京都大学 / 0048 / 新制・課程博士 / 博士(工学) / 甲第21308号 / 工博第4506号 / 新制||工||1701(附属図書館) / 京都大学大学院工学研究科都市環境工学専攻 / (主査)教授 田中 宏明, 教授 清水 芳久, 教授 伊藤 禎彦 / 学位規則第4条第1項該当 / Doctor of Philosophy (Engineering) / Kyoto University / DFAM

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All organisms have cell membranes which are composed of lipids. The length of lipids affects the elastic properties of the cell membrane which play an important role in cell's survival. For instance, membrane flexibility controls the amount of stress that a membrane can sustain before pore formation. In the bacterial cell membranes, the pore formation is also induced by naturally occurring peptides and synthetic amphiphilic copolymers. For this reason, they are one of the most anticipated novel antimicrobial materials. Understanding the mechanism of their action is essential for their use against microbes. Using coarse-grained simulations and a mean field model, we study lipid bilayer membranes under the variation of stress and tail length, as well as their interaction with flexible amphiphilic copolymers. We used a polymer brush model to describe the free energy of the membrane in terms of entropic contributions and hydrophobic interactions. As the stress is increased on the membranes, at high stresses, the membrane transits to a stable pore state in agreement with simulation results. The increased hydrophobic interaction energy at the interface at high stresses leads to the formation of a pore. The hydrophobic interactions induce a contraction stress and the entropy of lipid tails induces a repulsive stress on the membrane. The simulations show that the entropic contribution to the stress, at its positive values, decreases as the length of lipid tails is increased. This increases the tendency of the membrane with the longer lipids to withstand larger stresses before rupturing into pores, as the internal repulsive stress is reduced. We show that copolymers can enhance the pore stability by decreasing the line tension due to the weak adsorption along the rim of the pore. The bilayers studied in our simulations do not require high copolymer concentration at the pores nor any self-organization of the copolymers to open the pore. This is in contrast to the commonly known barrel stave model where the copolymers are assumed to be strongly localised at the rim of the pore. In the presence of the copolymers, we observe a meta-stable pore state of membrane. This happens at a specific concentration of copolymers depending upon the stress acting on the membrane. If the concentration is further increased from this value, then, the membrane shifts to a stable pore state. An increase in the probability of pore formation is observed as the length of copolymers or stress on the membrane are increased. Both the solvent and copolymer permeability increase as the pore becomes stable.

