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Determination of structure and dynamics of biomolecules by theoretical calculations of NMR spectroscopic parameters
Benda, Ladislav ; Sychrovský, Vladimír (advisor) ; Munzarová, Markéta (referee) ; Hrabal, Richard (referee)
iv Abstract Subject: Determination of structure and dynamics of biomolecules by theoretical calcu- lations of NMR spectroscopic parameters Author: Ladislav Benda, ladislav.benda@gmail.com Department/Institute: Institute of Organic Chemistry and Biochemistry, AS CR Supervisor: Dr. Vladim'ır Sychrovsk'y, Institute of Organic Chemistry and Biochemistry, AS CR, vladimir.sychrovsky@uochb.cas.cz Abstract: This doctoral work was focused on theoretical modeling of nuclear magnetic resonance (NMR) parameters in peptides and nucleic acids. Dependences of NMR para- meters on molecular structure and solvation were primarily modeled. Great emphasis was put on the comparison of the calculated data with the NMR experiment. The molecular models studied included the l-alanyl-l-alanine di-peptide (AA) and the phosphate group of nucleic acid backbone. Conformations of all three charged forms of AA in solution were determined and the respective pH-induced changes of experimental NMR chemical shifts and nuclear spin-spin coupling constants were explained. Dependences of NMR cross-correlated relaxation rates on the AA backbone geometry were calibrated. The 31 P NMR parameters in nucleic acid phosphate were systematically calculated in dependence on the backbone conformation and the phosphate solvation pattern. Qualitative rules...
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Structure and function of C-type lectin NK cell receptors studied by recombinant expression and protein crystallography
Vaněk, Ondřej ; Bezouška, Karel (advisor) ; Hrabal, Richard (referee) ; Bařinka, Cyril (referee)
Department of Biochemistry, Faculty of Science, Charles University in Prague 2010 Structure and function of C-type lectin NK cell receptors studied by recombinant expression and protein crystallography Abstract of Ph.D. thesis Ondřej Vaněk Supervisor: Prof. RNDr. Karel Bezouška, DSc. Natural killer cells (NK cells) were found out for their ability to spontaneously kill certain allogeneic tumour cell lines, without any previous sensitization. NK cells are part of non- adaptive immune response with very short reaction time against pathogens such as viruses, intracellular bacteria, parasites, and they are responsible for elimination of certain tumour cells and thus they are able to fight against malignancy and formation of metastasis. Activity of NK cells is regulated by the balance between activation and inhibitory signals mediated by the NK cell surface receptors. From the structural point of view, the majority of NK cell surface receptors could be classified as the C-type lectin or immunoglobulin-like receptors. One of many C-type lectin subgroups are type II lymphocyte receptors that are expressed on the NK cell surface. This study had two main aims. The first one was to find suitable expression and purification systems for selected C-type lectin receptors of NK cells and the other one was to perform their...
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Měření C-13 NMR relaxací karbonylových skupin v proteinech
Grocký, Marián ; Hrabal, Richard (referee)
Title: Measurement of 13 C NMR relaxation of Carbonyl Groups in Proteins Author: Marián Grocký Department: Department of Low Temperature Physics Supervisor: RNDr. Jan Lang, PhD. Supervisor's email address: Jan.Lang@mff.cuni.cz Abstract: I have investigated measurement methods of 13 C NMR longitudial and transversal relaxation constants in proteins labeled by 13 C, 15 N. The Mason-Pfizer Matrix protein (M-PMV) has been studied in it's wild form (WT) and mutated form (R55F) by these methods in order to reveal its dynamics. It has been known that point mutation of arginine for phenylalanine at the 55th position of matrix protein changes virus's life cycle. Reproduction of M-PMV than resembles HIV virus reproduction. Nitrogen T1, T2 and NOE relaxation experiments have also been carried out. All relaxation data were used for Lipari-Szabó model-free approach in order to get and compare carbonyl and amide group motion parameters. There has been found a high similarity between carbonyl and nitrogen motion parameters within WT protein. Nitrogen data of R55F protein approved higher mobility of particular sequences in that protein, which is assumed to be responsible for changes in mutant's life cycle. Both carbonyl and nitrogen data significantly enlarged our current knowledge of dynamics of both WT and R55F...
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Structural study of S6A mutant of matrix protein from Mason-Pfizer monkey virus
Kamal, Rašíd ; Hrabal, Richard (advisor) ; Ulbrich, Pavel (referee)
Mason-Pfizer monkey virus (M-PMV) belongs to the morphogenetic type D retroviruses which produce viral particles in the cytoplasm. This process is temporally and spatially separated from the cytoplasmic membrane budding and therefore M-PMV is a suitable model organism for studying the life cycle of retroviruses. Matrix protein, which is N-terminal portion of Gag polyprotein precursor, plays a central role in this life cycle. One of the key areas of the protein is its myristoylated N-terminus which is particularly important for binding to the cytoplasmic membrane during budding from host cells. A hydrogen bond exists between serine 6 and glutamate 9 of the wild-type protein. We have studied its influence on the structure and molecular mechanics of the corresponding area of the protein by means of disruption of this interaction by replacing serine 6 with alanine. This thesis describes the preparation of recombinant mutant of the M-PMV matrix protein, resonance assignment of its backbone atoms with nuclear magnetic resonance spectroscopy and compares observed secondary structure with that of other mutants and the wild type.
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