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.

京都大学 / 新制・課程博士 / 博士(理学) / 甲第25136号 / 理博第5043号 / 新制||理||1719(附属図書館) / 京都大学大学院理学研究科化学専攻 / (主査)教授 寺嶋 正秀, 教授 林 重彦, 教授 渡邊 一也 / 学位規則第4条第1項該当 / Doctor of Agricultural Science / Kyoto University / DGAM

The Rem, Rem2, Rad, and Gem/Kir GTPases, comprise a novel subfamily of the small Ras-related GTP-binding proteins known as the RGK GTPases, and have been shown to function as potent negative regulators of high voltage-activated (HVA) Ca2+ channels upon overexpression. HVA Ca2+ channels modulate Ca2+ influx in response to membrane depolarization to regulate a wide variety of cellular functions and they minimally consist of a pore-forming α1 subunit, an intracellular β subunit, and a transmembrane complex α2/δ subunit. While the mechanisms underlying RGK-mediated Ca2+ channel regulation remain poorly defined, it appears that both membrane localization and the binding of accessory Ca2+ channel β subunits (CaVβ) are required for suppression of Ca2+ channel currents. We identified a direct interaction between Rem and the L-type Cavα1 C-terminus (CCT), but not the CCT from CaV3.2 T-type channels. Deletion mapping studies suggest that the conserved CB-IQ domain is required for Rem:CCT association, a region known to contribute to both Ca2+-dependent channel inactivation and facilitation through interactions of Ca2+-bound calmodulin (CaM) with the proximal CCT. Furthermore, both Rem2 and Rad GTPases display similar patterns of CCT binding, suggesting that CCT represents a common binding partner for all RGK proteins. While previous studies have found that association of the Rem C-terminus with the plasma membrane is required for channel inhibition, it is not required for CaVβ- subunit binding. However, Rem:CCT association is well correlated with the plasma membrane localization of Rem and more importantly, Rem-mediated channel inhibition upon overexpression. Moreover, co-expression of the proximal CB-IQ containing region of CCT (residues 1507-1669) in HIT-T15 cells partially relieves Rem blockade of ionic current. Interestingly, Ca2+/CaM disrupts Rem:CCT association in vitro. Moreover, CaM overexpression partially relieves Rem-mediated L-type Ca2+ channel inhibition and Rem overexpression alters the kinetics of calcium-dependent inactivation. Together, these data suggest that the association of Rem with the CCT represents a crucial molecular determinant for Rem-mediated L-type Ca2+ channel regulation and provides new insights into this novel channel regulatory process. These studies also suggest that instead of acting as complete Ca2+ channel blockers, RGK proteins may function as endogenous regulators for the channel inactivation machinery.

The L-type calcium channel (LTCC) provides trigger Ca2+ for sarcoplasmic reticulum Ca2+-release and LTCC function is influenced by interacting proteins including the LTCC Distal Carboxyl-terminus (DCT) and calmodulin. DCT is proteolytically cleaved, and re-associates with the LTCC complex to regulate calcium channel function. DCT reduces LTCC barium current (IBa,L) in reconstituted channel complexes, yet the contribution of DCT to ICa,L in cardiomyocyte systems is unexplored. This study tests the hypothesis that DCT attenuates cardiomyocyte ICa,L. We measured LTCC current and Ca2+ transients with DCT co-expressed in murine cardiomyocytes. We also heterologously co-expressed DCT and CaV1.2 constructs with truncations corresponding to the predicted proteolytic cleavage site, CaV1.2Δ1801, and a shorter deletion corresponding to well-studied construct, CaV1.2Δ1733. DCT inhibited IBa,L in cardiomyocytes, and in HEK 293 cells expressing CaV1.2Δ1801 and CaV1.2Δ1733. Ca2+-CaM relieved DCT block in cardiomyocytes and HEK cells. The selective block of IBa,L combined with Ca2+-CaM effects suggested that DCT-mediated blockade may be relieved under conditions of elevated Ca2+. We therefore tested the hypothesis that DCT block is dynamic, increasing under relatively low Ca2+, and show that DCT reduced diastolic Ca2+ at low stimulation frequencies but spared high frequency Ca2+-entry. DCT reduction of diastolic Ca2+ and relief of block at high pacing frequencies, and under conditions of supraphysiological bath Ca2+ suggests that a physiological function of DCT is to increase the dynamic range of Ca2+ transients in response to elevated pacing frequencies. Our data motivates the new hypothesis that DCT is a native reverse use-dependent inhibitor of LTCC current.

