L’appréhension des mécanismes d’action biologiques des protéines membranaires nécessite de comprendre les interactions des xénobiotiques avec ces protéines et avec les membranes lipidiques. Les méthodes expérimentales sont parfois coûteuses et ne permettent d’obtenir que des informations partielles sur les interactions xénobiotiques-membrane-protéine. La modélisation moléculaire est une sérieuse alternative. Les simulations de dynamique moléculaire et de dynamique biaisées ont ouvert de nombreuses perspectives en permettant de décrire ces interactions moléculaires à l’échelle atomique. Grâce à des simulations de dynamique moléculaire, nous avons été capables de construire un modèle de transporteur humain ABC : ABCC4/MRP4. Cette protéine a été choisie pour sa présence dans le rein, notamment, et son importance clinique. Nous avons évalué l’influence du cholestérol sur cette protéine. L’étude de domaines spécifiques et l’impact d’un polymorphisme a été reliée à l’activité de transport de cette protéine. Nous avons également étudié l’interaction de xénobiotiques avec ce transporteur humain. Le cycle de transport des transporteurs ABC a été examiné afin de comprendre leur fonctionnement. L’incorporation de cholestérol a montré un impact significatif sur la protéine humaine ABCC4/MRP4 et sur les xénobiotiques étudiés. L’importance de domaines constituant la protéine ABCC4/MRP4 ainsi que l’importance de résidus individuels a clairement été prouvée. Nous avons également pu observer des intermédiaires du cycle de transport d’un transporteur ABC conjointement avec des changements structuraux. / Understanding the biological mechanisms of action of membrane proteins requires the comprehension of the interactions of xenobiotics with these proteins and with lipid membranes. Experimental methods are often demanding and only partially respond to xenobiotic-membrane-protein interactions. In silico molecular modeling is a serious alternative to tackle these issues. Molecular dynamics (MD) and biased dynamics simulations have opened many perspectives by providing an atomistic description of these intermolecular interactions. Using MD simulations, we built a model of the human ABC ABCC4/MRP4 transporter. We explored the influence of cholesterol on this protein as well as the impact of a polymorphism known to shut down the transport activity of this protein. We also studied the interaction of xenobiotics with this human transporter. The transport cycle of the ABC transporters was investigated in an attempt to better understand how it works.Interactions between lipid membranes and xenobiotics were explored by examining their ability to incorporate lipid membranes. Lipid mixtures with cholesterol showed a significant impact on the human protein ABCC4/MRP4 and on the xenobiotics studied. The importance of regions, domains constituting the ABCC4/MRP4 protein as well as the importance of specific residues has been clearly demonstrated. We also observed intermediates in the transport cycle of an ABC transporter in conjunction with structural changes occurring during this cycle.

