Mutations in the gene encoding the cystic fibrosis transmembrane conductance regulator protein (CFTR) cause cystic fibrosis (CF), the most common life-shortening genetic disease among Caucasians. Although general features of the structure of CFTR have been predicted from homology models, the conformational changes that result in channel opening and closing have yet to be resolved. We created new closed- and open-state homology models of CFTR, and performed targeted molecular dynamics simulations of the conformational transitions in a channel opening event. The simulations predict a conformational wave that starts at the nucleotide binding domains and ends with the formation of an open conduction pathway. Experimentally confirmed changes in side-chain interactions are observed in all major domains of the protein. We also identified unique-to-CFTR substitutions that may have led to channel activity in CFTR. Molecular modeling and simulations are used to compare the effects of these substitutions against a canonical ABC transporter, and suggest that gain of channel function in CFTR may have risen from loss of ATPase function at its NBDs. The models and simulation add to our understanding of the mechanism of ATP-dependent gating in this disease-relevant ion channel.

The ATP-binding cassette (ABC) transporter, ABCA1, plays a pivotal role in reverse cholesterol transport, which is the elimination of excess sterols from peripheral cells and their transport to the liver for elimination. Early studies failed to detect significant ATPase activity, prompting the suggestion that ABCA1 was an ATP-regulated receptor, rather than an active transporter. We have provided evidence that ABCA1 can bind ATP and trap its hydrolysis product, ADP, in the presence of either ortho-vanadate or beryllium fluoride and Mg2+ or Mn2+. We have also shown that both nucleotide-binding domains (NBDs) trap nucleotide comparably, suggesting that ABCA1 is a functional ATPase. In addition, we have shown that ABCA1 can directly transport 25-hydroxycholesterol (25-OHC) in an ATP-dependent manner using a membrane vesicle uptake assay, and can do so when the physiological substrate acceptor apoA-I is replaced with BSA as a non-specific binding protein. Although more than 50 naturally occurring missense mutations and polymorphisms in ABCA1 have been identified in individuals with HDL-C levels within the lowest 5th percentile of the general population, the extent to which many of these mutations affect ABCA1 function is not known and cannot be predicted. Naturally occurring extracellular loop (ECL) mutations W590S and C1477R have both been shown to effectively eliminate the ability to mediate lipid efflux, despite the fact that the W590S mutant protein retains the ability to bind apoA-I. We show that neither mutant can transport nor efflux 25-OHC, whether in the presence of apoA-I or BSA, despite apparently full retention of the ability to bind and trap nucleotide. This suggests that these two ECL mutations inhibit transport by a mechanism that is independent of their effect on apoA-I binding. By introduction of naturally occurring mutations in the NBDs, we show that although some mutations associated with Tangier Disease, such as N935S, essentially eliminate nucleotide trapping and substrate translocation, other polymorphisms such as L1026P and T2073A associated with low HDL-C, appear to be fully functional. Lastly, we observed differences in the behaviour of both wild-type and mutant forms of ABCA1-GFP depending on whether they were expressed in insect or mammalian cell lines. / Thesis (Ph.D, Pathology & Molecular Medicine) -- Queen's University, 2010-02-12 11:14:11.381

The aims of this thesis were to study the in vivo relevance of membrane transporters for intestinal absorption and the hepatic disposition of drugs in humans and preclinical models. Fexofenadine is a substrate for ABCB1 (P-glycoprotein) and members of the organic anion transporting polypeptide (OATP/SLCO) family. It is marginally metabolised in humans. The influence of known inhibitors of ABCB1 and OATPs on the membrane transport and pharmacokinetics of fexofenadine was investigated in Caco-2 and porcine models and in humans. The permeability of fexofenadine remained low, even when significantly altered by the addition of an inhibitor. Using the Loc-I-Gut® technique in vivo in humans, it was possible to see that the jejunal effective permeability of fexofenadine was unchanged when given with verapamil. However, the systemic exposure and apparent absorption rate of fexofenadine increased. This suggests that the first-pass liver extraction of fexofenadine was reduced by verapamil, probably through the inhibition of sinusoidal OATP-mediated and/or canalicular ABCB1-mediated secretion. The unchanged permeability can be explained by simultaneous inhibition of jejunal apical OATP-uptake and ABCB1-efflux, which would leave fexofenadine to be transported by passive trancellular diffusion. A Loc-I-Gut® perfusion in the porcine model enabling blood sampling in the portal and hepatic veins and bile collection revealed increased jejunal permeability, but no subsequent verapamil-induced elevation in the systemic exposure of fexofenadine. This indicates a species-related difference in the localisation of and/or the substrate specificity of fexofenadine for the transporters involved. The absence of an effect on the first-pass liver extraction in the porcine model might be caused by the observed lower liver exposure of verapamil. Finally, a novel intubation technique enabling dosing of fexofenadine in the jejunum, ileum and the colon showed that fexofenadine was absorbed less along the length the intestine in agreement with the properties of a low permeability drug.

