Thesis (M. Sc. (Biochemistry, Microbiology and Biotechnology))--Rhodes University, 2005. / A research report submitted in partial fulfilment of the requirements for the degree of Master of Science (in Bioinformatics and Computational Molecular Biology).

Thesis (Ph. D.)--University of Chicago, Dept. of Neurobiology, Pharmacology and Physiology, December 2002. / Includes bibliographical references. Also available on the Internet.

Thesis (Ph. D.)--University of California, San Diego and San Diego State University, 2006. / Vita. Includes bibliographical references (leaves 90-106).

Thesis (Ph.D.) OGI School of Science & Engineering at OHSU, October 2007. / Includes bibliographical references (leaves 132-158).

Thesis (Ph.D. (Biochemistry)) - Rhodes University, 2007.

Orientador: Carlos Henrique Inacio Ramos / Dissertação (mestrado) - Universidade Estadual de Campinas, Instituto de Biologia / Made available in DSpace on 2018-08-17T21:47:21Z (GMT). No. of bitstreams: 1 Seraphim_ThiagoVargas_M.pdf: 4293116 bytes, checksum: bd401fff62b6ce29029ac35de3bc753a (MD5) Previous issue date: 2011 / Resumo: O enovelamento protéico é essencial para a correta função biológica das proteínas. A existência de um ambiente com alta concentração dos mais diferentes tipos de moléculas, dentro da célula, e de diversos tipos de situações de estresse, podem agir induzindo a formação de espécies improdutivas na via de enovelamento, como proteínas mal enoveladas e/ou até mesmo agregados protéicos. Para controlar estes eventos, há a maquinaria de chaperonas moleculares, que tem por objetivo garantir a homeostase protéica celular. As chaperonas moleculares são capazes de ligar e estabilizar um polipeptídio, mas sem contribuir com informações para a sua conformação final. Dentro desta maquinaria, o sistema Hsp70 tem um papel central, sendo responsável por receber proteínas desenoveladas ou mal enoveladas de outras chaperonas, podendo auxiliar no reenovelamento e direcionamento para outras chaperonas moleculares ou para degradação. A Hsp70 é regulada por co-chaperonas, como a Hsp40, que é responsável pela entrega de proteínas clientes à Hsp70 e pelo estímulo da atividade ATPase, essencial para a funcionalidade da Hsp70. Este trabalho apresenta a caracterização de uma Hsp40 tipo I de cana-de-açúcar, nomeada SHsp40, e o estudo de uma Hsp40 tipo II de levedura e seus mutantes, a fim de entender a relação estrutura-função destas proteínas. A SHsp40 foi expressa em E. coli, purificada e obtida enovelada, como verificado por dicroísmo circular. Além disso, a SHsp40 apresentou atividade chaperona em experimentos de proteção ao substrato desenovelado e se comportou como um dímero alongado em solução, como mostrado por SEC-MALS e pela determinação do fator de Perrin. Experimentos de desenovelamento térmico monitorado pelo sinal de CD a 222 nm revelaram que a SHsp40 possui pelo menos um intermediário, e a fluorescência de tioflavina T e bis-ANS mostraram que este intermediário é rico em folhas ? e parcialmente desenovelado, características de espécies na via de formação de fibrilas. A SHsp40 agregada foi examinada por microscopia eletrônica de varredura, que comprovou sua capacidade de formar de fibrilas. Este trabalho também contribuiu para o estudo de uma Hsp40 tipo II de levedura, Sis1, e seus mutantes de deleção, Sis1?124-174 e Sis1?121-257. Ensaios de fluorescência estática do triptofano, fotoapagamento e anisotropia mostraram que a deleção do domínio G/M não afetou a estrutura e hidrodinâmica de Sis1?124-174 em relação à proteína selvagem. Estudos de estabilidade destas proteínas, realizado anteriormente em nosso grupo de pesquisa e complementado neste trabalho pelo uso da técnica de SEC-MALS, mostrou que Sis1 e Sis1?124-174 foram mais estáveis que Sis1?121-257, mutante que o domínio G/M e subdomínio CTDI estão ausentes / Abstract: Correct protein folding is essential for proper protein biological function. There is a crowded environment and many types of molecules inside the cell and a variety of external stresses can act inducing unproductive species, as unfolded and/or misfolded proteins and even protein aggregates. To control these undesired events and ensures the protein homeostasis there is a molecular chaperone machinery. Molecular chaperones are able to bind and stabilize polypeptides but with no contributions for their final conformations. Inside this machinery, the Hsp70 system has a central role and is responsible to receive unfolded or misfolded proteins from other chaperones, helping in protein refolding and delivering the clients to other chaperones and even protein targeting for degradation. Hsp70 is regulated by its co-chaperones, such as Hsp40, which is responsible to client proteins deliver to Hsp70 and stimulation of its ATPase activity, essential processes for Hsp70 function. This work presents a sugarcane type I Hsp40 characterization, named SHsp40, and studies of an yeast type II Hsp40 and its mutants in order to understand the structure-function relationship of these proteins. The SHsp40 was expressed in E. coli, purified and obtained folded, as verified by circular dichroism. Furthermore, SHsp40 presented chaperone activity in unfolded substrate protection experiments and behaved as an elongated dimer in solution, as shown by SEC-MALS and estimated by Perrin factor. Thermal-induced unfolding experiments monitored by CD signal at 222 nm revealed that SHsp40 has at least one intermediate which is populated and tioflavin T and bis-ANS fluorescence showed that this intermediate is ? sheet-rich and partially folded, such as intermediate species in the fibril formation pathway. The aggregated SHsp40 was examined by scanning electron microscopy, wich proved its ability to fibril formation. This work also contributed for the study of an yeast type II Hsp40, Sis1, and its deletion mutants, Sis1?124-174 and Sis1?121-257. Steady-state tryptophan fluorescence, quenching and anisotropy assays showed that the G/M domain deletion did not affect the structure and hydrodynamic properties of Sis1?124-174 in relation to the wild type protein. Stability studies of these proteins, previously performed in our research group and complemented in this work by using the SEC-MALS technique, showed that Sis1 and Sis1?124-174 were more stable than Sis1?121-257, a mutant with the G/M domain and CTDI subdomain absents / Mestrado / Bioquimica / Mestre em Biologia Funcional e Molecular