Intracellular transport of membrane-bound vesicles and organelles is a process fundamental for many cellular functions including cell morphogenesis and signaling. The transport is mediated by ensembles of motor proteins, such as kinesins, walking on microtubule tracks. When transporting membrane-bound cargo inside a cell, the motors are linked to diffusive lipid bilayers either directly or via adaptor molecules. The fluidity of the lipid bilayers induces loose inter-motor coupling which is likely to impact the collective motor dynamics and may induce cooperativity. Here, we investigate the influence of loose coupling of kinesin motors on its transport characteristics. In the first part of this thesis, we used truncated kinesin-1 motors with a streptavidin-binding-peptide (SBP) tag and performed gliding motility assays on streptavidin-loaded biotinylated supported lipid bilayers (SLBs), so called ‘membrane-anchored’ gliding motility assays. We show that the membrane-anchored motors act cooperatively; the microtubule gliding velocity increases with increasing motor density. This is in contrast to the transport behavior of multiple motors rigidly bound to a substrate. There, the motility is either insensitive to the motor density or shows negative interference at higher motor density, depending on the structure of the motors. The cooperativity in transport driven by membrane-anchored motors can be explained as following: while stepping on a microtubule, membrane-anchored motors slip backwards in the viscous membrane, thus propelling the microtubule in the solution at a velocity, given by the difference of the motor stepping velocity and the slipping velocity. The motor stepping on the microtubule occurs at maximal stepping velocity because the load on the membrane-anchored motors is minute. Thus, the slipping velocity of membrane-anchored motors determines the microtubule gliding velocity. At steady state, the drag force on the microtubule in the solution is equal to the collective drag force on the membrane-anchored motors slipping in the viscous membrane. As a consequence, at low motor density, membrane-anchored motors slip back faster to balance the drag force of the microtubule in the solution. This results in a microtubule gliding velocity significantly lower than the maximal stepping velocity of the individual motors. In contrast, at high motor density, the microtubules are propelled faster with velocities equal to the maximal stepping velocity of individual motors. Because, in this case, the collective drag force on the motors even at very low slipping velocity, is large enough to balance the microtubule drag in the solution. The theoretical model developed based on this explanation is in good agreement with the experimental data of gliding velocities at different motor densities. The model gives information about the distance that the diffusing motors can isotropically reach to bind to a microtubule, which for membrane-anchored kinesin-1 is ~0.3 µm, an order of magnitude higher as compared to rigidly bound motors, owing to the lateral mobility of motors on the membrane. In addition, the model can be used to predict the number of motors involved in transport of a microtubule based on its gliding velocity. In the second part of the thesis, we investigated the effect of loose inter-motor coupling on the transport behavior of KIF16B, a recently discovered kinesin motor with an inherent lipid-binding domain. Recent studies based on cell biological and cell extract experiments, have postulated that cargo binding of KIF16B is required to activate and dimerize the motor, making it a superprocessive motor. Here, we demonstrate that recombinant full-length KIF16B is a dimer even in the absence of cargo or additional proteins. The KIF16B dimers are active and processive, which demonstrates that the motors are not auto-inhibited in our experiments. Thus, in cells and cell extracts Kif16B may be inhibited by additional factors, which are removed upon cargo binding. Single molecule analysis of KIF16B-GFP reveals that the motors are not superprocessive but exhibit a processivity similar to kinesin-1 indicating that additional factors are most likely necessary to achieve superprocessivity. Transport on membrane-anchored KIF16B motors exhibited a similar cooperative behavior as membrane-anchored kinesin-1 where the microtubule gliding velocity increased with increasing motor density. Taken together, our results demonstrate that the loose coupling of motors via lipid bilayers provides flexibility to cytoskeletal transport systems and induces cooperativity in multi-motor transport. Moreover, our ‘membrane-anchored’ gliding motility assays can be used to study the effects of lipid diffusivity (e.g. the presence of lipid micro-domains and rafts), lipid composition, and adaptor proteins on the collective dynamics of different motors.:Abstract vii 1 Introduction 1 1.1 Intracellular transport driven by motor proteins 2 1.2 Attachment of motor proteins to cargo 13 1.3 In vitro approaches to study transport by motor proteins 16 1.4 Aim of this study 23 2 Transport by kinesin-1 anchored to supported lipid bilayers 24 2.1 Formation and characterization of biotinylated SLBs 26 2.2 Anchoring kinesin-1 to biotinylated SLBs 28 2.3 Gliding motility of microtubules by kinesin-1 linked to SLBs 34 2.4 Theoretical description of gliding motility on diffusing motor proteins 40 2.5 Comparison of the gliding velocity between experiment and theory 46 2.6 Gliding motility on phase-separated SLBs 53 2.7 Discussion 55 3 Transport by KIF16B with an inherent lipid-binding domain 62 3.2 Biophysical characterization of KIF16B 70 3.3 Gliding motility of microtubules by KIF16B linked to SLBs 78 3.4 Transport of SUVs and lipid-coated beads attached to KIF16B 87 3.5 Discussion 90 4 Conclusion and outlook 96 5 Materials and methods 99 5.1 Reagents and solutions 99 5.2 Molecular biology 100 5.3 Protein expression and purification 104 5.4 In vitro motility assays 110 5.5 Image acquisition and data analysis 118 References 126 List of figures 141 List of tables 143 Abbreviations and symbols 144 Acknowledgements 147

