Study of Drosophila melanogaster circadian clock regulation
Every organism on earth is regulated my an internal clock system which controls metabolic, physiologycal, sleep and wake cycles. This clock is controlled by many protein-protein interactions and post translation modifications. Both flies and humans have retained homologous genes for over 60% of their genome, including genes related to circadian rhythm. The circadian rhythm in both flies and humans regulated by conserved feedback loops forming heterodimeric protein complexes. These complexes contain large intrinsically disordered regions making them hard to study using x-ray crystallography, Cryo-Em OR NMR methods. In this project the aim is to study heterodimeric protein complexes in Drosophila melanogaster using homology modelling in using alphafold2 multimer. Alphafold2 is able to conduct thorough sequence alignment against protein databases to generate protein structures with high accuracy to the level of crystal structures. To run alphafold2 locally successfully, the algorithm required high power Graphics Processing Units. Running alphafold2 in Berzelius ensures complete prediction with output of all data files and models. The expected results include high quality protein-protein complex models and statistical data files that can be used for analysis.