Thesis (Ph. D.)--University of Washington, 1998. / Vita. Includes bibliographical references (leaves [100]-113).

La résistance des cellules cancéreuses à la chimiothérapie est une cause majeure de l’échec thérapeutique. Des études suggèrent qu’une adaptation du métabolisme énergétique pourrait jouer un rôle dans cette résistance. Ce travail de thèse montre que la résistance des cellules cancéreuses mammaires MCF-7dox à la doxorubicine est associée à une diminution de l’activité du complexe I de la chaîne respiratoire mitochondriale et à un métabolisme des cardiolipines (CL) particulier (diminution de la quantité de CL et augmentation de la quantité de MLCL, la forme immature des CL). Nos résultats montrent aussi que les mitochondries des cellules MCF-7dox expriment deux pompes d’efflux ATP-dépendantes (BCRP et MRP1) qui participent à limiter la quantité de doxorubicine accumulée dans ces mitochondries. De plus, l’activité de ces deux transporteurs dépend partiellement de l’ATP mitochondrial dont l’efficacité de synthèse est améliorée dans les cellules MCF-7dox. D’autre part, nous montrons que l’effet sensibilisant du DHA à la doxorubicine dans les cellules MCF-7dox implique un stress oxydant mitochondrial et s’accompagne d’une diminution de l’efficacité de la synthèse d’ATP. / Resistance of cancer cells to chemotherapy is a major cause of treatment failure. Studies have suggested that an adaptation of energy metabolism may play a role in the development of this resistance. The present work shows that resistance of the breast cancer cell line MCF-7dox to doxorubicin is associated with decreased activity of the mitochondrial respiratory chain complex I and particularly altered cardiolipin (CL) metabolism, (decreased CL levels and increased MLCL levels, the immature form of the CL). Our results also show that mitochondria from MCF-7dox cells express two ATP-dependent efflux pumps (BCRP and MRP1) limiting the accumulation of doxorubicin in these mitochondria. In addition, the activity of these two transporters is partially dependent on mitochondrial ATP synthesis which efficiency is improved in MCF-7dox cells. Moreover, we show that the sensitizing effect of DHA to doxorubicin in MCF-7dox cells is regulated by mitochondrial oxidative stress and is accompanied by a decrease in ATP synthesis efficiency.

