Integrity of the human genome is frequently threatened by endogenous and exogenous DNA damaging reagents that may lead to genome instability and cancer. Cells have evolved multiple mechanisms to repair DNA damage or to eliminate the damaged cells beyond repair and to prevent diverse diseases. Among these are ataxia telangiectasia and Rad3-related (ATR)-mediated DNA damage checkpoint and nucleotide excision repair (NER) that are the major pathways by which cells handle ultraviolet C (UV-C)- or other exogenous genotoxin-induced bulky DNA damage. However, it is unclear how these 2 pathways may be coordinated. In this study we show that ATR physically interacts with NER factor xeroderma pigmentosum group A (XPA) where an ATR phosphorylation site on serine 196 is located. Phosphorylation of XPA on serine 196 is required for repair of UV-induced DNA damage. In addition, a K188A point mutation of XPA that disrupts the ATR-XPA interaction inhibits the UV-induced XPA phosphorylation and DNA repair. Moreover, we show that depletion of p53, a downstream checkpoint of ATR, and inhibition of p53 transcriptional activities reduced the UV-induced XPA import. Furthermore, we found that the ATR-directed XPA nuclear import happens primarily in the S phase of the cell cycle. In effort to determine the mechanism involved in the XPA nuclear import, we found that, in addition to the nuclear localization signal (NLS) of XPA, importin-α4 is required for the UV-induced XPA nuclear import in an ATR-dependent manner. These data suggest that NER could be regulated by the ATR-dependent checkpoint via modulation of XPA phosphorylation and nuclear import. In a separate study we show that, upon UV damage, cytoplasmic ATR translocates to mitochondria, blocks the recruitment of proapoptotic Bcl-2–associated X (Bax) protein to mitochondria and prevents the loss of mitochondrial membrane potential (ΔΨ) and apoptosis. Bax-depletion reduces the effect of ATR on ΔΨ. Remarkably, the cytoplasmic ATR exhibits no checkpoint kinase activity, a hallmark function of nuclear ATR. Silencing of ATR’s kinase activity failed to affect Bax relocalization to mitochondria. These results reveal a novel checkpoint-independent antiapoptotic function of ATR at mitochondria in the cellular response to DNA damage.

Apoptosis is essential for development and the maintenance of cellular homeostasis and is frequently dysregulated in disease states. Proteins of the BCL-2 family are key modulators of this process and are thus ideal therapeutic targets. In response to diverse apoptotic stimuli, the pro-apoptotic member of BCL-2 family, BAX, redistributes from the cytosol to the mitochondria or endoplasmic reticulum and primes cells for death. The structural changes that enable this lethal protein to transition from a cytosolic form to a membrane-bound form remain poorly understood. Elucidating this process is a necessary step in the development of BAX as a novel therapeutic target for the treatment of cancer, as well as autoimmune and neurodegenerative disorders. A three-part study, utilizing computational modeling and biological assays, was used to examine how BAX, and similar proteins, transition to membranes. The first part tested the hypothesis that the C-terminal α9 helix regulates the distribution and activity of BAX by functioning as a "molecular switch" to trigger conformational changes that enable the protein to redistribute from the cytosol to mitochondrial membrane. Computational analysis, tested in biological assays, revealed a new finding: that the α9 helix can dock into a hydrophobic groove of BAX in two opposite directions – in a self-associated, forward orientation and a previously, unknown reverse orientation that enables dimerization and apoptosis. Peptides, made to mimic the α9-helix, were able to induce the mitochondrial translocation of BAX, but not when key residues in the hydrophobic groove were mutated. Such findings indicate that the α9 helix of BAX can function as a "molecular switch" to mediate occupancy of the hydrophobic groove and regulate the membrane-binding activity of BAX. This new discovery contributes to the understanding of how BAX functions during apoptosis and can lead to the design of new therapeutic approaches based on manipulating the occupancy of the hydrophobic groove. The second and third parts of the study used computational modeling to examine how the helical stability of proteins relates to their ability to functionally transition. Analysis of BAX, as a prototypical transitioning protein, revealed that it has a broad variation in the distribution of its helical interaction energy. This observation led to the hypothesis tested, that proteins which undergo 3D structural transitions during execution of their function have broad variations in the distribution of their helical interaction energies. The result of this study, after examination of a large group of all-alpha proteins, was the development of a novel, predictive computational method, based on measuring helical interactions energies, which can be used to identify new proteins that undergo structural transitioning in the execution of their function. When this method was used to examine transitioning in other members the BCL-2 family, a strong agreement with the published experimental findings resulted. Further, it was revealed that the binding of a ligand, such as a small peptide, to a protein can have significant stabilizing or destabilizing influences that impact upon the activation and function of the protein. This computational analysis thus contributes to a better understanding of the function and regulation of the BCL-2 family members and also offers the means by which peptide mimics that modulate protein activity can be designed for testing in therapeutic endeavors.