<p>The role of mechanical forces in the fate and function of adherent cells has been revealed to be a pivotal factor in understanding cell biology. Cells require certain physical cues to be present in their microenvironment or the cell will begin apoptosis. Mechanical signals from the environment are interpreted at the cellular level and biochemical responses are made due to the information from outside the cell, this process is known as mechanotransduction. Misinterpretation of physical cues has been indicated in many disease states, including heart disease and asthma. When a cell is bound to the ECM, proteins such as integrins are engaged at static and stable adhesion sites. These tight and static anchoring points found at the ECM exist in stark contrast to the dynamic conditions seen at intercellular junctions. Intercellular junctions, such as gap and adherens junctions, are formed between cells to act as a mechanism to relay information and exchange material. Due to the important role intercellular junctions play in processes of wound healing, epithelial-mesenchymal transition and cancer metastasis developing more sophisticated levels of understanding of these mechanisms would provide valuable insight.</p> <p>Complex biological processes, including immune cell signaling and cellular ECM adhesions, have been effectively replicated in model systems. These model systems have included the use of solid supported lipid bilayers and polymeric hydrogels that display cell adhesion molecules. Studies of cellular mechanotransduction at ECM adhesion sites has also been completed with covalently functionalized polymeric substrates of adjustable elasticity. However, developing model systems that allow the accurate reproduction of properties seen at intercellular junctions, while also allowing the investigation of cellular mechanosensitivity has proven to be a difficult task. Previous work has shown that polymer-tethered lipid bilayers (PTLBs) are a viable material to allow the replication of the dynamics and adhesion seen at intercellular junctions. Although efforts have been made to produce PTLBs with different mechanical properties, there is currently not a material with sufficient tunable elastic properties for the study of cellular mechanotransduction.</p> <p>To establish a system that allows the study of stiffness effects across a biologically relevant range (~0.50 – 40 kPa) while maintaining the dynamic properties seen at cell-to-cell junctions, polymer gel-tethered bilayers (PGTBs) were developed. A fabrication strategy was established to allow the incorporation of a hydrogel support with easily tunable stiffness and a tethered lipid bilayer coating, which produced a powerful platform to study the effects of stiffness at intercellular junctions. Careful attention was given to maintain the beneficial properties of membrane diffusion, and it was shown that on different linking architectures lipid bilayers could be established and diffusion was preserved. Microscopy-based FCS and FRAP methodology were utilized to measure lipid diffusion in these systems, while confocal microscopy was used to analyze cell spreading and adhesion. Three distinct architectures to link the lipid membrane to the underlying polyacrylamide hydrogel were pursued in this work, a non-covalent biotin-streptavidin system, a covalently linked design with fibronectin, and a direct covalent linkage utilizing crosslinker chemistry. In this work, it was shown that cells were able to spread and adhere on these substrates, with cell adhesion zones visualized under plated cells that demonstrate the capability of the cell to rearrange the presented linkers, while maintaining a stable material. Also confirmed is the tunability of the polymer hydrogel across a wide range of stiffness, this was shown by quantitative changes in cell spreading area in response to polymer properties.</p>

京都大学 / 新制・課程博士 / 博士(理学) / 甲第23405号 / 理博第4740号 / 新制||理||1679(附属図書館) / 京都大学大学院理学研究科生物科学専攻 / (主査)教授 高田 彰二, 教授 川口 真也, 准教授 立川 正志 / 学位規則第4条第1項該当 / Doctor of Science / Kyoto University / DFAM

京都大学 / 0048 / 新制・課程博士 / 博士(農学) / 甲第21379号 / 農博第2303号 / 新制||農||1071(附属図書館) / 学位論文||H30||N5152(農学部図書室) / 京都大学大学院農学研究科応用生命科学専攻 / (主査)教授 栗原 達夫, 教授 植田 充美, 教授 小川 順 / 学位規則第4条第1項該当 / Doctor of Agricultural Science / Kyoto University / DGAM

No description available.