The seaport of Bombay is often referred to as India's "Gothic City." Reminders of British colonial rule are seen throughout South Bombay in its Victorian architecture and sculpture. In the heart of Bombay lies the Victoria Terminus, a towering, hybrid railway station blending gothic and vernacular architectures. Built at the height of the British Empire, the terminus is evidence of the rapid modernization of Bombay through the philanthropy of the Parsis. This religious and ethnic minority became quick allies to the British Raj; their generous donations funded the construction of the "Gothic City." The British viewed the Parsis as their peers, not the colonized. However, Parsi-funded architectural ornament reveals that they saw themselves on equal footing with Bombay's indigenous populations. The Parsis sought to integrate Indian and British art, design, and culture. Through their arts patronage they created an artistic heritage unique to Bombay, as seen in the architectural crown of Bombay, the Victoria Terminus.The Parsi philanthropist, Sir Jamsetjee Jeejeebhoy was the most influential in Bombay's modern art world. He was chosen with other Indian elites to serve on the selection committee for the Great Exhibition of 1851 in London. He selected India's finest works to demonstrate India's rich tradition of the decorative arts. In turn, these works were viewed within the Indian Pavilion by the Victorian public and design reformer Owen Jones. Jones used many of the objects at the India Pavilion in his design book, The Grammar of Ornament. This book went on to inspire the eclectic architectural ornament of Victorian Britain and eventually Bombay. Jeejeebhoy sold the majority of the works from the exhibition to the Victorian and Albert Museum and the Department of Sciences and Art in South Kensington. The objects were studied by design students in South Kensington who were later hired by Jeejeebhoy to be instructors at the Bombay School of Art. This school taught academic European art alongside traditional Indian design forthe purpose of creating public art works. Thus, the Parsis were important cultural mediators who funded British and Indian craftsmen to create symbols of "progress," such as the Victoria Terminus, for a modern India.

Moral realism is the view that there are such things as moral facts. Moral realists have attempted to combat the skeptical problem of relativism, which is that the truth of an ethical value judgment is often, or always, subjective, that is, relative to the parties it involves. This essay presents, discusses, and criticizes Hilary Putnam’s attempt at maintaining moral realism while at the same time maintaining a degree of epistemological relativism. Putnam’s positive account originates in moral epistemology, at the heart of which lies truth, as idealized rational acceptability or truth under ideal conditions. The bridge between moral epistemology and normative ethics stems from Putnam’s disintegration of facts and values. His theory is finalized in the construction of a normative moral theory, in which the central notion is incessant self-criticism in order to maintain rationality. After presenting Putnam’s core thesis, the criticism raised by Richard Rorty, is deliberated upon. Rorty is critical of Putnam’s attempt at holding on to objectivity, because he does not understand how objective knowledge can be both relative to a conceptual scheme, and at the same time objective. The conclusion is that Putnam is unable to maintain his notion of truth as idealized rational acceptability and is forced into epistemological relativism. Putnam’s normative ethics has characteristics in common with virtue ethics, and is of much interest regardless of whether it can be grounded epistemologically or not.

