A malária é a doença parasitária mais comum no mundo e é causada por protozoários do gênero Plasmodium spp., sendo transmitida por dípteros do gênero Anopheles spp. para hospedeiros vertebrados. Ambos, parasitas e vetores, têm desenvolvido resistência aos tratamentos e medidas profiláticas, respectivamente, indicando a necessidade de novas formas de controle. Chaperonas moleculares e co-chaperonas são interessantes alvos de estudo para desenvolvimento de terapias mais eficazes, uma vez que estas biomoléculas desempenham papel importante no processo de adaptação e sobrevivência do protozoário. As chaperonas da família Hsp90 participam de vários processos fisiológicos, que não somente auxiliar o enovelamento de proteínas clientes. Cada protômero da Hsp90 é composto por três domínios denominados N, M e C, e a proteína se organiza na forma de homodímeros flexíveis. As co-chaperonas são proteínas auxiliares, essenciais para modulação do ciclo funcional da Hsp90. A co-chaperona Aha1 (do inglês Activator of the Hsp90-ATPase activity 1) estabiliza a Hsp90 em um estado conformacional intermediário e estimula a atividade ATPásica da mesma. Neste contexto, é usual a busca por inibidores potenciais diretos e indiretos para Hsp90 e por respostas sobre seu mecanismo de inibição. O objetivo deste trabalho foi a obtenção e caracterização bioquímica e biofísica da proteína Hsp90 recombinante de Plasmodium falciparum (PfHsp90) e construções PfHsp90NM e PfHsp90M, além do mapeamento da interação com a co-chaperona Aha4 de P. falciparum (PfAha4). Os experimentos de caracterização estrutural revelam que o domínio N é menos estável termicamente do que o domínio M e também é o mais rico em estrutura secundária do tipo hélice α. A PfHsp90 comporta-se majoritariamente como homodímero alongado e flexível em solução, sendo o domínio C essencial para a dimerização, todavia as construções PfHsp90NM e PfHsp90M comportam-se como monômeros. Ensaios de fluorescência revelaram que as construções exibem diferenças na estabilidade química e que possuem estrutura terciária local com seus triptofanos parcialmente expostos ao solvente. A atividade ATPásica da PfHsp90 foi estimulada por PfAha4, e a interação entre elas foi resolvida com estequiometria de duas moléculas de PfAha4 por dímero de PfHsp90. Tal interação foi entalpicamente dirigida, ocorrendo liberação de moléculas de água, com interação mediada principalmente por contatos hidrofóbicos. O mapeamento das regiões de contato sugere que o cerne da interação ocorra entre a PfAha4 e o domínio M da PfHsp90. As diferenças exibidas pela PfHsp90 com relação as propriedades de proteínas ortólogas podem ter relação com os resíduos de aminoácidos que conectam os domínios N e M em sua estrutura, devido a sua flexibilidade, tamanho e composição. / Malaria is the most common parasitic disease in the world and is caused by protozoa of the genus Plasmodium spp., and transmitted by dipterans of the genus Anopheles spp. for vertebrate hosts. Both parasites and vectors have developed resistance to treatments and prophylactic measures, respectively, indicating the need for new forms of control. Molecular chaperones and co-chaperones are interesting targets for the development of more effective therapies, since these biomolecules play an important role in the process of adaptation and survival of the protozoan. The chaperones of the Hsp90 family participate in several physiological processes, which not only aid in the folding of client proteins. Each Hsp90 protomer have three domains called N, M and C, and the protein is organized as flexible homodimers. Co-chaperones are assistant proteins, they are essential for modulating the functional cycle of Hsp90. The Aha1 (Activator of the Hsp90-ATPase activity 1) co-chaperone stabilizes Hsp90 in an intermediate conformational state and stimulates the ATPase activity thereof. In this context, it is usual the search for direct and indirect potential inhibitors for Hsp90 and for responses about its inhibition mechanism. The objective of this