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The nuclear pore complex (NPC) is a proteinaceous gateway embedded in the nuclear envelope (NE) that regulates nucleocytoplasmic transport of molecules in eukaryotes. The NPC is formed by hundreds of proteins that are classified into approximately thirty different types of proteins called nucleoporin (Nup), each presents in multiples of eight copies. These nucleoporins are divided into two categories: the scaffold Nups forming the main structure of the NPC and the phenylalanine-glycine (FG) Nups that contain multiple repeats of intrinsically disordered and hydrophobic FG domains. These FG-Nups constitute the selective permeability barrier in the central channel of the NPC, which mediates the nuclear import of proteins into the nucleus, and the nuclear export of mRNA and pre-ribosomal subunits out of the nucleus. However, the precise copies of these Nups and their specific roles in the nucleocytoplasmic transport mechanism remain largely unknown. Moreover, the dysfunctional nuclear transport and the mutations of Nups have been closely associated with numerous human diseases, such as cancer, tumor and liver cirrhosis. We have developed and employed live-cell high-speed single-molecule microscopy to elucidate these critical questions remained in the nuclear transport and provide the fundamental knowledge for developing therapies. In this dissertation, I will present my major findings for the following three research projects: 1) determine the dynamic components of FG-Nups in native NPCs; 2) track the nucleocytoplasmic transport of transcription factor Smad proteins under ligand-activated conditions; and 3) elucidate the relationship between the nuclear export of mRNA and the presence and absence of specific Nups in live cells.Determination of the dynamic components for FG-Nups in native NPCs. Scaffold Nups have been intensively studied with electron microscopy to reveal their spatial positions and architecture in the past decades. However, the spatial organization of FG-Nups remains obscure due to the challenge of probing these disordered and dynamic polypeptides in live NPCs. By employing high-speed single-molecule microscopy and a live cell HaloTag labeling technique, I have mapped the spatial distribution for all eleven known mammalian FG-Nups within individual NPCs. Results show that all FG-Nups within NPCs are distinct in conformations and organized to form a ~300nm long hourglass shaped toroidal channel through the nuclear envelope. Exceptionally, the two remaining Nups (Nup98 and hCG1) almost extend through the entire NPC and largely overlap with all other FG-Nups in their spatial distributions. These results provide a complete map of FG-Nup organization within the NPC and also offer structural and functional insights into nucleocytoplasmic transport models. Tracking of the nucleocytoplasmic transport of Smad proteins under ligand-activated conditions. The inducement of transforming growth factor β1 (TGF-β1) was reported to cause the nuclear accumulation of Smad2/Smad4 heterocomplexes. However, the relationship between nuclear accumulation and the nucleocytoplasmic transport kinetics of Smad proteins in the presence of TGF-β1 remains obscure. By combining a high-speed single-molecule tracking microscopy technique (FRET), I tracked the entire TGF-β1-induced process of Smad2/Smad4 heterocomplex formation, as well as their transport through nuclear pore complex in live cells. The FRET results have revealed that in TGF-β1-treated cells, Smad2/Smad4 heterocomplexes formed in the cytoplasm, imported through the nuclear pore complexes as entireties, and finally dissociated in the nucleus. Moreover, it was found that basal-state Smad2 or Smad4 cannot accumulate in the nucleus without the presence of TGF-β1, mainly because both of them have an approximately twofold higher nuclear export efficiency compared to their nuclear import. Remarkably and reversely, heterocomplexes of Smad2/Smad4 induced by TGF-β1 can rapidly concentrate in the nucleus because of their almost fourfold higher nuclear import rate in comparison with their nuclear export rate. Thus, these single-molecule tracking data elucidate the basic molecular mechanism to understand nuclear transport and accumulation of Smad protein. Elucidation of the relationship between the nuclear export of mRNA and the presence and absence of specific Nups in live cells. In addition to explore the dynamic organization of NPC, in vivo characterization of the exact copy number and the specific function of each nucleoporin in the nuclear pore complex (NPC) remains desirable and challenging. Using live-cell high-speed super-resolution single-molecule microscopy, we first quantify the native copies of nuclear basket FG-Nups (Nup153, Nup50 and Tpr). Second, with same imaging technique and the auxin-inducible degradation strategies, I track the nuclear export of mRNA through native NPCs in absence of these FG-Nups. I found that these FG-Nups proteins possess the stoichiometric ratio of 1:1:1 and play distinct roles in the nuclear export of mRNAs in live cells. Tpr’s absence in the NPC dominantly reduces nuclear mRNA’s probability of entering the NPC for export. Complete depletion of Nup153 causes mRNA’s successful nuclear export efficiency dropped approximately four folds. Remarkably, the relationship between mRNA’s successful export efficiency and the copy number of Nup153 is not linear but instead follows a sigmoid function, in which mRNA can gain its maximum successful export efficiency as Nup153 increased from zero to around half of their full copies in the NPC. Lastly, the absence of Tpr or Nup153 also alters mRNA’s export routes through the NPC, but the removal of only Nup50 has almost no impact upon mRNA export route and kinetics. / Biology

