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Interaction of Cytochromes P450 with Flavodoxin: a theoretical study
Culka, Martin ; Martínek, Václav (advisor) ; Chmelík, Josef (referee)
Cytochromes P450 are diverse group of heme enzymes found in most species on Earth. In humans they are involved in metabolism of foreign compounds or steroids, bacteria employ cytochromes P450 for utilization of various hydrophobic substrates. General reaction catalyzed by cytochromes P450 is monooxygenation, when one atom of oxygen molecule is introduced into the substrate, while the other is reduced producing water. NADPH:cytochrome P450 oxidoreductase or cytochrome b5 usually serves as an electron donor providing electrons needed for activation of oxygen in eukaryotic organisms, in bacteria small FeS proteins or flavoproteins are these electron donors. It was shown earlier that bacterial electron donor flavodoxin could also interact with human cytochromes P450 in vitro. This thesis employs molecular modeling techniques to support a hypothesis that flavodoxin is responsible for reduction of human (1A2, 2A6, 2A13, 2C9, 2C19, 3A4) and bacterial (101A1 a 176A1) cytochromes P450 heterologously expressed in Escherichia coli. An initial guess of possible mutual orientations of cytochrome P450 and flavodoxin was predicted using information-driven protein-protein docking. The stability of these complexes was examined by directed dissociation method. The most stable orientation for each cytochrome P450 was further...
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The study of the association behavior of the amphiphilic copolymers in solutions containing low molar compounds by means of computer simulations.
Šindelka, Karel
Title: The study of the association behaviour of the amphiphilic copolymers in solutions containing low molar compounds by means of computer simulations. Author: Mgr. Karel Šindelka Department: Faculty of Science, Charles University Supervisor: Doc. Ing. Zuzana Limpouchová, Csc. Abstract This doctoral thesis focuses on the study of electrostatic self- and co-assembly in complex polymer solutions containing polyelectrolyte (PE) block copolymers together with surfactants, neutral homopolymers, or oppositely charged PEs using the dissipative particle dynamics (DPD). It was shown that the electro- static self-assembly depends not only on the cooperative interactions of oppo- sitely charged PE chains, but also on the amphiphilicity of PE species or on the polymer block compatibility, among other properties. PEs with incompatible blocks create well-defined core-shell structures, while large ill-defined crew-cut aggregates form from PEs with compatible blocks In non-stoichiometric mixtures of PEs with incompatible blocks, co-assembled nanoparticles are smaller than in stoichiometric mixtures and are charged. The destabilization of larger aggregates depends on how the PE charge surplus is introduced: the effect is strongest when the density of the surplus PE charge on the PE chains is increased and weakest when the...
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Influence of Solvent on Deformation Behavior of Hydrogels
Kulovaná, Eva ; Bartlová, Milada (referee) ; Mráček, Aleš (referee) ; Žídek, Jan (advisor)
The thesis deals with molecular dynamic simulation of the influence of water on the deformation of hydrogels. Hydrogels are model materials formed from macromolecular networks solvated with water. It was found that water can form bridges between macromolecules that take the form of temporary ionic crosslinks. These bridges affect the behavior of the network during deformation. Water bridges are water molecules that have a limited radius of motion in the space between two macromolecules. The concentration of the water bridges was regulated by a partial charge on the macromolecular chain in the organic network. Bridges are a type of interaction that is relatively strong but significantly delocalized. It is not possible to dissociate the water bridge, after dissociation it will be re-created in another place in a short time. The influence of water bridges was compared with other types of network crosslinks, especially covalent and physical bonds. Covalent crosslinks are modeled as a simple binding interaction between two macromolecules. They are undissociable and are local throughout the simulation. Physical bonds are modeled as micelles, where hydrophobic groups form the core and hydrophilic groups form the micelle shell. Physical bonds have the nature of dissociable bonds that are local. Different types of crosslinks have different effects on deformation properties. The deformation of a network containing a combination of two types of crosslinks was simulated: (i) physically-covalent, (ii) ionically-covalent, and (iii) physically-ionic networks and (iv) ternary physically-covalent-ion networks. For individual and combined networks, the behavior depending on simple networks was verified. The number of water bridges was fundamentally affected by the primary structure of the chains. When the PEG chain was replaced with hydrophobic polyoxymethylene (POM) or polyoxytrimethylene (POTM), their solvation and mechanical behavior deteriorated.
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Quantum mechanical study of the electron hopingp rocesses of heterocyclic molecules.Simulation of absorption and emission spectra.
Tichý, Ondřej ; Burda, Jaroslav (advisor) ; Profant, Václav (referee)
This thesis is about computing lifetimes of excited states of molecules by using semiempirical methods in simulations of molecular dynamics. Pyrimidine nucleobases and three aza- derivatives were chosen as reference molecules. Simulations of molecular dynamics by program MNDO99 were performed with these molecules and static spectra were computed by programs Gaussian and Orca. All the examined molecules have femtosecond lifetimes of second excited states, pyrimidine nucleobases have also short lifetimes of first excited states in hundreds of femtoseconds. The computed first excited states of aza-derivatives have lifetimes in tens or hundreds of picoseconds and suggest that the higher stability of the states is related to the smaller number of amino groups attached to the ring.
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Modeling of an influence of a phospholipid membrane composition on the structure and dynamics of cytochromes P450s.