work was the biochemical and biophysical characterization of the Hsp90 recombinant protein of Plasmodium falciparum (PfHsp90) and PfHsp90NM and PfHsp90M constructions, as well as to map interactions with the Aha4 co-chaperone of P falciparum (PfAha4). Structural characterization experiments show that the N domain is less thermally stable than the M domain and is also the richest in α-helix secondary structure. PfHsp90 behaves mostly as elongated and flexible homodimer in solution, domain C is essential for dimerization, on the other hand the constructs PfHsp90NM and PfHsp90M behave as monomers. Fluorescence assays revealed that the constructs exhibit differences in chemical stability and that have local tertiary structure with their tryptophans partially exposed to the solvent. The ATPase activity of PfHsp90 was stimulated by PfAha4, and the interaction between them was resolved with stoichiometry of two molecules of PfAha4 by PfHsp90 dimer. Such interaction was enthalpically driven, releasing of water molecules, with interaction mediated mainly by hydrophobic contacts. The mapping of contact regions suggests that the core of the interaction occurs between PfAha4 and the M domain of PfHsp90. The differences exhibited by PfHsp90 concerning the properties of orthologous proteins, may be related to the amino acid residues that connect the N and M domains in its structure, due to its flexibility, size and composition.

Neurons need to be maintained to persist throughout adulthood for proper brain function. However neuronal activity, injury and aging exert physical stress on the nervous system, which compromise nervous system function. Healthy neurons are able to maintain their integrity throughout the lifespan of the animal, suggesting the existence of a maintenance mechanism that allows neurons to sustain or even repair damage. A forward genetic screening in Drosophila identified mutations in a gene called nmnat that cause a rapid and severe neurodegeneration immediately post neuronal differentiation and development. NMNAT protein was required to maintain neuronal integrity in an activity-dependent manner. When probing for the exact role of NMNAT in neuronal maintenance, a novel stress responsive chaperone function was identified, in addition to its essential housekeeping NAD synthase role. In this work, the mechanism of NMNAT-mediated neuroprotection is investigated. First, the transcriptional regulation of Drosophila NMNAT during acute stress is analyzed. Here, both stress transcription factors heat shock factor (HSF) and hypoxia inducible factor alpha (HIF1-α) have been shown to upregulate NMNAT during stress through a heat shock element in the nmnat promoter. In addition, the role of NMNAT for stress tolerance in Drosophila is revealed. Second, to elucidate the neuroprotective capacity of NMNAT in neurodegenerative disease, mouse models of tauopathy have been used. In the P301L Tau-transgenic mouse model, the levels of endogenous NMNAT2 have been studied at various ages to link a reduction in NMNAT2 as a precursor for neurodegeneration. The underlying mechanism of NMNAT2 downregulation is further studied in this model. Third, using Drosophila model of Tauopathy, the protective capacity of both wild type and enzyme-inactive NMNAT in ameliorating the pathological and behavioral impairments from Tau-induced neurodegeneration were studied extensively. The possible protective mechanism of NMNAT is uncovered by identifying novel interactions of NMNAT with hyperphosphorylated and ubiquitinated Tau in regulating the levels of toxic Tau species. Finally, this study also identified endogenous proteins that NMNAT interacts with to provide insight into a neuroprotective chaperone role of NMNAT. Together, these studies improve our understanding of the mechanisms of neuronal maintenance, by providing a comprehensive investigation of the stress-responsive regulation of NMNAT in both Drosophila and mammalian models, and its role as a chaperone both in protein foldopathies and in healthy neurons.