L’objectif de cette thèse était de développer et d’optimiser de nouvelles méthodologies et approches analytiques afin d’améliorer le potentiel de l’analyse protéomique pour les études biologiques.La première partie de ce travail est consacrée à la détermination massive et exacte de la position N-Terminale des protéines (N-Terminome). Pour cela, nous avons utilisé et développé une approche basée sur une dérivation N-Terminale au TMPP. Cette méthodologie de marquage de la position N-Terminale a permis d’aborder l’étude des clivages protéolytiques des protéines exportées par le parasite P. falciparum (pathogène de la malaria) dans le globule rouge.Afin de permettre une exploitation automatique à haut débit des données de MS/MS, nous avons élaboré une nouvelle méthodologie (dénommée dN-TOP). Celle-Ci repose sur l’utilisation de TMPP portant des isotopes stables et permet ainsi d’accéder à la détermination des positions N-Terminales pour des études de N-Terminome à large échelle.La seconde partie est dédiée aux développements de différentes stratégies analytiques de quantification, aussi bien au niveau peptidique qu’au niveau protéique, appliquées à une série de problématiques biologiques. Ces optimisations ont été réalisées dans le contexte de l’étude des complexes protéiques, du dosage de prion par SRM, de quantification des glycations d’anticorps monoclonaux thérapeutiques et de l’hémoglobine HbA2 pour la standardisation des méthodes de référence. / The objective of this Ph.D. thesis was to develop and optimize new methodologies and analytical approaches to improve the potential of the mass spectrometry based proteomics.The first part of this work focused on the development of the N-Termini proteomics. This topic was addressed with a specific N-Termini chemical derivatization based on TMPP. We have shown that our method allowed both specific N-Terminomics and classical proteomics studies in the same experiment.This N-Terminus methodology was applied to study the proteolytic cleavages of the exported proteins in P. falciparum, a parasite responsible for the malaria.In order to automatize the complex and tedious informatics processsing of the MS/SM data of ourTMPP based N-Terminomics method, we have introduced a new approach (named dN-TOP), based on the use of a stable isotope labeled TMPP which made now N-Terminome proteomics compatible with high throughput studies.The second part addresses quantitative aspects of proteomics. It describes the optimization of quantitative methods at the peptide level or at the protein level for five different proteomic studies in the context of protein complex subunits, targeted SRM based prion, quantification of monoclonal antibodies glycation and hemoglobin HbA2 for reference measurement methods standardization.

Argonautes (AGOs) are present in all domains of life. Like their eukaryotic counterparts, archaeal and eubacterial AGOs adopt a similar global architecture and bind small nucleic acids. In many eukaryotes, AGOs, guided by short RNA sequences, defend cells against transposons and viruses. In the eubacterium Thermus thermophilus, the DNA-guided Argonaute TtAgo defends against transformation by DNA plasmids. We find that TtAgo also participates in DNA replication. In vivo, TtAgo binds 15–18 nt DNA guides derived from the chromosomal region where replication terminates, and TtAgo complexed to short DNA guides enhances target finding and prefers to bind targets with full complementarity. Additionally, TtAgo associates with proteins known to act in DNA replication. When gyrase, the sole T. thermophilus type II topoisomerase, is inhibited, TtAgo allows the bacterium to finish replicating its circular genome. In contrast, loss of both gyrase and TtAgo activity slows growth and produces long, segmented filaments in which the individual bacteria are linked by DNA. Furthermore, wild-type T. thermophilus outcompetes an otherwise isogenic strain lacking TtAgo. Finally, at physiologic temperature in vitro, we find TtAgo possesses highest affinity for fully complementary targets. We propose that terminus-derived guides binding in such a fashion localize TtAgo, and that the primary role of TtAgo is to help T. thermophilus disentangle the catenated circular chromosomes generated by DNA replication.

Primary subject of this master`s thesis is to manage increasing traffic volumes between streets Korejská and Zborovská. The most appropriate solution seems to be connecting the Korejská and Hradecká street. Next aim of this work is to design terminus station and transfer terminal for passengers between trolleybus (lines n.34 and n.36) and North-south rail diameter (future express train line connecting north and south suburbs with city centre).

A closer look at innovation for and from emerging markets respectively developing economies reveals that a variety of different terms and concepts related to this type of innovation exist. The goal of my conceptual paper is to present a comprehensive overview of related terms and concepts and to suggest theoretical based classification criteria in order to differentiate them. After a first investigation in relation to innovation for and from emerging markets the keywords ‘reverse’, ‘frugal’, ‘jugaad’, and ‘bottom of the pyramid / bottom of pyramid / bop’ were identified and used for searching the database of Google Scholar. For further investigation only texts were considered with at least eight various terms. 19 different texts were identified which classified for a further analysis. As results 33 identified terms in relation to innovation for and from emerging markets, various spellings and synonyms and references with at least two mentions in the identified texts are presented. As theoretical based classification criteria ‘market orientation’, ‘determinants’ (of innovation for and from emerging market)’, ‘nature’ (of innovation for and from emerging markets), sophistication’, ‘sustainability’, ‘novelty’ and ‘innovator type’ were identified.