No description available.

<p>Apoptosis plays a key role in the regulation and development of healthy multicellular organisms throughout their lifetimes. The mitochondria play a key role in this cellular process, as it contains proapoptotic factors, which once released into the cytosol of the cell, results in the death of the cell. The Bcl-2 family of proteins play a key role in apoptosis, acting as the gateway between life and death of the cell. Proteins such as tBid and Bax act to permeabilize the mitochondrial outer membrane (MOM), releasing the proapoptotic factors into the cell’s cytosol. The interactions between these proteins and the mitochondrial outer membrane have yet to be fully understood. The lipid composition and cholesterol content of the membrane effectively inhibit or promote pore formation by Bax. Specifically, the addition of cholesterol into the membrane inhibits pore formation. This thesis attempts to further understand the effects cholesterol has on the structure of the MOM, and link those changes to the inhibited activity of Bax pore formation. MOM-like lipid bilayers were studied under varying temperatures and with the addition of cholesterol using x-ray reflectivity. Increasing temperatures from 10°C to 30°C resulted in bilayer thinning, as did decreasing cholesterol concentrations below 30%. From 10°C to 20°C, bilayer thickness showed a bell shaped profile, and changed to a linear decrease above about 20°C. This may assist Bax in pore formation, as it has also been observed to cause bilayer thinning. Increasing Cholesterol concentrations up to 30% resulted in little variation in bilayer thickness though hindrance of Bax pore formation is observed at content levels as low as 8%. Thus it is unlikely that bilayer thickening by cholesterol causes the inhibition of Bax pore formation. In addition, cholesterol was observed to increase the electron density of the core of the bilayer at concentration levels above 25%.</p> / Master of Science (MSc)

<p>Bcl-2 family of proteins regulate apoptosis at the level of the mitochondrial outer membrane (MOM) through both protein-protein and protein-membrane interactions. While the role of the membrane as the “locus of action” has been recognized, the detailed molecular mechanisms and the consequences of the interactions of Bcl-2 family members with the membrane are yet to be fully understood. The findings presented here focus on the dynamic interactions of Bcl-2 proteins, most notably tBid with the MOM, and their functional significance on mitochondrial outer membrane permeabilization. We show that the activation of tBid is a multi-step process that is regulated by MOM lipids and proteins. The rate-limiting step in the activation of tBid is an elaborate conformational change that is facilitated by Mtch2, and is required for the activation and recruitment of Bax to the MOM. Furthermore, we demonstrate that binding of both tBid and Bax to the membrane is reversible and is governed by dynamic equilibria that potentially contribute to the propagation of the permeabilization signal within the cell for the regulation of apoptosis. We report that the transfer of tBid between membranes is accelerated by Bax and restricted by Bcl-XL, whereas the transfer of Bax between membranes is slower than and not influenced by tBid. Finally, by studying the effect of varying lipid composition on Bax-mediated permeabilization, we establish that electrostatic interactions mediate the binding of both tBid and Bim to the membrane. We demonstrate that while Bim does not exhibit any preference for a specific anionic lipid, tBid requires cardiolipin in order to undergo its conformational change at the membrane in the absence of Mtch2. Taken together, our work contributes to the growing understanding of the dynamic interactions and changes in conformation of Bcl-2 proteins at the MOM.</p> / Doctor of Science (PhD)

