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Dissertation: The Functions of Proteins Using Methods of Structural Bioinformatics

25.04.2008

In her dissertation Structural Bioinformatics in the Study of Protein Function and Evolution, Susanna Repo studied the development of the functions of amino acid decarboxylases during evolution. Amino acid decarboxylases are enzymes that function in the metabolism of amino acids. Each of them catalyzes their specific amino acid precisely and generates an evolutionary tree with separate branches for each decarboxylase. Using this tree, Repo categorized unknown decarboxylase sequences and proposed what substance they catalyze. In addition, she studied the ligand binding properties of proteins and nucleus receptors that bind biotine and examined, using docking studies, how these proteins interact with small molecules.

The results indicate that the prognoses based on experimental data can help to achieve a more detailed picture of the functions of proteins. In addition, Repo presented and analyzed the advantages and defects of computer-based methods used in studies.

Susanna Repo applied structural bioinformatics methods in her study. Structural bioinformatics is a subfield of bioinformatics and is based on the study of three-dimensional protein structures, which is crucial for the protein functions. As a result, the properties that affect the abilities of protein to function in a cell can be identified by studying the structure. Using this information, it can be attempted to alter the function of proteins. In addition, many medicinal molecules that prevent the function of a certain protein have been found using this method. Furthermore, the protein structure includes much information about the evolution of the protein family in question and the study of the structures can crucially help to identify distant relationships within a protein family when constructing a phylogenetic (evolutionary) family tree.

Susanna Repo’s dissertation was examined in Åbo Akademi University’s Faculty of Mathematics and Natural Sciences. Repo used CSC’s software services in her dissertation.

 Väitöskuva Repo

The three-dimensional structure of an avidin protein is presented in the picture. One molecule used in the study is docked to the protein, i.e. 4-hydroxyl-3-nitroazobenzene-3-carboxylic acid. © Repo


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