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Development of selected CD markers and their role in the phylogenesis of human immune system
Podolská, Tereza ; Růžičková, Šárka (advisor) ; Vinkler, Michal (referee)
In the first part of the thesis we investigated the origin of selected surface CD markers of human, namely CD19, CD20, CD21, CD24, CD27 and CD38 molecules. In addition, nucleotide and amino acid sequences of these molecules were compared using in silico approach. Bioinformatic databases of sequences of selected molecules at DNA, mRNA and protein level, such as GeneBank, NCBI BLAST, Homologene and OrthoDB, have been used. The intent was to identify at the domain level the first organism in which it is possible to find the searched molecule. At the N-terminal domain of the CD38 of birds, a sequence showing significant similarity to the archaebacterial flagellin domain was found. This flagellin sequence in the CD38 avian molecule is located in the region of transmembrane domain, indicating that the occurrence of this sequence might be related to the formation of the transmembrane domain. The approach used here could be implemented in comparative hybridization studies as a tool in the preparatory non-laboratory phase of the research of the presence of paralogs and orthologs in phylogenetically old species. Keywords: CD marker, immunocyte, B lymphocyte, innate and adaptive immunity, sequence database, amino acid, nucleotide
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Clustering of aqueous aminoacids and similar molecules in the presence of phospholipid monolayers
Kukharchuk, Alexandra ; Cwiklik, Lukasz (advisor) ; Berka, Karel (referee)
Amino acid phenylalanine plays a key role in numerous biological processes and is also involved in amyloid fibril diseases. The aim of the thesis is to deepen our understanding of its behavior and partitioning at interfaces, and to investigate its clustering. Classical atomistic molecular dynamics simulations were performed for phenylalanine and three other aromatic molecules which chemical structure is derived from it - phenylglycine, phenylacetic acid and tyrosine. Molecules are simulated at both water-air and at water-DPPC-air interfaces. Phenylalanine, phenylglycine and phenylacetic acid demonstrate surface activity at the water-air interface, whereas tyrosine is not surface active. All molecules interact with the lipid monolayer at the water-DPPC-air interface but only phenylalanine penetrates deep into the monolayer. Formation of transient clusters is observed in the interfacial regions, mostly for phenylalanine. Powered by TCPDF (www.tcpdf.org)
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The metabolism of amino acids in parasitic and anaerobic protists
Jakubec, Dávid ; Šuťák, Róbert (advisor) ; Hrdý, Ivan (referee)
Parasitic protists are the cause of countless pathological conditions and economic issues in many parts of the world. While being phylogenetically unrelated, they share many similarities in their approach to satisfying the essential needs. Unlike the much studied energy metabolism, amino acids utilisation pathways are rather unexplored areas. This review shows that in many cases, the parasitic life style has not had the same impact on the amino acid metabolism as it did on the energy metabolism of the protists, which is often severely reduced. Novel pathways have been found in many of the organisms in question, for the biosynthesis of amino acids deemed both essential and non-essential in humans. The arginine dihydrolase pathway found in Trichomonas and Giardia represents a complely new way of utilising the said amino acid. The metabolism of sulfur-containing amino acid has been a matter of intensive research for their non-proteogenic roles. Polyamines are organic nitrogenous compounds involved in many vital processes in the cells, including DNA replication and protein translation. The synthesis of polyamines and their derivatives is elucidated, as it is directly connected to the amino acid metabolism. Finally, the exploitation of the unique pathways described integrates the previous research with the aim...
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Intramolecular and intermolecular interactions in proteins
Fačkovec, Boris ; Vondrášek, Jiří (advisor) ; Berka, Karel (referee)
Folding free energy of a protein is a delicate balance between stabilizing and destabilizing non-covalent itneractions. In this work, we decompose folding free energy into physically meaningful contributions, in which we aim to find general trends. Empirical potential is used to calculate interaction energy between all protein fragments, which are classified based on their dominant term in multipolar expansion. Calculations are done using 1200 non-redundant structures from PDB database. Based on the general trends found in interactions between these fragments, we attempt to better understand relationships between interaction energies calculated using computational chemistry methods and their corresponding free energy contributions on stabilization. 1
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Enantioseparation and derivatization of selected amino acid.
Rozumová, Nela ; Loukotková, Lucie (referee) ; Bosáková, Zuzana (advisor)
The enantioseparation of native and derivatized form of D,L-valine was studied on chiral stationary phase, based on teicoplanin chiral selector. The most suitable mobile phase for the enantioseparation and quantification of underivatized D,L-valine was methanol/water 50/50 (v/v) and UV detection at 205 nm. LOD and LOQ for L- and D-enantiomers were evaluated, in order of hundredths of mg/ml. Derivatization of D,L-valine was done using 9-fluorenylmethylchloroformate (FMOC-Cl). For the enantioseparation of FMOC-D,L-valine the optimized mobile phase consisted of 37/63 (v/v) methanol/0,5% triethylamine acetate buffer (TEEA), pH 4,0. Quantification was carried out using fluorescence detection at the excitation wavelength of 254 nm and the emission wavelength of 314 nm. LOD and LOQ values for FMOC-L- and FMOC-D-valine were in the range from hundredths to tenths of μg/ml. The results show that much higher detection sensitivity was achieved after the derivatization procedure.
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Analysis of the Tools for Detecting Similarities between Tertiary Protein Structures
Trlica, Jiří ; Vogel, Ivan (referee) ; Bendl, Jaroslav (advisor)
Alignment of the three-dimensional structures of proteins is an essential task in bioinformatics. Because there are many tools offering this functionality, only a limited subset of them was chosen for comparison (DALI, LOCK 2, SPALIGN, MUSTANG and CLICK). These tools vary in the principle of calculation. Their performance was measured on three proteins, which represent main protein classes (all-α, all-β, α/β). These proteins were tested against a subset of PDB database containing 2 357 records. The results were visualized by ROC curves and the tools were compared by their area under ROC curve (AUC metric). According to this metric, the best results were obtained for SPALIGN.
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Clustering of Protein Sequences Based on Primary Structure of Proteins
Jurásek, Petr ; Stryka, Lukáš (referee) ; Burgetová, Ivana (advisor)
This master's thesis consider clustering of protein sequences based on primary structure of proteins. Studies the protein sequences from they primary structure. Describes methods for similarities in the amino acid sequences of proteins, cluster analysis and clustering algorithms. This thesis presents concept of distance function based on similarity of protein sequences and implements clustering algorithms ANGES, k-means, k-medoids in Python programming language.
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