Gücklhorn, David ; Jeřábek, Petr (advisor) ; Kulhánek, Petr (referee)
Cytochrome P450 1A2 is one the most important enzymes that take part in phase I of biotransformation of xenobiotics in human body. This enzyme is anchored in membrane via transmembrane α-helix. Composition of the phospholipid membrane can affect structure and dynamics of this enzyme. In this thesis optimized full-length all-atom model of cytochrome P450 1A2 in POPC (1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine) membrane was created based on crystal structure of catalytic domain of this enzyme. Methods of molecular dynamics were used for creation and optimization of the model which contained parts with unknown structure. The optimized model was subjected to thorough analysis of its structure and dynamics and compared to a similar model with DLPC (1,2-dilauroyl-sn-glycero-3- phosphocholine) membrane. The results show that the composition of the membrane significantly affects dynamics of transmembrane domain and its contact with catalytic domain. Usage of the thicker POPC membrane resulted in smaller contact between both domains which caused partial emergence of the catalytic domain from membrane. Penetration of palmitoyl chain of POPC into tunnel 2f was observed in one the trajectories. Analysis of pathways to active site of cytochrome P450 1A2 and the influence of the membrane composition on...
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Modelling Binding of Insulin Variants toward Insulin Receptor Based on Recent Structural Breakthroughs
Černeková, Michaela ; Lepšík, Martin (advisor) ; Biedermannová, Lada (referee)
Insulin receptor is a multi-domain signalling protein acting as a dimer. It comprises an extracellular ectodomain, a transmembrane domain and intracellular tyrosine kinase domain. Upon insulin binding, conformational changes in insulin as well as in insulin receptor occur and trigger the signaling cascade via the kinase domain. Abnormalities in insulin and insulin receptor function cause diabetes mellitus, a widespread disorder which can be consequence of genetic factors as well as lifestyle and is manifested by increased level of blood glucose. A common treatment of diabetes mellitus is via insulin analogues with different molecular properties. Insulin/insulin receptor interactions in the binding pocket are divided into two groups, so-called "site1" and "site2". The molecular details of the interactions in site1 are well known, while site2 residues are still not completely elucidated. It is important to shed light on the binding properties of insulin and insulin receptor, especially site2 interactions, because it could contribute to improved design of new insulin analogues. In this work, we used the very recent breakthroughs in the structural biology of insulin receptor to study the interactions by computational chemistry methods. It was thus possible to assess the noncovalent interactions and...
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The study of the association behavior of the amphiphilic copolymers in solutions containing low molar compounds by means of computer simulations.
Šindelka, Karel
Title: The study of the association behaviour of the amphiphilic copolymers in solutions containing low molar compounds by means of computer simulations. Author: Mgr. Karel Šindelka Department: Faculty of Science, Charles University Supervisor: Doc. Ing. Zuzana Limpouchová, Csc. Abstract This doctoral thesis focuses on the study of electrostatic self- and co-assembly in complex polymer solutions containing polyelectrolyte (PE) block copolymers together with surfactants, neutral homopolymers, or oppositely charged PEs using the dissipative particle dynamics (DPD). It was shown that the electro- static self-assembly depends not only on the cooperative interactions of oppo- sitely charged PE chains, but also on the amphiphilicity of PE species or on the polymer block compatibility, among other properties. PEs with incompatible blocks create well-defined core-shell structures, while large ill-defined crew-cut aggregates form from PEs with compatible blocks In non-stoichiometric mixtures of PEs with incompatible blocks, co-assembled nanoparticles are smaller than in stoichiometric mixtures and are charged. The destabilization of larger aggregates depends on how the PE charge surplus is introduced: the effect is strongest when the density of the surplus PE charge on the PE chains is increased and weakest when the...
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Pairing of biologically relevant ions in aqueous solutions
Baxová, Katarína ; Jungwirth, Pavel (advisor) ; Předota, Milan (referee)
Not accounting for the electronic polarizability due to divalent ions such as Ca2+ introduces a significant artifacts to force field-based molecular dynamic simulations of biological systems. Two newly developed parameter refinements were used to compute the free energy profile of the Ca2+ -Cl- ion dissociation in aqueous solutions, to be compared with a free energy profile obtained from ab-intio molecular dynamics and to data from neutron scattering. Next, the computational evidence for the existence of a local free energy min- imum representing a guanidinium-guanidinium contact ion pair in aqueous solu- tions is provided suggesting a global preference for a contact ion pair. Finally, the passive membrane penetration mechanism of oligoarginines was investigated on a cell membrane model systems - lipid vesicles - by fluorescent spectroscopy. In this study, a mechanistic link between membrane penetration and vesicle aggregation and fusion was found. 1
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The study of the association behavior of the amphiphilic copolymers in solutions containing low molar compounds by means of computer simulations.
Šindelka, Karel ; Limpouchová, Zuzana (advisor) ; Slavíček, Petr (referee) ; Vondrášek, Jiří (referee)
Title: The study of the association behaviour of the amphiphilic copolymers in solutions containing low molar compounds by means of computer simulations. Author: Mgr. Karel Šindelka Department: Faculty of Science, Charles University Supervisor: Doc. Ing. Zuzana Limpouchová, Csc. Abstract This doctoral thesis focuses on the study of electrostatic self- and co-assembly in complex polymer solutions containing polyelectrolyte (PE) block copolymers together with surfactants, neutral homopolymers, or oppositely charged PEs using the dissipative particle dynamics (DPD). It was shown that the electro- static self-assembly depends not only on the cooperative interactions of oppo- sitely charged PE chains, but also on the amphiphilicity of PE species or on the polymer block compatibility, among other properties. PEs with incompatible blocks create well-defined core-shell structures, while large ill-defined crew-cut aggregates form from PEs with compatible blocks In non-stoichiometric mixtures of PEs with incompatible blocks, co-assembled nanoparticles are smaller than in stoichiometric mixtures and are charged. The destabilization of larger aggregates depends on how the PE charge surplus is introduced: the effect is strongest when the density of the surplus PE charge on the PE chains is increased and weakest when the...
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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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