|
|
Interaction of Metal Cations in Bioorganic Environment. Computational Study Using Quantum Mechanics and Molecular MechanicsTools.
Futera, Zdeněk ; Burda, Jaroslav (advisor) ; Bouř, Petr (referee) ; Clark, Tim (referee)
Interactions of Metal Cations in Bioorganic Environment Computational Study Using Quantum Mechanics and Molecular Mechanics Tools Zdeněk Futera Biologically relevant interactions of piano-stool ruthenium(II) complexes with ds-DNA are studied by QM/MM computational technique. The whole re- action mechanism is divided into three phases - hydration of [RuII (η6 - benzene)(en)Cl]+ , consequent binding DNA and final intra-strand cross-link formation between two adjacent guanines. Free energy profiles of all reactions are explored by QM/MM MD umbrella sampling approach where the Ru(II) complex is described by DFT. For that purpose, special QM/MM software was developed to couple Gaussian and Amber programs. Calculated free energy barriers of Ru(II) hydration as well as DNA binding process are in good agreement with experimentally determined rate constants. Reaction pathway for cross-link formation was predicted that is feasible from both thermodynamical and kinetical point of view.
|
|
|
Preparation and Characterization of Protein Binders Mimicking Epitopes of HIV-1 Neutralizing Antibodies
Šulc, Josef ; Malý, Petr (advisor) ; Novotný, Marian (referee)
For three decades, the ongoing HIV pandemic has taken the lives of tens of millions of people. Still, more tens of millions are fighting this incurable disease today. Current failures in combating this global problem are caused mainly by the virus's extreme ability of mutation, its very effective molecular shield which repels the immune system's attacks, and its immense variability. A breakthrough, achieved relatively recently, is the discovery of the so-called broadly neutralizing antibodies against HIV-1, which carry a very efficient and broad neutralizing response. So far, it's not known how to elucidate the production of these antibodies in the infected hosts to quell or altogether eliminate the virus. This work deals with experimental results, which led to both in vivo and in vitro proof-of-concept of the so-called protein mimetics, the ability to imitate viral surface epitopes, and therefore stimulate an efficient immune response carried by targeted broadly neutralizing antibodies. This effect is mediated by recombinant binding proteins, based on the Myomedin scaffold. This work describes the selection and characterization of these binding proteins mimicking the epitopes of one of the most effective broadly neutralizing antibodies, 10E8. It shows that the binding affinities of selected...
|
|
|
Modeling interactions of proteins with ions and membranes
Kadlec, Jan ; Jungwirth, Pavel (advisor) ; Kolafa, Jiří (referee)
The protein recoverin, localized in the eye in the rod outer segment of the retina, is a neuronal calcium sensor involved in vision adaptation. Recoverin reversibly associates with cellular membranes via its calcium-activated myristoyl switch. This reversible interaction is vastly dependent on the concentration of calcium ions in the cytosol and on conformation of recoverin. By using methods of molecular dynamics simulations and free energy calculations this work presents a detailed analysis of the energetics of myristoyl insertion into a lipid bilayer and interactions of non-myristoylated recoverin with the membrane. These results are in a perfect agreement with experimental data. The thesis provides a piece of puzzle to the so far unexplored mechanism of myristamide insertion into the membrane and also to recoverin conformational change. It gives an important insight into binding of recoverin to a membrane, which has a significant biological role.
|
|
|
Modeling interactions of proteins with ions and membranes
Kadlec, Jan ; Jungwirth, Pavel (advisor) ; Kolafa, Jiří (referee)
The protein recoverin, localized in the eye in the rod outer segment of the retina, is a neuronal calcium sensor involved in vision adaptation. Recoverin reversibly associates with cellular membranes via its calcium-activated myristoyl switch. This reversible interaction is vastly dependent on the concentration of calcium ions in the cytosol and on conformation of recoverin. By using methods of molecular dynamics simulations and free energy calculations this work presents a detailed analysis of the energetics of myristoyl insertion into a lipid bilayer and interactions of non-myristoylated recoverin with the membrane. These results are in a perfect agreement with experimental data. The thesis provides a piece of puzzle to the so far unexplored mechanism of myristamide insertion into the membrane and also to recoverin conformational change. It gives an important insight into binding of recoverin to a membrane, which has a significant biological role.
|
|
|
Interaction of Metal Cations in Bioorganic Environment. Computational Study Using Quantum Mechanics and Molecular MechanicsTools.
Futera, Zdeněk ; Burda, Jaroslav (advisor) ; Bouř, Petr (referee) ; Clark, Tim (referee)
Interactions of Metal Cations in Bioorganic Environment Computational Study Using Quantum Mechanics and Molecular Mechanics Tools Zdeněk Futera Biologically relevant interactions of piano-stool ruthenium(II) complexes with ds-DNA are studied by QM/MM computational technique. The whole re- action mechanism is divided into three phases - hydration of [RuII (η6 - benzene)(en)Cl]+ , consequent binding DNA and final intra-strand cross-link formation between two adjacent guanines. Free energy profiles of all reactions are explored by QM/MM MD umbrella sampling approach where the Ru(II) complex is described by DFT. For that purpose, special QM/MM software was developed to couple Gaussian and Amber programs. Calculated free energy barriers of Ru(II) hydration as well as DNA binding process are in good agreement with experimentally determined rate constants. Reaction pathway for cross-link formation was predicted that is feasible from both thermodynamical and kinetical point of view.
|
guest ::
