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Cloning, expression and characterization of human serine racemase mutants
Nováková, Ilona ; Konvalinka, Jan (advisor) ; Brynda, Jiří (referee)
AAbbssttrraacctt Human serine racemase (hSR) is a cytosolic pyridoxal-5'-phosphate dependent enzyme localized in the central nervous system. It synthesizes D-serine, which is an endogenous coagonist for the N-methyl-D-aspartate (NMDA) receptors and plays a key role in excitatory neurotransmission in the brain. Thus, human serine racemase is a promising target for the treatment of neurodegenerative diseases connected with NMDA receptors. However, few specific inhibitors have been identified to date and the crystal structure of hSR has become available only very recently. We decided to perform a random mutagenesis to determine the amino acid residues critical for the enzyme activity. Ser 84 was reported as a catalytic residue along with Lys 56. After analysis of a double mutant S84G/P111L which retained its capability to convert L-serine to pyruvate, we prepared and characterized the single mutant S84G in order to exclude potential effect of the P111L mutation.on the activity of the analyzed enzyme. KKeeyy wwoorrddss:: D-serine; Serine racemase; PLP-dependent enzymes; Random mutagenesis; Racemases
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Production of mouse recombinant prion protein and analysis of its properties
Krejčiříková, Anna ; Konvalinka, Jan (advisor) ; Brynda, Jiří (referee)
Title: Production of mouse recombinant prion protein and analysis of its properties Author: Anna Krejčiříková Department: Department of Biochemistry Supervisor: doc. RNDr. Jan Konvalinka, CSc., Supervisor's e-mail: konval@uochb.cas.cz Consultant: dr. Ing. Karel Holada, IIM 1stFM CU Abstract: Although prion diseases represent only a small fraction of all known neurodegenra- tive illnesses, they deserve our attention mainly due to the fact that they are lethal, incurable by today, and having a potential to cause a serious epidemic. Even though this topic has been studied for many years, there are still many unanswered questions concerning both the mechanism, and the spread of prion diseases. The most promising current theory is the protein-only hypothesis, which explains the fundamental of the ill- ness by the conversion of cellular prion protein (PrPC ) into pathological prion protein (PrPSc ). The important tool in proving this theory is also a recombinant prion pro- tein. The presented thesis summarizes existing successes in the proving of protein-only hypothesis. In the experimental part, we prepared the mouse recombinant prion pro- tein (mrPrP) in E. coli bacteria. The structure of the purified and renaturated protein was verified by CD spectroscopy. Next, we focus on the effects of the...
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Structure Analysis of Plant Bifunctional Nuclease TBN1
Kovaľ, Tomáš ; Dohnálek, Jan (advisor) ; Brynda, Jiří (referee) ; Schneider, Bohdan (referee)
This work is dedicated to thorough structural analysis of plant bifunctional nuclease TBN1, the representative of plant nuclease I group. TBN1 along with homologous nucleases from this family plays an important role in plant cell life cycle and also shows considerable anticancerogenic effects. Two variants of TBN1 (wild type and N211D mutant) were studied. Properties of both variants in different solutions were analyzed. Both were successfully crystallized. Structures of both types of TBN1 were solved using X-ray diffraction. The phase problem was solved by Multi-wavelength anomalous dispersion using Zn2+ ions natively present in TBN1. Structural properties of TBN1 such as fold, active site composition, effect of glycosylation and surface electrostatic potential distribution were analyzed. Reaction mechanism of TBN1 was proposed on the basis of structural properties and comparisons with similar structures.
