Comparison of sequences and structures between NS3-NS2B of various Flaviviruses

Le, Thai Thuy Anh

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Comparison of sequences and structures between NS3-NS2B of various Flaviviruses

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Flavivirus is a genus of virus that belong to the Flaviviridae family, a family of positive single-stranded, enveloped RNA viruses that transmit to humans through arthropods as their vectors. There has been recorded of more than 70 flaviviruses, with some of them causing potentially fatal human illness: yellow fever virus (YFV), West Nile virus (WNV), Dengue virus (DENV), Zika virus (ZIKV), and Murray Valley encephalitis virus (MVEV). In flavivirus, non-structural (NS) proteins have been found to play a vital role in the proliferation and transmission of flavivirus. The complex NS2B-NS3 protein is associated with the endoplasmic reticulum membrane and possesses dual functions for processing RNA and polyprotein. This article is a comparison in structures and sequences between various NS3 proteins among various human-borne flaviviruses and one swine-borne pestivirus, utilizing 3D structural modeling programs USCF Chimera, and global sequence alignment programs T-COFFEE Expresso, and MUSCLES. Based on the structural and sequence analysis data, it was observed that the helicase domains of the Flavivirus species the most conserved domains in terms of structures and sequences, while the protease region display more variations and diversities. Interestingly, the DENV4 helicase domains share a higher percent identity and a lower RMSD value when compared to the Kunjin virus and MVEV helicase domains than when compared to the Aedes mosquito-borne group members such as ZIKV and YFV, despite that MVEV and Kunjin virus belong to the Culex mosquito-borne group.

This report represents the work of one or more WPI undergraduate students submitted to the faculty as evidence of completion of a degree requirement. WPI routinely publishes these reports on its website without editorial or peer review.

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