In silico structural and Interaction analysis of HPV 33 E2 DNA binding domain

Abstract

Human papillomavirus (HPV) is a virus which spreads from person to person through skin-to-skin contact. There are over 100 different types of HPV, with over 40 being transmitted by sexual contact and affecting the genitals, mouth, and throat. HPV is the most frequent sexually transmitted infection (STI), according to the Center for Disease Control and Prevention (CDC). HPV33 is a high-risk HPV strain within the same phylogenetic species (alpha-9) as HPV16 and accounts for approximately 5% of cervical cancer cases worldwide, with some variation in this proportion by geographical location. The aim was to study the structural aspects of the HPV33 E2 protein which is a major viral regulatory protein and proven to be responsible in viral induced neoplasia. The protein model was constructed on SWISMODELER. Various in silico studies were also carried out on the protein structure and its binding properties were checked with its target DNA molecules using online server PatchDock. The protein parameters and interaction dynamics were studied using PDBsum, and the interacting residues were determined by using Protein Ligand Interaction Profiler (PLIP). The protein was also cloned and purified and was subjected to fluorescence-based studies to check the binding of protein and target DNA.