado leptina, é um produto originário do tecido adiposo, circula pelo plasma e afeta o balanço energético interagindo em receptores presentes no hipotálamo. A leptina desempenha um papel importante na regulação de uma variedade de funções fisiológicas, incluindo controle de ingestão alimentar, temperatura corporal e manutenção do peso corporal. A ausência ou resistência a leptina pelo organismo causa obesidade mórbida, diabetes e hipogonadismo. A estrutura terciária da molécula da leptina revela a presença de quatro hélices, cujo padrão é típico das citocinas. Com o objetivo de identificar a região da molécula responsável pela expressão de sua atividade biológica foram sintetizados seis fragmentos peptídicos cujas estruturas foram escolhidas de acordo com a estrutura tridimensional da leptina. Em estudos anteriores do nosso grupo, dois peptídeos, AchLEP92- 115-NH2 (IV) e Ac-[Ser117]-hLEP116-140-NH2 (V), foram reconhecidos pelo receptor da leptina presentes em células HP-75, confirmando outros trabalhos da literatura que também apontavam que é nesta região da molécula que deve estar presente o epitopo funcional da leptina. Neste trabalho, uma nova série de fragmentos, cujas estruturas primárias estão contidas na região dos fragmentos IV e V, foram sintetizados e os efeitos dos mesmos na variação do peso corporal e no consumo de alimento quando administrados no ventrículo cerebral de ratos normais foram avaliados. Os peptídeos foram sintetizados pelo método da fase sólida manual pela estratégia t-Boc. Os mesmos foram purificados por cromatografia liquida de alta eficiência e foram caracterizados por análise de aminoácidos e cromatografia liquida acoplada a um espectrômetro de massas. Estudos conformacionais dos peptídeos também foram realizados por Dicroísmo Circular com o objetivo de correlacionar a estrutura com a atividade biológica dos fragmentos. Dentre os compostos estudados, o melhor resultado foi obtido com o fragmento AchLEP110- 119-NH2 (VI) que se mostrou ser mais ativo que a própia leptina e foi equipotente com o [D-Leu4]-OB3, que até então era o fragmento mais ativo descrito na literatura. Embora haja a necessidade de refinamentos, esse tipo de abordagem pode oferecer uma interessante base para o desenvolvimento de compostos correlacionados com a leptina com potencial de aplicação em estudos de obesidade humana ou na medicina veterinária. / The protein hormone produced by the ob-gene and denominated leptin, a product originating from adipose tissue, circulates in the plasma and affects the energy balance by interacting with the hypothalamus. Leptin plays an important role in the regulation of a variety of physiological functions, including food intake, body temperature and body weight maintenance. Total absence or resistance to leptin causes morbid obesity, diabetes and hypogonadism. The tertiary structure of the leptin molecule reveals the existence of a fourhelix bundle that is characteristic of the short-helix cytokines. To identify regions of the leptin molecule responsible for its bioactivity, we have synthesized six peptides based on the protein three-dimensional structure. Our results indicated that the fragments AchLEP92- 115-NH2 (IV) and Ac-[Ser117]-hLEP116-140-NH2 (V) were recognized by leptin receptor present in hp-75 cells, in agreement with the obtained by other authors, validating that this region of the molecule contain the functional epitope of the leptin molecule. In the present study, a new series of peptides encompassing the region of fragments IV and V of leptin were synthesized, and their effects on body weight and food intake were assessed when administered into the lateral cerebroventricle of normal rats. Peptides were synthesized by the solid phase methodology, purified by RP-HPLC and characterized by LC/ESI-MS. We also performed a conformational study of the peptides by circular dichroism in order to correlate the biological activity and secondary structure of the leptin fragments. Out off the new series of compounds, the best results were obtained with the fragment Ac-hLEP110-119-NH2 (VI) which showed to be more active than leptin and equipotent to [D-Leu4]-OB3 the most active leptin fragment described in the literature so far. Although the peptide fragments design needs refinement, this kind of approach may offer the basis for the development of leptin-related compounds with potential application in human obesity or veterinary medicine. / TEDE / BV UNIFESP: Teses e dissertações