Central to this research, 40 kDa Heat shock proteins (Hsp40s) are known to partner (or cochaperone) 70 kDa Heat shock proteins (Hsp70s), facilitating the selection and transfer of protein substrate to Hsp70 and the stimulation of the protein folding ability of Hsp70. Members of the diverse Hsp70-Hsp40 protein complement of Plasmodium falciparum have been implicated in the cytoprotection of this malaria parasite, and are thought to facilitate the protein folding, assembly and translocation tasks required by the parasite to commandeer the infected human erythrocyte subsequent to invasion. In particular, the parasite has evolved an expanded and specialised 43- member suite of Hsp40 proteins, 19 of which bear an identifiable export motif for secretion into the infected erythrocyte cytoplasm where they potentially interact with human Hsp70. Although type I Hsp40 proteins are representative of typical regulators of Hsp70 activity, only two of these proteins are apparent in the parasite’s Hsp40 complement. These include a characteristic type I Hsp40 termed PfHsp40, and a larger, atypical type I Hsp40 termed Pfj1. Both Hsp40 proteins are predicted to be parasite-resident and are most likely to facilitate the co-chaperone regulation of the highly abundant and stress-inducible Hsp70 homolog, PfHsp70-I. In this work, the co-chaperone functionality of PfHsp40 and Pfj1 was elucidated using in vivo and in vitro assays. Purified recombinant PfHsp40 was shown to stimulate the ATPase activity of PfHsp70-I in in vitro single turnover and steady state ATPase assays, and co-operate with PfHsp70-I in in vitro aggregation suppression assays. In these in vitro assays, heterologous partnerships could be demonstrated between PfHsp70-I and the human Hsp40, Hsj1a, and human Hsp70 and PfHsp40, suggesting a common mode of Hsp70-Hsp40 interaction in the parasite and host organism. The functionality of the signature Hsp40 domain, the Jdomain, of Pfj1 was demonstrated by its ability to replace the equivalent domain of the A. tumefaciens Hsp40, Agt DnaJ, in interactions with the prokaryotic Hsp70, DnaK, in the thermosensitive dnaJ cbpA E. coli OD259 deletion strain. An H33Q mutation introduced into the invariant and crucial HPD tripeptide motif abrogated the functionality of the J-domain in the in vivo complementation system. These findings provide the first evidence for the conservation of the prototypical mode of J-domain based interaction of Hsp40 with Hsp70 in P. falciparum. Immunofluorescence staining revealed the localisation of PfHsp40 to the parasite cytoplasm, and Pfj1 to the parasite cytoplasm and nucleus in cultured intraerythrocytic stage P. falciparum parasites. PfHsp70-I was also shown to localise to the parasite cytoplasm and nucleus in these stages, consistent with the literature. Overall we propose that PfHsp40 and Pfj1 co-localise with and regulate the chaperone activity of PfHsp70-I in P. falciparum. This is the first study to identify and provide evidence for a functional Hsp70-Hsp40 partnership in P. falciparum, and provides a platform for future studies to elucidate the importance of these chaperone partnerships in the establishment and survival of the parasite in the intraerythrocytic-stages of development.