Mitochondrial outer membrane permeabilization (MOMP) is regulated by protein-protein and protein-membrane interactions between Bcl-2 family proteins. These interactions are governed by the concentrations and relative binding affinities of the proteins for each other. These affinities are altered by conformation changes of Bcl-2 family proteins resulting from interactions with each other and with membranes. How Bcl-2 proteins transition into and out of the conformations that controls their functions, and ultimately the fate of the cell, is not well understood. Here, kinetic analysis of the pore-forming Bcl-2 family member, Bax, revealed that Bax undergoes a conformational rearrangement through at least one structurally distinct intermediate that is a necessary precursor to pore formation. We discover that four cancer-associated Bax point mutants are trapped in the intermediate state, suggesting that transitions into and out of this intermediate can be modulated independently with consequences for the execution of apoptosis. Furthermore we report that the conformation changes Bax undergoes can be regulated by phosphorylation of Bax on residue S184 by the pro-survival kinase, Akt. Phosphorylation converts Bax into an anti-apoptotic protein that functions in a dominant-negative fashion. Bioinformatics revealed that in human cancers, higher levels of Bax are positively associated with high levels of PI3K/AKT pathway genes representing an added mechanism for cancer cells to evade apoptosis. Additionally we studied the interactions between Bax, the anti-apoptotic protein Bcl-XL, the sensitizer BH3 protein Bad and the BH3 activator protein Bid. We uncover a new mechanism of apoptosis regulation whereby Bad binds to one monomer of a Bcl-XL dimer eliciting an activating conformation change in a tBid bound to the other monomer of the Bcl-XL dimer. This allows Bad to function as a non-competitive inhibitor of Bcl-XL, and represents a novel mechanism that significantly enhances the potency of Bad to elicit apoptosis. / Thesis / Doctor of Philosophy (PhD) / Every day the human body creates billions of cells replacing damaged or unwanted cells. The death of these cells is tightly controlled and can result in disease when misregulated. Cancers arise when there is too little cell death and neurodegenerative diseases, such as Alzheimer’s, arise from too much cell death. Much research, including this thesis, is focused on understanding how cells die because once understood, cell death can be manipulated to treat disease. Cell death ironically occurs at the mitochondria, a cellular organ normally responsible for creating the energy required for the cell to live. When cell death is initiated, the mitochondria get holes poked into them, releasing pro-death factors that irreversibly commit the cell to dying. The work presented here uncovers new information about the regulation of the hole poking process, how it is blocked in breast cancer and how the process may be modulated to treat cancers.

<p> Bax is a pro-apoptotic protein believed to permeabilize mitochondria during apoptosis. The mechanism Bax uses is not well understood. In this work, we use fluorescence techniques to shed light on how tBid activates Bax and we examine the topology of the pore-forming domain of Bax. </p> <p> The manner in which tBid promotes apoptosis via Bax activation is not known. Study of tBid and Bax interaction using a new FRET pair showed that the proteins only interacted in the presence ofmembranes. The Bax pore was shown to have a variable size distribution. A fluorescence technique of simultaneously measuring pore formation, Bax insertion and FRET showed that tBid interaction with Bax occurred before all the Bax inserted or formed pores in the liposomes. A chronological order is proposed for Bax pore formation. tBid first binds to liposomes. tBid proceeds to interact with Bax, and Bax inserts into the membrane. After insertion, Bax oligomerizes and forms small pores. More Bax is recruited and the pores become larger. </p> <p> The two central hairpin helices of Bax, helices 5 and 6, are known as the pore-forming domain. We used cysteine scanning with the environment sensitive fluoroprobe NBD to gain insight into the topology of these helices. Fluorescence intensity changes and emission blue shifts showed that residues in these helices undergo conformational reorganization during pore formation. In the activated oligomeric conformation, fluorescence lifetimes showed that helix 5 was more inaccessible to water than helix 6. Cobalt, a cationic NBD quencher, effectively quenched residues in the pore-forming domain, consistent with a pore that is lined with anionic lipid head groups. Quenching with nitroxide groups at various lipid depths showed that residues on helix 6 were most quenched by a shallow quencher, while residues on helix 5 were quenched by deeper quenchers. Compared to beta sheet pore-forming proteins, the data obtained suggests that Bax and possibly other alpha helical pore-forming proteins form a lipidic pore in a dynamic environment. Combined together, the data suggest a model for Bax in which helix 5 spans the bilayer, and helix 6 is buried just below the lipid headgroups of a toroidal pore. </p> / Thesis / Master of Science (MSc)

No description available.