This thesis was made to get a deeper understanding of how chaperones interact with unstable, aggregation prone, misfolded proteins involved in human disease. Over the last two decades, there has been much focus on misfolding diseases within the fields of biochemistry and molecular biotechnology research. It has become obvious that proteins that misfold (as a consequence of a mutation or outer factors), are the cause of many diseases. Molecular chaperones are proteins that have been defined as agents that help other proteins to fold correctly and to prevent aggregation. Their role in the misfolding disease process has been the subject for this thesis. Transthyretin (TTR) is a protein found in human plasma and in cerebrospinal fluid. It works as a transport protein, transporting thyroxin and holo-retinol binding protein. The structure of TTR consists of four identical subunits connected through hydrogen bonds and hydrophobic interactions. Over 100 point mutations in the TTR gene are associated with amyloidosis often involving peripheral neurodegeneration (familial amyloidotic polyneuropathy (FAP)). Amyloidosis represents a group of diseases leading to extra cellular deposition of fibrillar protein known as amyloid. We used human SH-SY5Y neuroblastoma cells as a model for neurodegeneration. Various conformers of TTR were incubated with the cells for different amounts of time. The experiments showed that early prefibrillar oligomers of TTR induced apoptosis when neuroblastoma cells were exposed to these species whereas mature fibrils were not cytotoxic. We also found increased expression of the molecular chaperone BiP in cells challenged with TTR oligomers. Point mutations destabilize TTR and result in monomers that are unstable and prone to aggregate. TTR D18G is naturally occurring and the most destabilized TTR mutant found to date. It leads to central nervous system (CNS) amyloidosis. The CNS phenotype is rare for TTR amyloid disease. Most proteins associated with amyloid disease are secreted proteins and secreted proteins must pass the quality control check within the endoplasmic reticulum (ER). BiP is a Hsp70 molecular chaperone situated in the ER. BiP is one of the most important components of the quality control system in the cell. We have used TTR D18G as a model for understanding how an extremely aggregation prone protein is handled by BiP. We have shown that BiP can selectively capture TTR D18G during co-expression in both E. coli and during over expression in human 293T cells and collects the mutant in oligomeric states. We have also shown that degradation of TTR D18G in human 293T cells occurs slower in presence of BiP, that BiP is present in amyloid deposition in human brain and mitigates cytotoxicity of TTR D18G oligomers. / Denna avhandling handlar om proteiner. Särskilt de som inte fungerar som de ska utan har blivit vad man kallar ”felveckade”. Anledningen till att proteiner veckas fel beror ofta (men inte alltid) på mutationer i arvsmassan. Felveckade proteiner kan leda till sjukdomar hos människor och djur (man brukar tala om amyloidsjukdomar), ofta av neurologisk karaktär. Exempel på amyloidsjukdomar är polyneuropati, där perifera nervsystemet är drabbat, vilket leder till begränsad rörelseförmåga och senare till förlamning; och Alzheimer´s sjukdom, där centrala nervsystemet är drabbat och leder till begränsad tankeförmåga och minnesförluster. Studierna som presenteras i denna avhandling har gått ut på att få en bättre förståelse för hur felveckade proteiner interagerar med det som vi har naturligt i cellerna och som fungerar som skyddande, hjälpande proteiner, så kallade chaperoner. Transtyretin (TTR) är ett protein som cirkulerar i blodet och transporterar tyroxin (som är ett hormon som bland annat har betydelse för ämnesomsättningen) samt retinol-bindande protein (vitamin A). I TTR genen har man funnit över 100 punktmutationer, vilka har kopplats samman med amyloidsjukdomar, bland annat ”Skellefteåsjukan”. Mutationer i TTR genen leder ofta till att proteinet blir instabilt vilket leder till upplösning av TTR tetrameren till monomerer. Dessa monomerer kan därefter sammanfogas på nytt men denna gång på ett sätt som är farligt för organismen. I denna avhandling har fokus legat på en mutation som kallas TTR D18G, vilken har identifierats i olika delar av världen och leder till en dödlig form av amyloidos i centrala nervsystemet. Det chaperon som vi har studerat benämns BiP och är beläget i en cellkomponent som kallas för det endoplasmatiska retiklet (ER). I ER finns cellens kontrollsystem i vilket det ses till att felveckade proteiner inte släpps ut utan istället bryts ned. Denna avhandling har visat att BiP kan fånga upp TTR D18G inuti celler och där samla mutanten i lösliga partiklar som i detta fall är ofarliga för cellen. Avhandligen har också visat att nedbrytningen av TTR D18G sker mycket långsammare när BiP finns i riklig mängd.