The extant coelacanths have a close resemblance to the coelacanth fossil records dating back to 230mya. Like their predecessors, the extant coelacanths inhabit rocky caves at a depth of 100-300m below sea level. In the Comoros, the water temperature at these depths is estimated to fluctuate between 14-20°C. High-level adaptation to these environment and lack of competition are thought to have led to the morphological uniformity and slow change throughout the history of the coelacanths. Under stress conditions, proteins unfold or misfold leading to the formation of aggregates. Molecular chaperones facilitate the correct folding of other proteins so that they can attain a stable tertiary structure. In addition, molecular chaperones aid the refolding of denatured proteins and the degradation of terminally misfolded protein after cellular stress. Heat shock proteins form one of the major classes of molecular chaperones. Here we show that, despite high-level adaptation to a unique habitat and slow change, the genome of the coelacanth encodes the major and highly conserved molecular chaperone, Hsp70. Latimeria menadoensis and Latimeria chalumnae contain intronless hsp70 genes encoding Hsp70 proteins archetypal of known Hsp70s. Based on the coelacanth codon usage, we have shown that bacterial protein expression systems, particularly Escherichia coli, may not be appropriate for the overproduction of coelacanth Hsp70s and coelacanth proteins in general. Also interesting, was the discovery that like the rat Hsc70, the L. menadoensis Hsp70 could not reverse thermal sensitivity in a temperate sensitive E. coli DnaK mutant strain, BB2362. We also report the successful isolation of a 1.2 kb region of L. menadoensis hsp70 upstream regulatory region. This region contain three putative heat shock elements, a TATA- box and two CAAT-boxes. This regulatory region resembled the Xenopus, mouse, and particularly tilapia hsp70 promoters, all of which have been shown to drive the expression of reporter genes in a heat dependent manner. Taken together, this data is the first to strongly suggest an inducible Hsp70-base cytoprotection mechanism in the coelacanth. It further provides basis to formulate testable predictions about the regulation, structure and function of Hsp70s in the living fossil, Latimeria.