O transplante autólogo de tecido ovariano constitui alternativa relevante na preservação da fertilidade e da função hormonal ovariana em mulheres sujeitas à falência ovariana prematura e infertilidade, por causas malignas, tratamentos adjuvantes ou cirurgias. É a única opção para crianças, fase pré-puberal e para mulheres que não podem retardar a quimioterapia ou não podem ser submetidas à estimulação do ciclo. O transplante ovariano autólogo pode ser, quanto ao local de reimplantação, ortotópico ou heterotópico e, quanto à conservação, a fresco ou após o período de criopreservação. As várias etapas envolvidas neste transplante são estudadas mundialmente na atualidade, como a retirada e preservação do tecido ovariano, as técnicas de criopreservação, o local apropriado para o reimplante e as possibilidades de redução da perda folicular. A avaliação da apoptose - morte celular programada - é útil na avaliação da rejeição e viabilidade dos enxertos de transplantes estabelecidos na prática clínica, tanto autólogos como heterólogos. Com o intuito de utilizar animais de maior porte, conseguir seguimento de médio prazo e realizar os procedimentos cirúrgicos por via laparoscópica, padrão ouro em humanos, o presente estudo utilizou como modelo experimental fêmeas suínas, em idade reprodutiva, da raça Minipig. Este projeto teve como propósito avaliar a influência da criopreservação e do local de implante na qualidade e na viabilidade do transplante autólogo de ovário, a fresco e após criopreservação, no tecido celular subcutâneo e na região intraperitoneal peri-infundibular. Foram avaliados a quantidade e a densidade folicular dos implantes e os aspectos morfológicos e histomorfométricos, bem como a apoptose, por meio da imunoexpressão de proteínas proapoptóticas- Bax e antiapoptóticas-Bcl-2, além da Caspase 3-clivada, fase final das vias extrínseca e intrínseca dos mecanismos de apoptose.Quarenta animais foram divididos em cinco grupos: Controle com ooforectomia (Grupo I), ooforectomia e transplante a fresco subcutâneo (Grupo II), a ooforectomia e transplante fresco intraperitoneal (Grupo III), ooforectomia e transplante criopreservado subcutâneo (Grupo IV) e ooforectomia e transplante criopreservado intraperitoneal (GrupoV). Os resultados mostraram que independente da técnica empregada, havia folículos em desenvolvimento e corpos lúteos em todos os tecidos ovarianos transplantados; que a contagem de folículos antrais não degenerados foi menor nos grupos após criopreservação em relação ao grupo controle e que a imunoexpressão sugestiva de apoptose ocorreu em todos os grupos transplantados, sendo maior nos transplantes intraperitoneais. Concluiu-se que a técnica utilizada para o transplante de ovário e criopreservação foi viável no modelo suíno, em tecido celular subcutâneo e na região intraperitoneal peri-infundibular. O transplante autólogo heterotópico subcutâneo apresentou melhores taxas de apoptose que o transplante ortotópico. / Autotransplantation of ovarian tissue is an important alternative to preserve fertility and hormonal ovarian function in women undergoing ovarian failure and premature infertilidade, because of cancer or surgery. It is the only option for infants, pre-pubertal patients and for women who can not delay chemotherapy or not may be subjected to stimulation of the cycle. The various steps involved in the transplant are studied worldwide today, as the removal and preservation of ovarian tissue, the techniques of cryopreservation, the appropriate site and mechanisms to reduce follicular loss. Assessment of apoptosis - programmed cell death-is useful in the study of the viability of the grafts and rejection of transplants established in clinical practice, both autologous and heterologous. In order to use larger animals, getting following medium term (over 21 days) and to perform surgical procedures by laparoscopy (gold standard in humans), this study used an experimental model sows, reproductive age, Minipig race. This project aims to evaluate the influence of cryopreservation and implantation site of the quality and viability of ovarian autografts, fresh and after cryopreservation, at subcutaneous site and at intraperitoneal site. We analyzed the quantity and density of follicular implants and the morphological and histomorphometric as well as apoptosis, by proteins immunoexpression antiapoptotic and proapoptotic. Forty animals were divided into five groups: Control with oophorectomy (Group I), oophorectomy and fresh transplantation to subcutaneous site (Group II), oophorectomy and fresh transplantation to intraperitoneal site (Group III), oophorectomy and transplantation of cryopreserved ovarian tissue to subcutaneous site (Group IV) and oophorectomy and transplantation of cryopreserved ovarian tissue to intraperitoneal site (Group V). We concluded that the autologous ovarian transplantation was feasible in the technical proposals, in subcutaneous and intraperitoneal site in the porcine model; that regardless of the technique, there was developing follicles and corpora lutea in all ovarian tissue transplanted; that antral non-degenerate follicle count was lower in groups after cryopreservation that in the control group and that the immunoexpression of apotposis occurred in all transplanted groups, more evident in intraperitoneal transplants