The accumulation of the microtubule associated protein tau has been implicated in several neurological disorders; however, its interaction with chaperones along its normal degradation pathway remains largely uncharacterized at single residue resolution. In this study, nuclear magnetic resonance (NMR) spectroscopy was used to probe the interaction between tau, the molecular chaperone Hsp90, and the immunophilin FKBP51. Resonance intensity changes were observed for specific residues in the heteronuclear single quantum coherence (HSQC) spectra of 15N-labeled tau in the presence of Hsp90 and/or FKBP51. Analysis of the HSQC spectra identified the two hydrophobic hexapeptide motifs located at residues V275 - K280 and V306 - K311 in tau's C-terminal assembly domain as the sites of an interaction with both Hsp90 and FKBP51. Resonances that show reduced intensities did not experience line broadening, which suggests that slow chemical exchange is occurring with a bound conformation that is not observable due to the molecular weight of the complex. We have also investigated the role of the PPIase domain alone in binding to tau and found that specific residues within the PPIase active site experience significant reductions in intensity upon addition of tau. The experimental data is collectively used to propose a structural model for ternary complex formation between tau, Hsp90, and FKBP51.

Numerous essential cellular processes, such as gene regulation and tRNA processing, are carried out by structured RNAs. While in vitro most RNAs become kinetically trapped in non-functional misfolded states that render them inactive on a biologically-relevant time scale, RNAs folding in vivo do not share this same outcome. RNAs do indeed misfold in the cell; however, chaperone proteins promote escape from these non-native states and foster folding to functional conformations. DEAD-box proteins are ATP-dependent RNA chaperone proteins that function by disrupting structure, which can facilitate structural conversions. Here, studies with both local and global focuses are used to uncover mechanistic features of DEAD-box proteins CYT-19 and Mss116p. Both of these proteins are general RNA chaperones as they each have the ability to facilitate proper folding of multiple structured RNAs. The first study probes how DEAD-box proteins interact with a simple duplex substrate. Separating the strands of a duplex is an ATP-dependent process and is central to structural disruption by DEAD-box proteins. Here, how ATP is utilized during duplex separation is monitored by comparing ATP hydrolysis rates with strand separation rates. Results indicate that one ATP molecule is sufficient for complete separation of a 6-11 base pair RNA duplex. Under some conditions, ATP binding in the absence of hydrolysis is sufficient for duplex separation. Next, focus is shifted to a more global perspective as the function of Mss116p is probed in the folding of a cognate group II intron substrate, aI5[gamma], under near-physiological conditions. Three catalytically-active constructs of aI5[gamma] are used and catalysis serves as a proxy for folding. Folding of all constructs is promoted by the presence of Mss116p and ATP. In vitro and in vivo results indicate that a local unfolding event is promoted by Mss116p, stimulating formation of the native state. Lastly, orthogonal methods that probe physical features of RNA are used to provide insight into the structural intermediates with which Mss116p acts. / text

Chromatin structure is crucial to regulate access to the genome for processes such as a transcription, recombination, DNA repair, and DNA replication. Spt6, a key factor involved in regulating chromatin structure, is conserved throughout eukaryotes. Spt6 has been shown to function in many aspects of gene expression, including nucleosome assembly, transcription initiation and elongation, and mRNA processing and export. In addition, Spt6 has several conserved domains; however, little is known about their functions. I have performed a structure-function analysis of Spt6 using three separate approaches. First, I employed a random insertion mutagenesis that has identified sixty-seven mutants. While these mutants did not provide information regarding known domains, some have phenotypes that may prove useful for future study. Second, in a collaborative project with Romier lab, I studied the functional