Tauopathies are neurodegenerative diseases that affect millions of people around the world. Tauopathies include more than 20 neurodegenerative diseases. Some of the most common tauopathies are Alzheimer’s disease (AD), frontotemporal dementia (FTD), chronic traumatic encephalopathy (CTE), Pick’s disease, corticobasal degeneration, progressive supranuclear palsy (PSP), agyrophillic grain disease, and amyotrophic lateral sclerosis (ALS). These diseases can cause significant memory loss, behavioral changes, motor deficits and speech impairments. Tauopathies stem from accumulation of the microtubule associated protein tau (MAPT). Tau stabilizes microtubules and helps with axonal transport. In a disease state tau becomes hyperphosphorylated and truncated leading to its aggregation. More recently tau has been shown to propagate from cell to cell potentially acting as a signaling molecule that contributes to disease progression. In addition during disease, tau mislocalizes to dendrites leading to synaptic dysfunction. This mislocalization may also lead to subsequent neurodegeneration. Today, many strategies have been implemented to treat tauopathies. Some of these strategies include kinase inhibitors, immunotherapy, tau aggregation inhibitors, and microtubule-stabilizing compounds. However none these strategies have been effective in stopping tau pathology nor do they address tau degradation pathways. Therefore we hypothesized that utilizing small molecules that target degradation pathways such as autophagy or proteasomal degradation would improve clearance of aberrant tau. We previously showed that a natural product (+)-aR,11S-myricanol (1) from Myrica cerifica (bayberry/southern wax myrtle) root bark reduced levels of tau. In this study we discovered that 1 is composed of two enantiomers and two possible atropisomers. We found that one enantiomer (-)-aS,11R-myricanol (3) was responsible for the anti-tau activity of 1 in multiple models of tauopathy. We also found that 3 selectively targets and lowers specific tau species. To better understand how these tau species were being reduced we took a non-biased approach and subjected 3 treated samples to stable isotope labeling by amino acids in cell culture (SILAC) mass spectrometry (MS) proteomic analysis. We found that autophagy pathways were most affected by 3 and that 3 was predicted to mimic the drug rapamycin, a well-established macroautophagy activator. In addition we confirmed our MS findings by simultaneously giving 3 treated cells an autophagy inhibitor which blocked 3’s tau reductions. Moreover we created a tetralin derivative of 1, 13, that produced the same effects on tau as 3 but did not rely upon stereochemistry for its activity. This work supports targeting the autophagy degradation pathway as a viable approach to improving aberrant tau accumulation. In order to further support our hypothesis, we collected and screened several known heat shock protein 70 (Hsp70) inhibitors and tau aggregation inhibitors for cellular anti-tau activity. While it is known that Hsp70 inhibition facilitates tau clearance through proteasomal degradation, it is not known what role tau aggregation inhibition plays in the cellular degradation of tau. Moreover understanding which inhibitory activity contributes most to tau degradation would lead to the creation of better drug scaffolds. In this study, we found that several Hsp70 inhibitors from different scaffold backbones had varying effects on tau degradation. The rhodacyanine and phenothiazine compounds were most effective at lowering cellular tau while the adenosine analog, sulfonamide, dihyropyrimidine, piperidine-3-carboxamide, phenoxy-N-arylacetamide, and flavonol, were not as effective. We also examined the effects of several tau aggregation inhibitor scaffolds such as the carbocyanine, oleuropein, anthraquinone, aminothienopyridazine, hydroxytyrosol and rhodanine on tau expression reduction. We found that none had effective tau reductions except the carbocyanine. However when we performed a lactate dehydrogenase (LDH) assay, carbocyanine was shown to be extremely toxic. These results lead us to further investigate if the tau expression reducing Hsp70 inhibitors had anti-tau aggregation activity and if the tau aggregation inhibitors had any Hsp70 inhibitory activity. We discovered that many of the Hsp70 inhibitors also had anti-tau aggregation activity while none of the aggregation inhibitors had Hsp70 inhibitory activity. We found a positive correlation between tau expression reductions and anti-tau aggregation activity for the Hsp70 inhibitors. Our work demonstrates that both Hsp70 activity and tau aggregation in vitro best predicts anti-tau activity of small molecules. Also these dual acting Hsp70 inhibitors support our hypothesis that targeting the degradation pathways can improve tau clearance. Overall, this work indicates the importance of targeting degradation pathways to improve tau clearance. Utilizing small molecules that have dual activities against tau could prove beneficial as a novel therapeutic approach to treat tauopathies. In addition using small molecules that target different degradation pathways simultaneously could be another viable therapeutic strategy for treatment of tauopathies.