O transplante autólogo de tecido ovariano constitui alternativa relevante na preservação da fertilidade e da função hormonal ovariana em mulheres sujeitas à falência ovariana prematura e infertilidade, por causas malignas, tratamentos adjuvantes ou cirurgias. É a única opção para crianças, fase pré-puberal e para mulheres que não podem retardar a quimioterapia ou não podem ser submetidas à estimulação do ciclo. O transplante ovariano autólogo pode ser, quanto ao local de reimplantação, ortotópico ou heterotópico e, quanto à conservação, a fresco ou após o período de criopreservação. As várias etapas envolvidas neste transplante são estudadas mundialmente na atualidade, como a retirada e preservação do tecido ovariano, as técnicas de criopreservação, o local apropriado para o reimplante e as possibilidades de redução da perda folicular. A avaliação da apoptose - morte celular programada - é útil na avaliação da rejeição e viabilidade dos enxertos de transplantes estabelecidos na prática clínica, tanto autólogos como heterólogos. Com o intuito de utilizar animais de maior porte, conseguir seguimento de médio prazo e realizar os procedimentos cirúrgicos por via laparoscópica, padrão ouro em humanos, o presente estudo utilizou como modelo experimental fêmeas suínas, em idade reprodutiva, da raça Minipig. Este projeto teve como propósito avaliar a influência da criopreservação e do local de implante na qualidade e na viabilidade do transplante autólogo de ovário, a fresco e após criopreservação, no tecido celular subcutâneo e na região intraperitoneal peri-infundibular. Foram avaliados a quantidade e a densidade folicular dos implantes e os aspectos morfológicos e histomorfométricos, bem como a apoptose, por meio da imunoexpressão de proteínas proapoptóticas- Bax e antiapoptóticas-Bcl-2, além da Caspase 3-clivada, fase final das vias extrínseca e intrínseca dos mecanismos de apoptose.Quarenta animais foram divididos em cinco grupos: Controle com ooforectomia (Grupo I), ooforectomia e transplante a fresco subcutâneo (Grupo II), a ooforectomia e transplante fresco intraperitoneal (Grupo III), ooforectomia e transplante criopreservado subcutâneo (Grupo IV) e ooforectomia e transplante criopreservado intraperitoneal (GrupoV). Os resultados mostraram que independente da técnica empregada, havia folículos em desenvolvimento e corpos lúteos em todos os tecidos ovarianos transplantados; que a contagem de folículos antrais não degenerados foi menor nos grupos após criopreservação em relação ao grupo controle e que a imunoexpressão sugestiva de apoptose ocorreu em todos os grupos transplantados, sendo maior nos transplantes intraperitoneais. Concluiu-se que a técnica utilizada para o transplante de ovário e criopreservação foi viável no modelo suíno, em tecido celular subcutâneo e na região intraperitoneal peri-infundibular. O transplante autólogo heterotópico subcutâneo apresentou melhores taxas de apoptose que o transplante ortotópico. / Autotransplantation of ovarian tissue is an important alternative to preserve fertility and hormonal ovarian function in women undergoing ovarian failure and premature infertilidade, because of cancer or surgery. It is the only option for infants, pre-pubertal patients and for women who can not delay chemotherapy or not may be subjected to stimulation of the cycle. The various steps involved in the transplant are studied worldwide today, as the removal and preservation of ovarian tissue, the techniques of cryopreservation, the appropriate site and mechanisms to reduce follicular loss. Assessment of apoptosis - programmed cell death-is useful in the study of the viability of the grafts and rejection of transplants established in clinical practice, both autologous and heterologous. In order to use larger animals, getting following medium term (over 21 days) and to perform surgical procedures by laparoscopy (gold standard in humans), this study used an experimental model sows, reproductive age, Minipig race. This project aims to evaluate the influence of cryopreservation and implantation site of the quality and viability of ovarian autografts, fresh and after cryopreservation, at subcutaneous site and at intraperitoneal site. We analyzed the quantity and density of follicular implants and the morphological and histomorphometric as well as apoptosis, by proteins immunoexpression antiapoptotic and proapoptotic. Forty animals were divided into five groups: Control with oophorectomy (Group I), oophorectomy and fresh transplantation to subcutaneous site (Group II), oophorectomy and fresh transplantation to intraperitoneal site (Group III), oophorectomy and transplantation of cryopreserved ovarian tissue to subcutaneous site (Group IV) and oophorectomy and transplantation of cryopreserved ovarian tissue to intraperitoneal site (Group V). We concluded that the autologous ovarian transplantation was feasible in the technical proposals, in subcutaneous and intraperitoneal site in the porcine model; that regardless of the technique, there was developing follicles and corpora lutea in all ovarian tissue transplanted; that antral non-degenerate follicle count was lower in groups after cryopreservation that in the control group and that the immunoexpression of apotposis occurred in all transplanted groups, more evident in intraperitoneal transplants