The rapid development of micro/nanofabrication techniques have enabled engineering of material interfacial properties. Micro/nanostructures with unique electrical, mechanical, thermal, magnetic, optical, and biological properties, have found applications in a wide range of fields such as electronics, photonics, biological/chemical sensing, tissue engineering, and diagnostics, etc. As such, numerous strategies have been developed for structuring materials into micro/nano- scale. However, the challenge still lies in the high cost, low throughput, complexity in fabrication, and difficulty in scaling up. This thesis aims to explore fabrication strategies for micro/nanostructured surfaces that are versatile, simple, and inexpensive. The thin film stencil lift-off technique with both Parylene and self-adhesive vinyl has been explored for this purpose. Further applications of the resulted micro/nanostructured surfaces are also presented in this thesis. Through improved Parylene stencil fabrication process, both spontaneously phase-segregated and arbitrary binary supported lipid bilayer patterns have been achieved. Also, the microstructured Parylene surfaces have been ddemonstrated for patterning stacked SLBs that are either homogeneous or phase-segregated. Without any lithography technique involved, vinyl stencil lift-off offers as a facile and inexpensive benchtop method for patterning thin films such as metal and glassy films. Combining the thermal shrinking of shape memory polymer, the patterned feature sizes are further decreased by 60% in both x and y dimensions, pushing the patterning resolution to down to sub-100 μm range. In addition, the shrinking process induces micro/nanostructures onto the deposited thin film, and the structure sizes are easily tunable with film thickness deposited. Further applications of such patterned micro/nanostructured surfaces has also been explored. The structured gold films have served as high-surface-area electrodes for electrochemical sensing. By introducing photoresist as a sacrificial layer, the structured gold thin films can be lifted off and transferred onto elastomeric substrate, and serve stretchable and flexible sensors. Such sensing devices exhibit great stability and reproducibility even when working under external strain. Finally, the micro/nanostructured glassy surfaces have been employed as substrate for cell growth to study topographical effect on cell morphology. It has been concluded that rougher surfaces lead to cell elongation, and finer structures promote filopodia generation. These results underscore the strength and suitability of thin film stencil lift-off as a powerful technique for creating micro- and nanostructured surfaces. These structured surfaces could find applications in many other areas, due to their great properties such as tunable structure size, high surface area, flexibility, and long-term stability. / Thesis / Doctor of Philosophy (PhD)

Life is soft. From the fluid-like structure of lipid bilayers to the flexible folding of proteins, the realm of nanoscale soft matter is a complex and vibrant area of research. The lure of personalized medicine, advanced sensing technology, and understanding life at a fundamental level pushes research forward. This work considers to areas: (1) lipid bilayer dynamics in the presence of substrate defects and (2) the inverse temperature transition of elastic proteins. Molecular dynamics simulations as well as umbrella sampling were employed. The behavior of the bilayers discussed in the work provides evidence that small defects on confining surfaces can promote nucleation of lipid tethers. Results the second part of this work indicate elastin-like peptides experiencing inverse temperature transitions may be capable of performing amounts of work similar to RNA polymerase; additionally, resilin's inverse temperature transition may be closely linked to the molecule's ability to efficiently transmit energy through the similar coil-β secondary structure transition seen in both cases. These insights into the inverse transition temperature are relevant for the design of bio-inspired sensors and energy storage devices. / Master of Science

No description available.

<p>Biological membranes play host to a number of processes essential for cellular function and are the most important biological interface. The structurally complex and highly dynamic nature of the membrane poses significant measurement challenges, requiring an experimental technique capable of accessing very short, nanometer length scales, and fast, micro-pico second time scales.</p> <p>The experimental work presented in this thesis uses a variety of neutron scattering techniques to study the structure and dynamics of biologically relevant model membrane systems. The main body of this work can be sub-divided into two distinct topics: (1) lateral diffusion of lipid molecules in a bilayer; and (2) the measurement of domains in the membrane.</p> <p>Diffusion is the fundamental mechanism for lipids and proteins to move throughout the lipid matrix of a biological membrane. Despite a strong effort to model lipid diffusion, there is still no coherent model which describes the motion of lipid molecules from less than a lipid-lipid distance to macroscopic length scales. The experiments presented on this topic attempt to extend the range over which diffusion is typically measured by neutron scattering, to initiate the development of a more complete lipid diffusion model.</p> <p>Lipid domains and rafts are thought be platforms for many cellular functions; however, their small size and transient nature makes them notoriously difficult to observe. The penultimate chapter of this thesis provides evidence supporting the existence of domains in a model lipid/cholesterol system by probing of the dynamics of the system. The challenge of observing these structures directly was addressed by modifying the traditional neutron triple-axis spectrometry setup to increase its sensitivity to systems with short-range order. This technique was employed to examine the coexistence of fluid and gel domains in a single-component lipid bilayer system, as well as the presence of highly ordered lipid domains in a model membrane containing cholesterol.</p> / Doctor of Philosophy (PhD)