National Repository of Grey Literature 14 records found  1 - 10next  jump to record: Search took 0.00 seconds. 
Study of Ligands for Phosphatases from the Haloacid Dehalogenase Superfamily
Brinsa, Vítězslav ; Maloy Řezáčová, Pavlína (advisor) ; Vaněk, Ondřej (referee)
Phosphatases of the haloacid dehalogenase superfamily are one of the cell's tools for dephosphorylation of many diverse endogenous and exogenous compounds. This work is aimed at enzymes Tt82 and cytosolic purine 5'-nucleotidase II (cN-II), two members of this large enzyme superfamily. The Tt82 originates in the hyperthermophilic archaeon Thermococcus thioreducens. Up to date, there is only a small amount of knowledge about properties and biological function of this enzyme. Based on its sequence and structure, it was predicted that the Tt82 should possess a phosphatase catalytic activity. Consequently, potential substrates of the Tt82 were proposed by the molecular docking. In this work, the phosphatase activity of the Tt82 was confirmed together with several of its substrates: AMP, D-glucose 1-phosphate, D-glucose 6-phosphate and p-nitrophenyl phosphate (pNPP). Activity towards AMP and pNPP was then characterized by steady-state kinetics at 37 řC and 60 řC. In consistence with its thermophilic origin, the Tt82 showed markedly higher activity towards both substrates at 60 řC. Nonetheless, the effectivity of the Tt82 catalytic activity towards these substrates was actually very low. This leads to assumption, that the identified substrates are probably not biologically relevant. On the other hand, it is quite...
Structural studies of transcription factors implicated in regulation of metabolism of pancreatic beta cells
Duchoslav, Vojtěch ; Maloy Řezáčová, Pavlína (advisor) ; Vaněk, Ondřej (referee)
Nkx6.1 is a homeodomain protein (37.8 kDa) and an important transcription factor, which regulates transcription of key genes in pancreatic ß-cells. Insufficient expression of this protein leads to reduced glucose uptake from blood as a consequence of suppressed transcription of the glucose transporter Glut2 and impaired glucose metabolism. Furthermore, the proliferation of pancreatic ß-cells is suppressed due to insufficient transcription of Cyclin D2, a protein regulating the mitosis. Moreover, the biosynthesis of insulin is impaired duet he diminished transcription of the genes coding for Ero1lb a Slc30a8, which as a consequence leads to reduced production of the mature insulin. Nkx6.1 could play a role in the pathogenesis of the type 2 diabetes , where ß-cells show diminished ability to compensate high demand for insulin. This malfunction is the cause of an insufficient ability to secrete insulin and death of pancreatic cells. Perhaps driven by misregulation of transcription of the genes that are involved in the mentioned processes. Nkx6.1 recognizes a strictly conserved 8-base pair DNA sequence (TTAATTAC). Its binding to DNA is regulated by an acidic domain at the C-terminus. Within the bachelor thesis, the resonances were assigned to the backbone atoms of the Nkx6.1 protein using nuclear...
Structural studies of selected signaling protein complexes.
Pšenáková, Katarína ; Obšil, Tomáš (advisor) ; Hrabal, Richard (referee) ; Maloy Řezáčová, Pavlína (referee)
The ability of proteins to bind other molecules in response to various stimuli in their microenvironment serves as a platform for extensive regulatory networks coordinating downstream cell actions. The correct function of these signaling pathways depends mostly on noncovalent interactions often affecting the structure of proteins and protein complexes. Understanding the molecular mechanism of a protein function in cell signaling therefore often depends on our knowledge of a three-dimensional structure. In this doctoral thesis, I present the work that led to the understanding of several protein-protein and protein-ligand interactions implicated in cell signaling at the molecular level. I applied nuclear magnetic resonance spectroscopy, small angle X-ray scattering and other biophysical methods to determine the molecular basis of inhibition of four signaling proteins: Calcium/Calmodulin (Ca2+ /CaM)-dependent protein kinase kinase 2 (CaMKK2); protease Caspase-2; Forkhead transcription factor FOXO3, and Apoptosis signal-regulating protein kinase 1 (ASK1). In particular, I investigated the distinct roles of 14-3-3 and Ca2+ /CaM in the regulation of CaMKK2 activity. I also studied in detail the mechanism how 14-3-3 interferes with the caspase-2 oligomerization and its nuclear localization as well as...