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Cloning, expression and characterization of human serine racemase mutants
Nováková, Ilona ; Brynda, Jiří (referee) ; Konvalinka, Jan (advisor)
AAbbssttrraacctt Human serine racemase (hSR) is a cytosolic pyridoxal-5'-phosphate dependent enzyme localized in the central nervous system. It synthesizes D-serine, which is an endogenous coagonist for the N-methyl-D-aspartate (NMDA) receptors and plays a key role in excitatory neurotransmission in the brain. Thus, human serine racemase is a promising target for the treatment of neurodegenerative diseases connected with NMDA receptors. However, few specific inhibitors have been identified to date and the crystal structure of hSR has become available only very recently. We decided to perform a random mutagenesis to determine the amino acid residues critical for the enzyme activity. Ser 84 was reported as a catalytic residue along with Lys 56. After analysis of a double mutant S84G/P111L which retained its capability to convert L-serine to pyruvate, we prepared and characterized the single mutant S84G in order to exclude potential effect of the P111L mutation.on the activity of the analyzed enzyme. KKeeyy wwoorrddss:: D-serine; Serine racemase; PLP-dependent enzymes; Random mutagenesis; Racemases
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Production of mouse recombinant prion protein and analysis of its properties
Krejčiříková, Anna ; Brynda, Jiří (referee) ; Konvalinka, Jan (advisor)
Title: Production of mouse recombinant prion protein and analysis of its properties Author: Anna Krejčiříková Department: Department of Biochemistry Supervisor: doc. RNDr. Jan Konvalinka, CSc., Supervisor's e-mail: konval@uochb.cas.cz Consultant: dr. Ing. Karel Holada, IIM 1stFM CU Abstract: Although prion diseases represent only a small fraction of all known neurodegenra- tive illnesses, they deserve our attention mainly due to the fact that they are lethal, incurable by today, and having a potential to cause a serious epidemic. Even though this topic has been studied for many years, there are still many unanswered questions concerning both the mechanism, and the spread of prion diseases. The most promising current theory is the protein-only hypothesis, which explains the fundamental of the ill- ness by the conversion of cellular prion protein (PrPC ) into pathological prion protein (PrPSc ). The important tool in proving this theory is also a recombinant prion pro- tein. The presented thesis summarizes existing successes in the proving of protein-only hypothesis. In the experimental part, we prepared the mouse recombinant prion pro- tein (mrPrP) in E. coli bacteria. The structure of the purified and renaturated protein was verified by CD spectroscopy. Next, we focus on the effects of the...
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Crystallographic study of an anti=carbonic anhydrase IX monoclonal antibody M75
Štouračová, Renata ; Závada, Jan ; Závadová, Zuzana ; Pastoreková, S. ; Brynda, Jiří ; Fábry, Milan ; Král, Vlastimil ; Hořejší, Magdalena ; Sedláček, Juraj
Carbonic anhydrase IX (CA IX) is a cell surface protein, strongly associated with certain types of human carcinomas. Structural study of a CA IX-binding monoclonal antibody (mAb) M75, complexed with its epitope peptide may contribute toward elucidation of the role of CA IX. Monoclonal antibody M75 was obtained and proved to react excellently with native and denaturated CA IX. Using synthetic oligopeptides, the epitope of mAb M75 was localized in the proteoglycan domain of CA IX, in the region of a tandem repeat and identified as amino acids PGEEDLP. The Fab fragment was obtained by papain cleavage. We obtained crystals of free Fab M75 and Fab M75 complexed with two different epitope peptides. The data set for Fab M75 was collected and the structure solving is underway.
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Preliminary Crystallographic Study of ç-D-Crystalline Obtained from Patient`s Eye
Brynda, Jiří ; Řezáčová, Pavlína ; Štouračová, Renata ; Ondráček, Jan ; Kmoch, B. ; Asfaw, B. ; Elleder, M. ; Bezouška, K. ; Filipec, M. ; Sedláček, Juraj
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Vazba fenylnorstatinového inhibitoru na proteázu HIV-1: geometrie, protonace a interakce kapes podřadných míst analyzované při atomovém rozlišení
Brynda, Jiří ; Řezáčová, Pavlína ; Fábry, Milan ; Hořejší, Magdalena ; Štouračová, Renata ; Sedláček, Juraj ; Souček, Milan ; Hradilek, Martin ; Lepšík, Martin ; Konvalinka, Jan
The x-ray structure of a complex of HIV-1 protease (PR) with a phenylnorstatine inhibitor Z-Pns-Phe-Glu-Glu-NH2 has been determined at 1.03 A, the highest resolution so far reported for any HIV PR complex. The inhibiot shows subnanomolar Ki values for both the wild-type PR and the variant representing one of the most common mutations linked to resistance development. The structure displays a unique pattern of hydrogen bonding to the two catalytic aspartate residues. The high resolution permints to assess the donor/acceptor relations of this hydrogen bonding and to indicate a proton shared by the two catalytic residues. Structural mechanism for the unimpaired inhibition of the protease Val82Ala mutant is also suggested, based on energy calculations and analyses
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