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Cell-free expression of protein libraries made of different amino acid repertoires
Neuwirthová, Tereza ; Hlouchová, Klára (advisor) ; Míšek, Jiří (referee)
This bachelor thesis is an introduction to a project dealing with the influence of genetic code evolution (and the consequentamino acid repertoire in proteins) on the evolution of protein structure and function. The initial amino acid alphabet was apparently only half the size of the present alphabet and according to available metaanalyses it included only about 10 prebiotically present amino acids derived from potential exogenous or endogenous sources. This work includes mRNA transcription and cell-free expression of five randomized protein libraries (containing approximately 1011 variants). These libraries differ in their amino acid composition and reflect individual predicted stages of genetic code evolution. The main goal is to convert libraries from DNA to protein form to provide a source for library purification and their subsequent biophysical (occurrence of secondary and tertiary structure) and functional analyses. The whole research could theoretically contribute to a few basic questions not only in the fields of protein evolution but also in areas of synthetic biology or protein engineering. Keywords: Cell-free expression, proteins, genetic code evolution This thesis is written in Czech.
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Dynamers based on the reversible formation of hemiacetals
Nosek, Vladimír ; Drahoňovský, Dušan (advisor) ; Míšek, Jiří (referee)
This work deals with the design and synthesis of building blocks, usable for creating dynamic polymers based on the reversible formation of hemiacetals bond. Next part is focused on the study of the formation of hemiacetal between polyfunctional alcohols and trifluoromethylketones via NMR spectroscopy. Key words: constitutional dynamic chemistry, hemiacetals, trifluoromethylketones, diols and polyols
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Praparation and use of α-alkylidene-β-lactams in cross-metathesis
Kretschmer, Jan ; Veselý, Jan (advisor) ; Míšek, Jiří (referee)
The main topic of this thesis was preparation of α-alkyliden-β-lactams and their use in cross metathesis in a presence of transition metal catalyst. Kinugasa reaction as well as Morita- Baylis-Hillman derivatives were used for preparation of lactams. α-alkyliden-β-lactams were used in reactions with aliphatic alkens and for study of subsituent electronic effect on lactames in cross metathesis step. The formal total synthesis of Ezetimibe was also developed in this work.
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Synthesis of sulphanylaminoderivatives of cyclodextrines and computational simulations of their complexes formation
Provazníková, Adéla ; Jindřich, Jindřich (advisor) ; Míšek, Jiří (referee)
This master thesis deals with synthesis of 6I -N-monosubstituted β-CD bearing a linear spacer of various lenghts containing disulfidic bond and terminated by amine. Whole series was succesfully prepared by nucleophilic substitution of toluenesulfonyl group on tosyl β-CD by a spacer's amine group. In case of the shortest spacer (cystamine) 35 % yield was achieved. Synthesis of β-CD derivatives using longer and more lipophilic spacer derived from di-, tri- and tetraethylenglycol yielded 66 to 85 %. The oligoethylene spacers were prepared by standard chemical modifications. A separation method using n-butanol elution mixtures was optimized for isolation of β-CD derivatives. To better understand the β-CD derivative behavior in solution, molecular dynamics (MD) computations were used. The synthetized species were intended to be used for fluorescent sensor construction. For the same reason the inclusion of small organic molecules in β-CD cavity was studied with molecular dynamic simulations. MD method for computation of relative binding energy was optimized and gave values of right sign and order of magnitude.
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On Azahelicenes: Synthesis, Resolution, Properties and Applications
Míšek, Jiří
Mgr. Jiří Míšek PhD Thesis Abstract A novel and modular approach to azahelicenes has been developed. Using [2+2+2] cyclotrimerisation of appropriate triyne as a key step, azahelicenes 83, 84 and 85 have been prepared (Scheme 1). Scheme 1. Aza[6]helicenes 84 and 85 have shown to be sufficiently configurationally stable and have been resolve into individual enantiomers by the diastereoisomeric salt crystalisation and chiral HPLC. This allowed to determine exact values of racemisation barriers for both aza[6]helicenes 84 and 85. In general, both hexacyclic derivatives 84 and 85 are stable enough to be used in asymmetric transformations or chiral sensing. The ability of aza[6]helicenes 84 and 85 to serve as chiral ligands for transition metals has been proven by the preparation and X-ray analysis of corresponding silver complexes. Interesting chiral self-recogniton properties of aza[6]helicenes 84 in gas phase have been described using mass spectrometry techniques. In order to complement information about azahelicenes basicities, gas phase proton affinities of derivatives 84 and 85 and solution phase dissociation constants of azahelicenes 83, 84 and 85 have been determined. Eventually, the first utilization of azahelicene in asymmetric catalysis has been demonstrated by the successful use of optically pure...
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Characterization of organogold compounds
Shcherbachenko, Elena ; Roithová, Jana (advisor) ; Míšek, Jiří (referee)
Geminally diaurated complexes are important intermediates involved in some of the gold catalyzed reactions and therefore they have become a subject of the current research. The aim of this thesis was to assess the influence of electronic structure of an aryl ligand on the stability of gold complexes with three-center-two-electron interaction Au2C. A series of geminally diaurated complexes was obtained by a reaction of gold complex [(IPr)Au(NCMe)]BF4 (IPr = 1,3-bis(2,6-di-iso-propylphenyl)imidazol-2-ylidene) with arylboronic acids ArB(OH)2 bearing different substituents at the aryl group (Ar = para- O2NC6H4, para-NCC6H4, para-ClC6H4, C6H5, para-H3CC6H4, para-H3COC6H4, meta- O2NC6H4, meta-NCC6H4, meta-H3CC6H4, ortho-O2NC6H4, ortho-NCC6H4, ortho-H3CC6H4). Mass spectrometry (MS) was used as the main experimental method in this study. Appearance energies (AE) for the fragmentation of geminally diaurated complexes were estimated by the methods MS/MS. The obtained energies were plotted against the corresponding Hammett σ-constants to assess the correlation between the electronic structure of a given aryl ligand and the stability of the Au2C bond. It was found that structures of gold complexes derived from the cyanophenylboronic acids do not correspond to the geminally diaurated complexes but to the...
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Synthesis of cyclodextrin derivatives using methoxymethyl protecting groups
Kasal, Petr ; Jindřich, Jindřich (advisor) ; Míšek, Jiří (referee)
This work deals with the use of methoxymethyl protecting group in chemistry of cyclodextrins, where this group has not been used very often so far. The work deals with development of optimal methods for introduction and for subsequent removal of the group and shows its usefulness in the preparation of new 6I -O-monosubstituted cyclodextrin derivatives, which are hard to get by standard methods. Key words: cyclodextrin derivatives, methoxymethyl group, protecting group
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