Regulation of purine nucleotide metabolism as a pharmacological target
Brinsa, Vítězslav ; Maloy Řezáčová, Pavlína (advisor) ; Hlouchová, Klára (referee)
Purine nucleotides are essential basic building blocks for DNA and RNA synthesis. They can also serve as energy storage and transfer unit and play an important role in cell signalling and regulation of variety of biochemical processes. It is crucial for the cells to maintain a sufficient supply of purine nucleotides in order to secure its survival and cell division. Level of purine nucleotide pool in the human body is regulated via purine nucleotide metabolism, which consists of three coordinated processes: de novo synthesis pathway, salvage pathway and degradation pathway of purine nucleotides. Regulation of those three pathways is under control of various mechanisms including regulation on the level of enzyme expression, allosteric regulation of enzyme activity or forming a multienzime complexes, i. e. purinosomes in the de novo synthesis pathway. Phosphoribosyl pyrophosphate synthetase I (PRS-I) and cytosolic purine 5'-nucleotidase (cN-II) play an important role in purine nucleotide metabolism. These enzymes contribute significantly to the purine nucleotide pool regulation by means of their allostericaly regulated activity. Malfunctions of their catalytic activity are connected with various pathologies such as gout, hyperuricosuria, neurological dysfunctions and acute lymphoblastic leukaemia...
Use of specific inhibitors of carbonic anhydrase IX for fluorecent imaging of cancer cells
Pospíšilová, Klára ; Maloy Řezáčová, Pavlína (advisor) ; Novotný, Marian (referee)
Human carbonic anhydrases are metalloenzymes that are involved in many physiological processes in the body, but also play an important role in the pathogenesis of numerous diseases. Under regular conditions, expression of carbonic anhydrase IX (CAIX) is very limited, unlike that of other 14 human carbonic anhydrase isozymes. But in hypoxic tumors this enzyme is highly overexpressed on the cell surface. For this reason, this enzyme represents a good target for therapy and diagnosis of tumors and thus various anti-CAIX monoclonal antibodies and specific inhibitors are being developed. In this work we investigated the possibility to use fluorescent polymer conjugate carrying a CAIX specific inhibitor for florescent labeling of tumor cells. Specific binding of polymer conjugate to different cell lines was investigated by flow cytometry and confocal microscopy. Binding properties of the polymer conjugate was compared to CAIX specific monoclonal antibody M75 and its single-chain fragment scFv M75. Ability of the polymer conjugate to inhibit CAIX enzyme activity was also investigated. For these experiments, recombinant protein CAII was prepared and purified, which was also used for protein crystallization. Tests of inhibitory activities allowed to identify novel inhibitors CAIX with better inhibitory...
Structural studies of LEDGF/p75 interactions
Těšina, Petr ; Maloy Řezáčová, Pavlína (advisor) ; Obšil, Tomáš (referee) ; Spiwok, Vojtěch (referee)
3 ABSTRACT LEDGF/p75 protein is a human transcriptional co-activator and epigenetic reader associated with transcriptionally active chromatin. It is crucial for HIV integration and MLL1 fusion-driven leukemia development. Interactions of LEDGF/p75 with HIV integrase (HIV IN) and MLL1-menin complex are considered an attractive therapeutic target for drug development. LEDGF/p75 interacts with both HIV IN and MLL1-menin complex through its integrase binding domain (IBD). While the pathophysiological interactions of LEDGF/p75 IBD were intensively studied, little was known about the physiological ones. In addition to HIV IN and MLL1, the LEDGF/p75 IBD also interacts with JPO2, PogZ, ASK and MLL2. In search for specific inhibitors of LEDGF/p75 IBD interaction with HIV IN and MLL1, it is essential to obtain detailed information about its interactions with all binding partners. The IBD-MLL1-menin complex has been structurally characterized, but only partially. Using NMR spectroscopy, we identified and mapped a novel part of the IBD-MLL1 interface. This additional interface is able to maintain the interaction between LEDGF/p75 and MLL1 even without the presence of menin, which was considered necessary. Moreover, colony forming assays of primary leukemic blasts revealed that this additional interface is essential for...
Structural biology of the enzymes involved in mercaptopurine metabolism
Soldánová, Anna ; Maloy Řezáčová, Pavlína (advisor) ; Novotný, Marian (referee)
Mercaptopurine (6-mercaptopurine) together with azathioprine and 6-thioguanine belong to a group of widely used chemotherapeutics and immunosuppressants. However, insufficient therapy outcome or severe adverse effects such as myelosuppression are still being reported. Technological progress in DNA and RNA sequencing facilitates effective identification of causative genes responsible for the therapy failure, i.e., description of genetic variants for enzymes involved in metabolism of physiological purines as well as thiopurine drugs. Variants of these enzymes may substantially alter concentrations of cytotoxic forms of thiopurines, which affect therapy success rates. Currently, a number of mutations in genes that play role in thiopurine metabolism have been annotated. Nevertheless, molecular mechanisms underlying the effect of these mutations are not fully elucidated. Knowledge of 3D structure for these enzymes may shed light on the effect of the genetic variants to protein function and mechanisms modulating therapeutic efficacy of thiopurines. This thesis focuses mainly on biochemical and structural characterization of thiopurine-S-methyltransferase, fosfatase NUDT15 and cytosolic 5′-nucleotidase II. It summarizes current state of knowledge and emphasizes the importance of structural biology methods for...