roles of the Spt6 SH2 domains. I have shown that deletion of the region of Spt6 encoding the SH2 domains causes severe mutant phenotypes without affecting Spt6 protein levels, demonstrating the importance of the SH2 domains of Spt6. Third, in an additional collaboration with the Romier lab, I showed that mutations that alter the region of Spt6 that interacts with the conserved transcription factor Spn1 impair Spt6 functions in vivo. Overall, this multi-pronged structure-function analysis of Spt6 has provided new insights into the tandem SH2 domains of Spt6, the Spt6-Spn1 interaction, and the uses and limitations of insertion mutagenesis. In addition, I have attempted to explore a possible role for Spt6 in transcription-associated mutagenesis. After employing several types of in vivo assays, I conclude that a possible role for Spt6 in transcription-associated mutagenesis is uncertain, as the results (with respect to a role for Spt6) reproducibly vary depending on the assay used. Thus, understanding this aspect of Spt6 biology awaits better assays and understanding of transcription-associated mutagenesis. Overall, the work in this dissertation will serve to further elucidate the mechanisms of Spt6 in chromatin regulation, transcription, and DNA damage repair.

Biometals such as copper, cobalt and zinc are essential to life. These transition metals are used as cofactors in many enzymes. Nonetheless, these metals cause deleterious effects if their intracellular concentration exceeds the cells' requirement. Prokaryotic organisms usually employ efflux systems to maintain metals in appropriate intracellular concentrations.The Cus system of Escherichia coli plays a crucial part in the copper homeostasis of the organism. This system is a tetrapartite efflux system, which includes an additional component compared to similar efflux systems. This fourth component is a small periplasmic protein, CusF. CusF is essential for full copper resistance, yet its role within the Cus system has not been characterized. It could potentially serve in the role of a metallochaperone or as a regulator to the Cus system.To gain insight into the molecular mechanism of resistance of this system, I have structurally and biochemically characterized CusF. Using X-ray crystallography I determined the CusF structure. CusF displays a novel fold for a copper binding protein. Through multiple sequence alignment and NMR chemical shift experiments, I proposed a metal binding site in CusF, which I confirmed through determination of the structure of CusF-Ag(I). CusF displays a novel coordination of Ag(I) and Cu(I) through a Met2His motif and a cation-pi interaction between the metal ion and a tryptophan sidechain. Furthermore, I have shown that CusF binds Cu(I) and Ag(I) specifically and tightly.I investigated the role of the tryptophan at the binding site to establish its effect on metal binding and function of CusF. I have shown through competitive binding assays, NMR studies and through collaborative EXAFS studies that the tryptophan plays an essential role in CusF metal handling. The affinity of CusF for Cu(I) is influenced by this residue. Moreover, the tryptophan also caps the binding site such that oxidation of the bound metal as well access to adventitious ligands is prevented. In summary, these findings show that the structure and metal site of CusF are unique and are specifically designed to perform the function of CusF as a metallochaperone to the Cus system.

Enteropathogenic Escherichia coli (EPEC) is an enteric pathogen that causes potentially fatal infantile diarrhea. A type III secretion system is employed by EPEC to inject bacterial effector proteins directly into host intestinal epithelial cells. The multivalent chaperone, CesT, interacts with nine effectors and is a significant contributor to EPEC pathogenesis. A putative transcriptional promoter region was identified directly upstream of cesT. In silico analyses identified conserved elements that suggest the cesT promoter is recognized by ?70. Using transcriptional fusions to lux reporter genes I showed that the cesT promoter region is active under conditions known to induce virulence-gene expression. I conclude that the cesT promoter is active early during an in vitro assay, and regulated by different mechanisms than those affecting the Ptir operon promoter.

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