Glaucoma is a neurodegenerative protein misfolding disorder classified by increases in IOP, damage to retinal ganglion cells (RGCs), optic nerve (ON) head damage, and progressive irreversible blindness. Primary open-angle glaucoma (POAG) is the most common form of glaucoma, constituting over 90% of clinical cases. POAG is observed in patients where normal outflow channels, mainly the trabecular meshwork (TM), are exposed at the angle formed by the iris and cornea. However, due to TM cellular dysfunction, aqueous outflow resistance is increased preventing normal circulation of aqueous humor. Recent studies have shown that in 2-4% of POAG cases, increased intracellular levels of a secreted glycoprotein, called myocilin, are present in the TM. Myocilin is a 504aa glycoprotein, with an unknown precise function. Recent studies have postulated the importance of myocilin in oligodendrocyte differentiation, axonal myelination, and early apoptosis of retinal cells in development, but exact function is still widely debated. However, it is important to note that pathology associated with myocilin is only seen during POAG. Also, only cells of the TM exhibit toxicity when overexpressing mutant myocilin. In the normal eye, myocilin is secreted from the ER of TM cells, however, mutations in the MYOC gene lead to an aggregation-prone form of the protein, which is inefficiently processed and degraded from the ER, leading to build-up and associated toxicity. There are over 70 known MYOC mutations associated with glaucoma, with over 90% occurring in the C-terminal OLF domain. Some of the more common, pathological mutations are: I477N, Y437H, P370L, W286R, N480K. All of these mutations have been observed in patients with glaucoma, and all lead to build-up and aggregation of the mutant protein within the ER of TM cells. Recently, work out of our lab has discovered an interaction between mutant forms of myocilin and the chaperone Grp94. Grp94 is the resident Hsp90 isoform of the ER. Grp94 is an important chaperone in ER quality control, aiding in the output of properly folded secretory and membrane-bound proteins. Besides protein folding, other roles of Grp94 in the ER include: calcium buffering, roles in ER quality control (including targeting misfolded proteins for ERAD), peptide binding, and roles in ER stress. Generally, terminally misfolded proteins in the ER are degraded through ERAD; the Grp94 mediated shuttling of misfolded proteins to the ER trans-membrane machinery for ubiquitination and subsequent translocation to the cytosol for proteasomal degradation. However, in the case of POAG, ERAD is inefficient in mutant myocilin degradation, causing protein accumulation within the ER. In this study, we demonstrate that specific Grp94 inhibition of interaction with mutant or misfolded myocilin leads to myocilin degradation and subsequent lowering of protein accumulation in the TM, thus reducing downfield pathology associated with POAG. Grp94 preserves mutant myocilin in the ER of TM cells leading to protein accumulation and aggregation precipitating TM cellular dysfunction. We showed in various in vitro cell assays that Grp94 inhibition leads to a reduction in intracellular protein levels, while alleviating TM cellular toxicity. Furthermore, in the Tg-MYOCY437H mouse model of POAG, we showed that topical ocular administration of a specific Grp94 inhibitor alleviated glaucomatous pathologies, including elevated IOP, myocilin accumulation in the TM, reduced scotopic/photopic visual responses, and RGC health and viability. Finally, we have proven the importance of ER-stress pathway malfunction in the development of POAG pathology, while also discovering the involvement of the autophagy mechanism for myocilin degradation following Grp94 inhibition. Overall, this work proves that Grp94 is an important regulator of myocilin pathology during POAG. While there are no current therapeutics on the market that directly target the underlying POAG disease mechanism, specific Grp94 inhibition shows great promise and should be considered for human clinical trials. If successful, specific targeted Grp94 inhibition could be the first curative therapeutic options for patients suffering from myocilin-associated POAG.