Understanding the interaction of antibodies and transcription factors with their ligands through structural biology
Škerlová, Jana ; Maloy Řezáčová, Pavlína (advisor) ; Hrabal, Richard (referee) ; Obšil, Tomáš (referee)
Understanding protein function highly benefits from the knowledge of its three-dimensional structure, especially in the case of protein-ligand complexes. Structural biology methods such as X-ray crystallography, SAXS and NMR are therefore widely used for structural studies of protein-ligand interaction. In this work, these methods were used to understand two biological processes involving protein interactions: X-ray structural analysis was used to study binding of effector molecule to a prokaryotic transcription factor. NMR and SAXS techniques were used to study interaction of a monoclonal antibody with its protein antigen. Transcriptional regulator DeoR negatively regulates the expression of catabolic genes for the utilization of deoxyribonucleosides and deoxyribose in Bacillus subtilis. DeoR comprises an N-terminal DNA-binding domain and a C-terminal effector-binding domain (C-DeoR), and its function is regulated by binding of a small-molecular effector deoxyribose-5-phosphate. We determined crystal structures of C-DeoR both in the free form and in complex with deoxyribose-5-phosphate. Structural analysis revealed unique covalent binding of effector molecule through a reversible Schiff-base double bond with an effector-binding-site lysine residue. The physiological nature of this binding mode was...
Expression and characterization of recombinant capsid protein from HIV and its mutants: towards inhibition of virus assembly
Sivá, Monika ; Konvalinka, Jan (advisor) ; Maloy Řezáčová, Pavlína (referee)
Human immunodeficiency virus infection has been a threat to the world for the last thirty years. It causes a condition called acquired immunodeficiency syndrome leading to complete collapse of immune system and death if not treated. There are many anti-HIV drugs that are part of the combined antiretroviral treatment but they only slow down the progress of the infection. Although the success of all the 31 antiviral agents is remarkable, the cure is not efficient enough. The research of potencial new HIV drugs is now focusing on new targets of viral inhibition. The capsid protein is a potential target of virion assembly and maturation inhibitors due to its multimerization features. The N-terminal domains of six capsid proteins create hexamers. These are connected to each other by dimers of the C-terminal domains according to X-ray and NMR studies. There are inhibitors that bind to the C-terminal domain, alter its conformation and weaken the protein-protein interaction of the dimer. Protein calorimetry is a method that could detect and quantify protein-protein interactions and thus capsid protein dimerization and its inhibition. We expressed and purified recombinant wild-type capsid protein and its C-terminal domain that both dimerize in solution and crystals. Their dimerization constant was determined by...
Characterization of recombinant fragment of an antibody against CD3 marker.
Písačková, Jana ; Maloy Řezáčová, Pavlína (advisor) ; Obšil, Tomáš (referee)
Monoclonal antibody MEM-57 recognizes CD3 antigen expressed on peripheral blood T-lymphocytes. CD3 surface glycoprotein complex associates with T-cell receptor and is responsible for the transduction of activation signal. Antibody MEM-57 has, therefore, a large diagnostic and therapeutic potential. It could be used in autoimmune diseases diagnostics, for classification of T-cell leukemias and, as an immunosuppressant, in transplantation. The most promising therapeutic use of MEM-57 antibody would be the construction of a "Bispecific T-cell Engager" (BiTE) antibody format with potential application in cancer therapy. In this format, single-chain variable fragment (scFv) of MEM-57 would be fused with an anti-tumor antigen scFv. The thesis is focused on biochemical and biophysical characterization of MEM-57 antibody scFv fragment. Recombinant antibody fragment scFv MEM-57, equipped with the pelB leader sequence, c-myc tag and His5 tag, was produced from a pET22b(+) vector into the periplasmic space of E. coli BL21 (DE3). Two-step purification protocol, employing nickel chelation affinity chromatography and ion-exchange chromatography, was developed to obtain high yield of pure protein. The antigen binding activity of scFv MEM-57 was confirmed by flow cytometry. Structural information on scFv MEM-57...

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