Akrep Venom Peptidlerinin Kristalizasyonu, Yapısal Karakterizasyonu ve Benzeşim Modellemesi

Abstract

In this study, which was conducted to gather informationabout the structures of scorpion venoms, two peptides purified from two different types of scorpions of the same family were investigated. Of these scorpions from the Buthidae family, one belongs to the species Androctonus crassicauda while the other belongs to Buthacus macrocentrus. Venoms taken from the scorpions were purified by using high performance liquid chromatography system in Venom Search Laboratory at Eskişehir Osmangazi University.Acra3, one of the peptides analyzed within the study, was purified from Androctonus crassicauda. The prerequisite for solving the molecule and crystal structure of the peptide by X-ray crystallography is a well-ordered crystal that will diffract x-ray strongly. For this reason, crystallization experiments were performed with the goal of obtainingsingle crystals.Experiments were repeated under different conditions until a single crystal structure was formed. However, ivdetermination of the three dimensional structure could not be achieved since the crystal was not formed.Asthe second part of the study, small angle X-ray scattering (SAXS) method was used for the characterization of low-resolution structure (nanometer size)of Acra3 molecules in solution. SAXS intensity data measuredfrom the experiment which was performed on EMBL P12 BioSAXS beamlinein Hamburgwere analyzed via different programs. Due tothe aggregation in solution, gyration radius and molecular shape of a few aggregated molecules weredetermined.For Acra3 peptide, bioinformatics modelingalong with crystallization and SAXS experiments werealsocarried out. On the other hand, for Bu1 peptide only bioinformaticsmodeling was performed.As the final part of the thesis, it was aimed toestimate thesecondary and tertiary structures of both peptides by using bioinformatics approaches. Firstly, convenient template structures were found via different servers such as NCBI, EBI and Swiss model. To see the similarities between our peptides with others, multiple sequence alignment was performed by employing UniProtKB and ClustalW2 servers. Secondly, secondary structuresof the peptides were determined by homology modeling performed for each of them.