Orientador: Andréa Balan Fernandes / Dissertação (mestrado) - Universidade Estadual de Campinas, Instituto de Biologia / Made available in DSpace on 2018-08-17T16:02:06Z (GMT). No. of bitstreams: 1 Pegos_VanessaRodrigues_M.pdf: 19133775 bytes, checksum: abcda42c9097c7e59ea61175934c2304 (MD5) Previous issue date: 2011 / Resumo: A captação de sulfato em Escherichia coli é dependente do transportador do tipo ABC (do inglês, ATP Binding Cassete), SbpCysAWD, pertencente a um regulon que envolve 26 genes. Na ausência de sulfato, a bactéria induz a expressão de dois outros transportadores ABC, o de proteínas do sistema de transporte de alcanosulfonatos (SsuABCDE) e de sulfonatos alifáticos (TauABCDE), que são responsáveis pela captação, incorporação e oxidação destes compostos a sulfito e aldeído. Embora não comprovado funcionalmente, Xanthomonas axonopodis pv. citri apresenta todos os genes envolvidos neste regulon e, neste trabalho, dando continuidade à caracterização do transportador SsuABCDE, foi realizada pela primeira vez, a caracterização estrutural e funcional das enzimas SsuD e SsuE. Análises bioquímicas associadas às análises de bioinformática e modelagem molecular, revelaram que as enzimas SsuD e SsuE constituem um sistema de dois componentes, no qual a SsuD seria a óxido-redutase responsável pela oxidação do NAD(P)H, seguida da redução da FMN. A proteína foi expressa e purificada a partir de células de E. coli com massa molecular de 39 kDa, e se organiza na forma de um octâmero, conforme demonstrado por experimentos de espalhamento de raios X a baixo ângulo e ultra-centrifugação. O modelo da estrutura tridimensional da SsuD revela uma proteína com enovelamento barril-TIM, com conservação de resíduos que permitem a oligomerização e a interação com NAD(P)H, mas não com flavina. Ensaios enzimáticos mostraram que a SsuD liga NADP(Pbp) com alta afinidade (0,21 µM) e é capaz de oxidá-lo conforme os parâmetros cinéticos de Km: 0.1877 µM -1; Kcat: 7,192 s-1; Vmáx: 0.7911 µM/min; Kcat/Km: 3,8 x 107 m-1S-1. Ainda, foram obtidos cristais da SsuD em diferentes condições as quais estão em fase de refinamento. As análises de bioinformática da SsuE sugerem que ela seja a óxido-redutase do sistema. O trabalho ainda mostra a caracterização da proteína Pbp de X. axonopodis, do suposto sistema de transporte de fosfonatos. A Pbp foi expressa com massa molecular de 33 kDa, e as análises espectroscópicas revelaram alterações conformacionais na estrutura secundária na presença de fosfonatos e fosfato, bem como aumentada estabilidade térmica na presença de espermidina, usada nos ensaios de cristalização. Cristais foram obtidos em diferentes condições e devem ser usados para os testes de difração. Os resultados apresentados neste trabalho revelam dados de proteínas e sistemas de X. axonopodis ainda não estudados e serão importantes para direcionar futuros estudos sobre a função destas na bactéria, tanto em condições laboratoriais, como em testes in vivo, durante infecção na planta / Abstract: Sulfur uptake in Escherichia coli is dependent of the ABC transporter SbpCysAWD (ATP Binding Cassete), which belongs to a regulon with 26 genes. In the sulfate absence, the bacteria induces the expression of two other ABC transporters, for alkanesulfonates (SsuABCDE) and aliphatic sulfonates (TauABCDE), which are responsible for the uptake and oxidation of these compounds to sulfite and aldehyde. Although its functionality has been not showed, Xanthomonas axonopodis pv. citri has all the genes involved in this regulon, including the alkanesulfonate transporter and enzymes. In order to continue the characterization of this transport, this work shows for the first time, the structural and functional characterization of the proteins SsuD and SsuE. Biochemical analyses associated to the bioinformatics and molecular modeling tools revealed that the SsuD and SsuE form a two-components system, where SsuD is the oxidoreductase responsible for the NAD(P)H oxidation followed by the FMN reduction. The protein was expressed and purified from E. coli cells with a molecular mass of the 39 kDa and it is organized in a octamer, such was demonstrated by the small angle scattering X-ray and ultracentrifugation assays. The tri-dimensional model of SsuD reveals a TIM barrel folding and conservation of residues that allow the oligomerization and NADP interaction. Enzymatic assays showed a high affinity binding of SsuD and NADP (0,21 µM) and that the protein was able to obtain the cinetic parameters, such as Km: 0.1877µM -1; Kcat: 7,192 s-1; Vmáx: 0.7911 µM/min; Kcat/Km: 3,8x 10-7 m 1S-1. Indeed, SsuD crystals were obtained in different conditions. The work still shows the charactrization of the Pbp protein, from X. axonopodis, believed to be the fosfonate/fosfate binding protein. Pbp was expressed with a molecular mass of 33 kDa, and spectroscopic analyses revealed conformational changes at the secondary structure content in presence of fosfonates, as well as an increased thermal stability in presence of spermidine, which was used for the crystallization trials. Crystals were obtained but still not tested. All results presented in this work can bring some light to the strategies that X. axonopodis uses for growth and infection and they will direct our studies for laboratorial and in vivo analyses / Mestrado / Genetica de Microorganismos / Mestre em Genética e Biologia Molecular

