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Molecules in Cell Membranes
Timr, Štěpán ; Jungwirth, Pavel (advisor) ; Böckman, Rainer (referee) ; Ettrich, Rüdiger (referee)
Biological membranes are actively involved in a multitude of processes in living cells; therefore, a detailed characterization of their structure, dynamics, and function is essential for an understanding of living organisms at the molecular level. In this work, we made use of the high spatial and temporal resolution offered by computer simulations to investigate the behavior of several molecular species which associate with cellular membranes. Using a combination of classical molecular dynamics simulations and ab initio electronic structure calculations, we were able to characterize nonlinear optical properties of membrane- embedded fluorescent probes and thus contribute to establishing two-photon polarization microscopy as a tool of structural biology. Moreover, our molecular dynamics simulations provided an atomistic picture of the reversible membrane binding of recoverin, a neuronal calcium-sensing protein involved in vision adaptation, and they also yielded an important insight into the mechanism of its calcium-induced myristoyl switch. In addition, we examined the biological role of cholesterol oxidation and compared two methods of representing transmembrane voltage in molecular dynamics simulations.
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Simulation of processes in cellular membranes
Melcr, Josef ; Jungwirth, Pavel (advisor)
Simulation of processes in cellular membranes Abstract Many important processes in cells involve ions, e.g., fusion of synaptic vesi- cles with neuronal cell membranes is controlled by a divalent cation Ca2+ ; and the exchange of Na+ and K+ drives the the fast electrical signal transmis- sion in neurons. We have investigated model phospholipid membranes and their interactions with these biologically relevant ions. Using state-of-the-art molecular dynamics simulations, we accurately quantified their respective affinites towards neutral and negatively charged phospholipid bilayers. In order to achieve that, we developed a new model of phospholipids termed ECC-lipids, which accounts for the electronic polarization via the electronic continuum correction implemented as charge rescaling. Our simulations with this new force field reach for the first time a quantitative agreement with the experimental lipid electrometer concept for POPC as well as for POPS with all the studied cations. We have also examined the effects of transmembrane voltage on phospholipid bilayers. The electric field induced by the voltage exists exclusively in the hydrophobic region of the membrane, where it has an almost constant strength. This field affects the structure of nearby water molecules highlighting its importance in electroporation. 1
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Lipids - Creating Animations to Support Education in the Natural Sciences
Josífková, Hana ; Teplá, Milada (advisor) ; Martínek, Václav (referee)
The diploma thesis deals with the topic of lipids and it is focused on the processing in the form of educational materials (educational text and educational animations) for chemistry and biology on secondary school. It is devided into two parts. The theoretical part defines the key concepts serving as theoretical background: interdisciplinarity, visualization, animation. There is also performed the analysis of RVP G and the representation of the topic of the diploma thesis in this curricular document. The final chapter of the theoretical part is dedicated to determing the criteria for the analysis of the educational materials and the characteristics of the animation program Adobe Animate CC. The analysis of available educational materials is performed according to predetermined criteria in the practical part, specifically animations available on the Internet. There are also introduced the educational materials so as the complex file of educational animations created in the program Adobe Animate CC and the educational text that serves as a guiding material to educational animation program. The materials include methodological guide for users. The created materials focus on the topic of the lipids and biological membranes, they emphasize interdisciplinarity of chemistry and biology and also connect...
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Simulation of processes in cellular membranes
Melcr, Josef ; Jungwirth, Pavel (advisor)
Simulation of processes in cellular membranes Abstract Many important processes in cells involve ions, e.g., fusion of synaptic vesi- cles with neuronal cell membranes is controlled by a divalent cation Ca2+ ; and the exchange of Na+ and K+ drives the the fast electrical signal transmis- sion in neurons. We have investigated model phospholipid membranes and their interactions with these biologically relevant ions. Using state-of-the-art molecular dynamics simulations, we accurately quantified their respective affinites towards neutral and negatively charged phospholipid bilayers. In order to achieve that, we developed a new model of phospholipids termed ECC-lipids, which accounts for the electronic polarization via the electronic continuum correction implemented as charge rescaling. Our simulations with this new force field reach for the first time a quantitative agreement with the experimental lipid electrometer concept for POPC as well as for POPS with all the studied cations. We have also examined the effects of transmembrane voltage on phospholipid bilayers. The electric field induced by the voltage exists exclusively in the hydrophobic region of the membrane, where it has an almost constant strength. This field affects the structure of nearby water molecules highlighting its importance in electroporation. 1
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Simulation of processes in cellular membranes
Melcr, Josef ; Jungwirth, Pavel (advisor) ; Otyepka, Michal (referee) ; Tarek, Mounir (referee)
Simulation of processes in cellular membranes Abstract Many important processes in cells involve ions, e.g., fusion of synaptic vesi- cles with neuronal cell membranes is controlled by a divalent cation Ca2+ ; and the exchange of Na+ and K+ drives the the fast electrical signal transmis- sion in neurons. We have investigated model phospholipid membranes and their interactions with these biologically relevant ions. Using state-of-the-art molecular dynamics simulations, we accurately quantified their respective affinites towards neutral and negatively charged phospholipid bilayers. In order to achieve that, we developed a new model of phospholipids termed ECC-lipids, which accounts for the electronic polarization via the electronic continuum correction implemented as charge rescaling. Our simulations with this new force field reach for the first time a quantitative agreement with the experimental lipid electrometer concept for POPC as well as for POPS with all the studied cations. We have also examined the effects of transmembrane voltage on phospholipid bilayers. The electric field induced by the voltage exists exclusively in the hydrophobic region of the membrane, where it has an almost constant strength. This field affects the structure of nearby water molecules highlighting its importance in electroporation. 1
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Biological membranes and methods for their characterization - current approach.
