Date of Award
Master of Science (MS) in Biology
Jenna Lee Ridlen
The aim of this study is to create a homology model of VG35 serine protease and evaluate the evolutionary comparison of secondary structure on basis of protein model using YASARA. This method was furthermore used to predict the potential epitopes which can help in the investigation of future studies.
The VG35 was used to run a BLAST search which gave most resembled serine protease of different species which was then translated and modeled in YASARA. The modeled protein data was then used to determine the secondary structure. This was then used for evolutionary comparison of all proteins to VG35. Then potential epitope was found using DiscoTope 2.0.
Homology ribbon models were generated using YASARA for VG35 and 12 other serine protease proteins. This was then used to make a dataset of secondary structure which shows sheet, helix, turn, and coil of protein structure. This dataset was used to determine the conservation of other proteins to VG35. The homology ribbon models were used to find epitopes of VG35, VG172, and serine protease of Crotalus tigris.
The homology model helps to understand the difference in the structure of proteins and how it impacts the enzymatic activity of the proteins. This also helps in understanding the variants which lead to change in the secondary structure of proteins which can be caused during post-transcriptional process. The potential epitopes found can be used in future studies to design and develop anti-venom to target specific venom.