Submitted by Neusa Fagundes (neusa.fagundes@unioeste.br) on 2018-03-05T19:50:05Z No. of bitstreams: 2 Debora_Dudek2017.pdf: 1099947 bytes, checksum: eb7356b2bdfdfe7d3d4da8e48d12d05c (MD5) license_rdf: 0 bytes, checksum: d41d8cd98f00b204e9800998ecf8427e (MD5) / Made available in DSpace on 2018-03-05T19:50:05Z (GMT). No. of bitstreams: 2 Debora_Dudek2017.pdf: 1099947 bytes, checksum: eb7356b2bdfdfe7d3d4da8e48d12d05c (MD5) license_rdf: 0 bytes, checksum: d41d8cd98f00b204e9800998ecf8427e (MD5) Previous issue date: 2017-02-07 / Conselho Nacional de Pesquisa e Desenvolvimento Científico e Tecnológico - CNPq / Second generation bioethanol employs lignocellulosic materials in its preparation. One of the steps for these materials degradation utilizes cellulases produced by microorganisms. Among these, Trichoderma reesei fungus is one of the main cellulases producers used in industry. This fungus genetic modification can lead to enzimes production optimization, reducing cost and improving biofuels manufacture. Thus, the present work objective was delete the sequence encoding zinc fingers motifs of cellulase ACE1repressor transcription factor from T. reesei RUT-C30 fungus, seeking enzymatic production optimization. In primers construction for amplification ACE1 regions 5’ and 3' and the hph selection marker, which confers hygromycin B resistance, Joint Genome Institute - JGI site and the BioEdit ® program were used. The deletion cassette with pRS426 vector construction was mediated by Saccharomyces cerevisiae SC9721 yeast. After the cassette construction, T. reesei RUT-C30 transformation was made by protoplast and this transformation confirmation was effected by part of the hph using hphNestF and hphNestR amplification primers. After transformation with mutants obtained, endoglucanase, exoglucanase and total cellulase activity was quantified with carboxymethylcellulose substrates (CMC), microcrystalline cellulose (Avicel®) and Whatman paper filter (PF), respectively. The enzymatic production and biomass hydrolysis efficiency were performed comparing RUT-C30 strain for mutants. After deletion cassette construction, a 3501 bp fragment amplification confirmed the cassette formation. Posteriorly, RUT-C30 strain transformation, a 989 bp amplification was observed, confirming the 3 mutants target sequence deletion. With cellulase activity assay, 3 transformed strain showed higher enzymatic production when compared to RUT-C30 strain. In this comparison, a significant statistical difference was observed of RUT-C30Δace1-1 strain with Avicel® and PF (p <0.001) CMC (p <0.01), RUT-C30Δace1-2 strain with CMC (p<0,01) e PF (p<0,05), and RUT-C30Δace1-3 strain with Avicel (p<0,001), CMC and PF (p<0,01). The mutants also showed greater efficiency in biomass hydrolysis, with release sugar increase between 21 and 42%. Based on this study, mutants are promising for most efficient and viable ethanol production. Nevertheless, additional tests must be carried out to better understand these fungi applicability in the industrial level. / O bioetanol de segunda geração emprega materiais lignocelulósicos na sua elaboração. Uma das etapas para a degradação destes materiais utiliza celulases produzidas por microrganismos. Dentre estes, o fungo Trichoderma reesei é um dos principais produtores de celulases utilizadas na indústria. A modificação genética deste fungo pode levar à otimização da produção de suas enzimas, diminuindo o custo e melhorando a fabricação de biocombustíveis. Desta forma, o objetivo do trabalho foi deletar a região dos motivos dedos de zinco no gene que codifica o fator de transcrição repressor de celulase ACE1 do fungo T. reesei RUT-C30, buscando a otimização na produção enzimática. Na construção dos primers para amplificação das regiões 5’ e 3’ de ace1 e do marcador de seleção hph, que confere resistência à higromicina B, utilizou-se o site Joint Genome Institute – JGI e o programa BioEdit®. A construção do cassete de deleção com o vetor pRS426 foi mediado pela levedura Saccharomyces cerevisiae SC9721. Posteriormente, a construção do cassete, a transformação de T. reesei RUT-C30 foi realizada através de protoplasto e a confirmação desta transformação foi efetuada por amplificação de parte do hph utilizando os primers hphNestF e hphNestR. Após a transformação, com os mutantes obtidos, a atividade de endoglucanase, exoglucanase e celulase total foi quantificada com os substratos carboximetilcelulose (CMC), celulose microcristalina (Avicel®) e papel de filtro Whatman (PF), respectivamente. A produção enzimática e a eficiência na hidrólise da biomassa foram realizadas comparando-se a linhagem RUT-C30 aos mutantes. Após a construção do cassete de deleção, a amplificação de um fragmento de 3501 pb confirmou a formação do cassete. E, posteriormente à transformação da linhagem RUT-C30, o amplificado de 989 pb foi observado, confirmando a deleção da sequência alvo em 3 mutantes. Com o ensaio de atividade de celulases, as 3 linhagens transformadas mostraram maior produção enzimática quando comparadas à linhagem RUT-C30. Nessa comparação, foi observada diferença estatística significativa da linhagem RUT-C30Δace1-1 com Avicel® e PF (p<0,001), da linhagem RUTC30Δace1- 2 com CMC (p<0,01) e PF (p<0,05) e da linhagem RUT-C30Δace1-3 com Avicel (p<0,001), CMC e PF (p<0,01). Os mutantes também apresentaram maior eficiência na hidrólise da biomassa, com aumento na liberação de açúcar entre 21 e 42%. Com base nos dados deste estudo, os mutantes apresentam-se promissores para a produção mais eficiente e viável de etanol. Apesar disso, testes adicionais devem ser realizados para melhor entendimento da aplicabilidade destes fungos a nível industrial.