Skotnicová, Marie ; Konopásek, Ivo (advisor) ; Plocek, Vítězslav (referee)
Cell membrane of prokaryotes is immediately exposed to various environmental changes. To survive, the organism has to sufficiently react to these changes and adapt to them. On the level of the lipid bilayer it means changes of membrane fluidity induced by alterations of the lipid composition. Even a small alteration of acyl chains or polar heads of the phospholipids can alter the order of the lipid bilayer. Various biophysical techniques have been used to detect changes of the membrane fluidity and lipid composition. The purpose of this work is to summarize mechanism of adaptation induced by cold, heat and osmotic shock, as well as commonly used methods for detection of these changes. Studied organisms represent Gram- negative Escherichia coli and Gram-positive Bacillus subtilis. Key words biological membranes, membrane fluidity, adaptation of prokaryotic organisms to environmental changes, methods of characterization of biological membranes, membrane spectroscopy
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Molecules in Cell Membranes
Timr, Štěpán ; Jungwirth, Pavel (advisor) ; Böckman, Rainer (referee) ; Ettrich, Rüdiger (referee)
Biological membranes are actively involved in a multitude of processes in living cells; therefore, a detailed characterization of their structure, dynamics, and function is essential for an understanding of living organisms at the molecular level. In this work, we made use of the high spatial and temporal resolution offered by computer simulations to investigate the behavior of several molecular species which associate with cellular membranes. Using a combination of classical molecular dynamics simulations and ab initio electronic structure calculations, we were able to characterize nonlinear optical properties of membrane- embedded fluorescent probes and thus contribute to establishing two-photon polarization microscopy as a tool of structural biology. Moreover, our molecular dynamics simulations provided an atomistic picture of the reversible membrane binding of recoverin, a neuronal calcium-sensing protein involved in vision adaptation, and they also yielded an important insight into the mechanism of its calcium-induced myristoyl switch. In addition, we examined the biological role of cholesterol oxidation and compared two methods of representing transmembrane voltage in molecular dynamics simulations.
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Membrane interactions studied by advanced fluorescent techniques: From ions to macromolecules
Pokorná, Šárka ; Hudeček, Jiří (advisor) ; Konopásek, Ivo (referee) ; Benda, Aleš (referee)
Advanced fluorescence techniques were used to explore tree distinct topics concerning biological membrane and their interactions. Following thesis is according to the topic divided into three parts: 1) Ionic effects were studied employing time dependent fluorescence shift experiments and molecular dynamic simulations. Combination of these two approaches are suitable to reveal characteristic like mobility and hydration of particular bilayer segment, lipid packing or ion binding sites. Halide anions were reported to adsorb to the cationic lipid bilayer specifically, altering membrane mobility and organization. Changes in observed parameters follows Hofmeister order. Their effect is mediated either by direct ionic interaction (soft, polarizable ions) as well as via alteration of water structure (hard, non-polarizable ions) in proximity of ion molecule. Further, divalent calcium was shown to bind strongly to neutral and negatively charged lipid bilayers. Several types of binding sites depending on calcium concentration were identified. 2) Two complementary lipopeptides, CPK and CPE, incorporated into distinct lipid bilayers serve as a minimal model inducing membrane fusion. Effectiveness of fusion event might be influenced by lipopeptide-membrane and lipopeptide-lipopeptide interaction. To reveal...
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Conformational states of the opiod receptors
Provazníková, Adéla ; Hudeček, Jiří (advisor) ; Entlicher, Gustav (referee)
This Thesis elucidates the relationships between structure and function of opioid receptors. The mechanism of opioid receptor function could be better understood on the basis of the recent knowledge of their three-dimensional structure. In the first part of the Thesis, methods for membrane protein crystallization and X-ray structural analysis are reviewed with a special focus on in meso crystallization. Next, the three opioid receptor subtype crystal structures are described and analysed, starting with their general architecture and proceeding to the detailed description including the binding pocket for opioid ligands with the help of visualization with the PyMol software. In its third part, this Thesis re-examines the structure-function correlations predicted on the basis of site-directed mutagenesis (Décaillot F.M. et al, Nature Structural Biology 10, 629, 2003) in the light of now available crystal structure. This analysis is pointing to the potentially important contacts of aspartate D128, suggesting that ligand binding and receptor activation might involve changes in its interaction with tyrosine Y308.
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Functional activity of opioid receptors in membrane domains
Cechová, Kristína ; Hudeček, Jiří (advisor) ; Mrízová, Iveta (referee)
7 ABSTRACT In this Thesis, we examined the influence of morphine administration to the laboratory rats on the amount of µ-opioid receptors and caveolins in their cerebral cortex. Effect of morphine is known to be caused by its binding to opiod receptors, in particular to the µ subtype, and a long-term exposure to morphine reduces the functionality and number of these receptors as part of the resulting tolerance and addiction. Caveolins are proteins essential for formation of the membrane microdomains of caveolae, although it is known today that presence of these proteins is not limited to caveolae and their function is probably independent of these domains (they may participate in the regulation of cell signaling pathways, lipid transport, etc.). The function of caveolins in brain cells is not precisely known yet. In the experimental part of this work, we used the Western blot method to estimate the presence of caveolin-1 and caveolin-2 in the cerebral cortex of the rats after ten-days morphine application and in control animals. A significant increase of caveolin-1 was observed after morphine treatment as compared to control animals; a smaller, non-significant increase of caveolin-2 was also found. The amount of μ-opioid receptors in morphine affected animals was significantly decreased compared to...
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