|
|
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)
|
|
|
The effect of amino acid repertoire on protein structure and function
Treťjačenko, Vjačeslav ; Hlouchová, Klára (advisor) ; Obšil, Tomáš (referee) ; Pačes, Jan (referee)
To understand protein structure emergence is to comprehend the evolutionary transition from messy chemistry to the first heritable molecular systems. Early proteins were probably flexible in structure, promiscuous in activity and ambiguous in sequence. Moreover, first sequences were presumably composed of prebiotically plausible amino acids from endogenous and exogenous sources which form only a subset of the extant protein alphabet. Here we investigate the effect of most recent additions to the amino acid alphabet on protein structure/function relationship and the properties of random proteins as the evolutionary point-zero for the earliest sequences as well as for proteins emerging de novo from the non-coding parts of the genome. Random or never born proteins are of a special interest for the contemporary biology as they unveil the unexposed side of the protein sequence space. We constructed an in silico library of random proteins with the natural amino acid alphabet, analyzed its structure/disorder/aggregation content and selected 45 sequences for subsequent experimental preparation and biophysical characterization. We observed that structure content in random sequence space does not differ significantly from the natural proteins. However, the analyses of the aggregation propensity showed a...
|
|
| |
|
|
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)
|
guest ::