No description available.

Indiana University-Purdue University Indianapolis (IUPUI) / Human BCRP is one of the major ATP-binding cassette transporters involved in the development of multidrug resistance in cancer chemotherapy. Overexpression of BCRP in the tumor cell plasma membrane and apical membrane of the gastrointestinal tract leads to decreased intracellular accumulation of various anticancer drugs as well as reduced drug bioavailability. BCRP has been shown to exist on the plasma membrane as higher forms of homo-oligomers. In addition, the oligomerization domain of BCRP has been mapped to the carboxyl-terminal TM5-ECL3-TM6 and this truncated domain, when co-expressed with the full-length BCRP, displays a dominant inhibitory activity on BCRP function. Thus, the oligomerization of BCRP could be a promising target in reversing multidrug resistance mediated by BCRP. To further dissect the oligomerization domains of human BCRP and test the hypothesis that TM5, ECL3, and TM6 each plays a role in BCRP oligomerization and function, we engineered a series of BCRP domain-swapping constructs with alterations at TM5-ECL3-TM6 and further generated HEK293 cells stably expressing wild-type or each domain-swapping construct of BCRP. Using co-immunoprecipitation and chemical cross-linking, we found that TM5, ECL3, and TM6 all appear to partially contribute to BCRP oligomerization, which are responsible for the formation of oligomeric BCRP. However, only TM5 appears to be a major contributor to the transport activity and drug resistance mediated by BCRP, while ECL3 or TM6 is insufficient for BCRP functions. Taken together, these findings suggest that homo-oligomeric human BCRP may be formed by the interactions among TM5, ECL3 and TM6, and TM5 is a crucial domain for BCRP functions and BCRP-mediated drug resistance. These findings may further be used to explore targets for therapeutic development to reverse BCRP-mediated drug resistance and increase the bioavailability of anti-cancer drugs for better treatment of multidrug resistant cancers.

No description available.