Dry reforming of methane is an important reaction to generate syngas from two greenhouse gases. The syngas can be used in Fishcher-Tropsch synthesis to produce valueded chemicals. Chapter I reviews the catalytic conversion of methane and carbon dioxide to syngas, including DRM reaction chemistry, catalysts used in this process, catalyst deactivation, and the kinetics of DRM reaction. Chapter II discusses the development of bimodal pore NiCeMgAl catalysts for DRM reaction. Bimodal pore NiCeMgAl catalysts were synthesized via the refluxed co-precipitation method and systematically investigated the influence of active metal loading, calcination temperature, reduction temperature and gas hourly space velocity (GHSV) on the catalytic performance of DRM reaction. The Ni15CeMgAl sample with 15 wt% NiO loading was found to be active enough at 750 °C with a high CH4 conversion of 96.5%. The proper reduction temperature for the NiCeMgAl catalyst is either 550–650 °C or 850 °C. Higher calcination temperature favors the formation of NiAl2O4 and MgAl2O4 spinel structures. Compared with non-bimodal pore NiCeMgAl catalyst, bimodal pore NiCeMgAl catalyst has a longer stability in the feed gas without dilution. In chapter III, the kinetic behavior of bimodal pore NiCeMgAl catalyst for DRM reaction was investigated after the elimination of external and internal diffusion effects in a fixed-bed reactor as a function of temperature and partial pressures of reactants and products. A Langmuir-Hinshelwood model was developed assuming that the carbon deposition is ignorable but the RWGS reaction is non-ignorable and the removal of adsorbed carbon intermediate is the rate-determining step. A nonlinear least-square method was applied to solve the kinetic parameters. The derived kinetic expression fits the experimental data very well with a R2 above 0.97, and predicts the products flow rate satisfactorily. Chapter IV documents the results of in situ XRD study on the NiMgAl catalyst for DRM reaction. The phase evolution of a NiMgAl oxide catalyst at the reduction stage was qualitatively analysed and quantitatively determined by employing the continuous changes in XRD intensity and TPR information. The stable crystallite size of both active metal and spinel support is responsible for the long stability of NiMgAl catalyst without carbon deposition during the DRM reaction.

Alzheimer's Disease (AD) is a devastating neurodegenerative disease that is characterized by brain atrophy, neuronal and synaptic loss, cognitive decline, trouble handling activities of daily life, and ultimately leads to death. Worldwide, at least 30 million people suffer from AD, with 5.8 million suffering in the US alone. Despite extensive basic and clinical research, the underlying molecular mechanisms behind AD remain largely unknown. There are four FDA-approved compounds are used for alleviating symptoms but have no curative potency. The first potentially disease-modifying AD drug, aducanumb, was approved by FDA in June 2021. The main histopathological traits of AD are the Amyloid-beta (Aβ) peptide and the tau protein. Aβ aggregates to form extracellular plaques in brain parenchyma and vasculature while tau forms intraneuronal tangles. Aβ is produced by enzymatic cleavage of the amyloid precursor protein (APP) in the brain. Once APP cleavage occurs, Ab monomers either aggregate extracellularly to form buildups of sticky plaque or embed themselves within the neuronal cell membrane to form pores, causing homeostatic dysregulation and eventually cell death. The mechanism of membrane pores formed by Ab and the pore structure remain to be characterized. This study aims to analyze the structure of four Aβ species in lipid membranes. These are the most abundant form of Aβ, Aβ1-40, and the more cytotoxic form, Aβ1-42, as well as their pyroglutamylated counterparts, pEAβ3-40 and pEAβ3-42, which are hypertoxic. These peptides have been studied using biophysical approaches, i.e., circular dichroism, fluorescence spectroscopy, and Fourier transform infrared spectroscopy. Elucidation of the structure of Aβ membrane pores provides valuable insight into the mechanism of Aβ toxicity and may help develop novel therapies for the lethal mystery that is AD.

Porous materials or a porous media can be encountered in our everyday life, both in industrial and household systems and in the nature. Generally speaking all solid and semisolid materials are porous to some degree e.g. different dense rock types, plastics etc. Porous materials are constantly finding more and more applications, both in industry and research. Many commercially important process in the industry utilize porous media e.g. flow of fluids through porous media for separation process and porous catalyst supports. This has strongly contributed to the development of porous media with controlled properties, which can be utilized for understanding the behavior of liquids confined in the material, and the morphology of these synthetic materials. This thesis work brings some insight and understanding of porous materials i.e. Controlled Pore Glass (CPG). Report also contains a brief explanation of Nuclear Magnetic Resonance (NMR) spectroscopy, diffusion NMR and other techniques such as Mercury porosimetry. The first part of the thesis is focused on determining the required amount of liquid i.e. octanol needed to achieve full pore saturation for different CPGs with varying pore sizes. This was achieved by taking into account that the transverse relaxation time T2 is sensitive in the ms-ns of motional correlation times, and that there are physical factors in porous material which affect the T2. Second part, diffusion NMR is used to study self-diffusion of octanol confined in CPG, thus bringing some insight on mass transfer limitations within porous systems. The report present results obtained from experiments with NMR and Diffusion NMR, discusses the issues that can arise when investigating porous materials and suggest solutions

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