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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...
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Selection approaches in directed evolution of binding proteins
Huličiak, Maroš ; Malý, Petr (advisor) ; Hlouchová, Klára (referee)
Artificial binding proteins derived from small protein domains attract attention as a promising alternative to monoclonal antibodies and can be used in many kinds of applications. They are useful in diagnosis of human diseases, seem to be a clue for more efficient vaccine development preventing from global diseases such as AIDS, can exhibit a therapeutic potential or improve purification techniques. For the selection of protein variants with desired properties such as high specificity and binding affinity, more than 10 different selection techniques have been developed. So called display techniques such as phage display, yeast display, retroviral display or baculovirus display are based on protein expression from different vectors. Contrary that, ribosome display, mRNA display and CIS display are cell-free systems based on in vitro translation. Development of different selection approaches allows production of post- translationally glycosylated, phosphorylated and acetylated proteins, increased yield of the produced binders and improved their binding properties. The submitted work provides an overview of current selection techniques, compare their parametres regarding to combinatorial libraries, describes their advantageous properties and limitations, and focus on a practical utilization of...
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Protein domains utilizable for development of binding molecules
Dobešová, Petra ; Malý, Petr (advisor) ; Veverka, Václav (referee)
Small protein domains represent basic building blocks of naturally occurring proteins. Many of them exhibit excellent stability, lack disulfide bonds and their structures, therefore, represent attractive tools for generation of artificial binding molecules. First step in the production of novel binding proteins is the definition of a basic domain structure, called "scaffold", which is identified using in silico approaches, resulting in discovery of mutable amino acid residues. Then, randomization of such residues leads to design of a highly complex combinatorial library as a key tool for targeted selection of protein variants. Based on chosen selection approach, the particular protein variants can be tested for their ability to recognize the target molecule with high specificity and binding affinity. Small binding proteins lack post-translation modifications, exhibit thermal stability, are resistant to many organic solvents and can be produced on a mass scale in bacterial host cells. In addition, they can be easily modified and used in vivo with excellent tissue penetration. Due to these beneficial properties, small artificial binding proteins are extraordinary useful biotechnological tools and represent a promising alternative to monoclonal antibodies. The aim of this work is to summarize our knowledge on...
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