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Gene Searching - Web Application
Stiborová, Lucie ; Koutný, Jiří (referee) ; Burgetová, Ivana (advisor)
The aim of my Bachelor's Thesis is to create a user interface and to implement the web application with the genes' searching. This is the educational application when each user has a possibility of entering own nucleotide sequences or selecting a redefined chain. This application has to be able to read, process and decide on the existence of a potential gene. On the base of this simple statistic method the result is given back to the user.
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LacZ-alpha complementation peptide as a tool for molecular evolution studies
Ptáčková, Barbora ; Hlouchová, Klára (advisor) ; Vaněk, Ondřej (referee)
Proteins are the key structural and functional molecules of living organisms. Although the last decades have brought a lot of knowledge about their structural and functional characteristics, science still lacks very basic answers about how these properties evolved. Current predominant opinions suggest that early genetic code contained only a subset of today's canonical amino acids. Both exogenous and endogenous sources of prebiotic amino acids imply that even though the prebiotic amino acid repertoire was very broad, only about half of the proteinogenic amino acids were present. It follows that the ''evolutionary new'' amino acids were added to the genetic coding system only after the evolution of their biosynthetic pathways. From the current scientific knowledge it is unclear whether proteins composed of "evolutionary old" amino acids could serve basic metabolic functions and if today's proteins could be "reversely-evolved" to be composed of only such a subset of amino acids while maintaining their structural and functional integrity. These questions lie at the core of this study. This thesis aims to test a starting methodology that would randomize "new" amino acid positions by "old" amino acids in the sequence of LacZ-alpha peptide. This peptide was selected as a target model protein because it...
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Never Born Proteins: Occurence and characterization of secondary structure motifs
Treťjačenko, Vjačeslav ; Hlouchová, Klára (advisor) ; Kopecký, Vladimír (referee)
An experimental study on randomly generated protein sequences can provide important insights into the origin and mechanism of secondary structure formation and protein folding. In this study we bring biophysical characterization of five protein sequences selected from the in silico generated library of random chains. The sequences were selected on the basis of bioinformatic analysis in order to find the candidates with the maximum potential to possess secondary structure. This study shows that the random polypeptide sequences form stable secondary structures and in some show the signs of tertiary structure, such as hydrophobic core formation and distinctive oligomerization pattern. While the work presented in this thesis is work in progress on a larger study, the data already demonstrate that unevolved protein sequence space provides a lot of potential for secondary and tertiary structure formation that awaits its characterization. Powered by TCPDF (www.tcpdf.org)
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Synthesis of proteins containing non-canonical amino acids
Knetl, Adam ; Vopálenský, Václav (advisor) ; Plocek, Vítězslav (referee)
0 Abstract: Non-canonical amino acids allow the introduction of new chemical properties into proteins, which is useful both for studying proteins, and designing proteins. However, the synthesis of proteins containing non-canonical amino acids faces problems with decreased effectivity of translation. This thesis examines the role of genetic code for coding non-canonical amino acids, proteosynthesis and aminoacilation of tRNA and finally the non-canonical amino acids and their application in proteins while including examples.
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Never Born Proteins: Occurence and characterization of secondary structure motifs
Treťjačenko, Vjačeslav ; Hlouchová, Klára (advisor) ; Kopecký, Vladimír (referee)
An experimental study on randomly generated protein sequences can provide important insights into the origin and mechanism of secondary structure formation and protein folding. In this study we bring biophysical characterization of five protein sequences selected from the in silico generated library of random chains. The sequences were selected on the basis of bioinformatic analysis in order to find the candidates with the maximum potential to possess secondary structure. This study shows that the random polypeptide sequences form stable secondary structures and in some show the signs of tertiary structure, such as hydrophobic core formation and distinctive oligomerization pattern. While the work presented in this thesis is work in progress on a larger study, the data already demonstrate that unevolved protein sequence space provides a lot of potential for secondary and tertiary structure formation that awaits its characterization. Powered by TCPDF (www.tcpdf.org)
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LacZ-alpha complementation peptide as a tool for molecular evolution studies
Ptáčková, Barbora ; Hlouchová, Klára (advisor) ; Vaněk, Ondřej (referee)
Proteins are the key structural and functional molecules of living organisms. Although the last decades have brought a lot of knowledge about their structural and functional characteristics, science still lacks very basic answers about how these properties evolved. Current predominant opinions suggest that early genetic code contained only a subset of today's canonical amino acids. Both exogenous and endogenous sources of prebiotic amino acids imply that even though the prebiotic amino acid repertoire was very broad, only about half of the proteinogenic amino acids were present. It follows that the ''evolutionary new'' amino acids were added to the genetic coding system only after the evolution of their biosynthetic pathways. From the current scientific knowledge it is unclear whether proteins composed of "evolutionary old" amino acids could serve basic metabolic functions and if today's proteins could be "reversely-evolved" to be composed of only such a subset of amino acids while maintaining their structural and functional integrity. These questions lie at the core of this study. This thesis aims to test a starting methodology that would randomize "new" amino acid positions by "old" amino acids in the sequence of LacZ-alpha peptide. This peptide was selected as a target model protein because it...
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|
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Gene Searching - Web Application
Stiborová, Lucie ; Koutný, Jiří (referee) ; Burgetová, Ivana (advisor)
The aim of my Bachelor's Thesis is to create a user interface and to implement the web application with the genes' searching. This is the educational application when each user has a possibility of entering own nucleotide sequences or selecting a redefined chain. This application has to be able to read, process and decide on the existence of a potential gene. On the base of this simple statistic method the result is given back to the user.
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