Structural interpretation of the NS3 helicase ATP binding domain of Zika virus (ZIKV)

Afnan Shakoori, Nida Alsaffar

Abstract


Background: The Zika virus, a mosquito-borne virus, was discovered in Uganda and quickly spread to Asia and the Pacific. Zika is mainly transmitted by the bite of an infected Aedes species mosquito (Aedes aegypti and Aedes albopictus). These mosquitos bite both during the day and at night.

Methods: Numerous tools (SMART, Pfam, InterProScan and Scan Prosite, BepiPred-2.0 server, I-TASSER, PROCHECK, phyre 2, protparam, and GPS 6.0) were used to elaborate the content in this publication.

Results:  The results show that HABD (187 amino acids) is a DEAH-Box RNA helicase. We also used the Ramachandran plot to validate the epitope peptides and structure modeling. We also discovered the amino acid composition and various residues/parentages in the HABD protein phosphorylation site prediction and PK-specific phosphorylation sites (p-sites). 

Conclusion: The helicase ATP binding domain (HABD), HABD protein ATP binding sites, and epitope binding peptides are discussed in this work. There are five atoms in total: nitrogen, sulfur, hydrogen, carbon, and oxygen. Hydrogen atoms (1476) provide the most to the composition. We created a graph representing the protein's predicted phosphorylation sites (p-sites). Aside from the standard statistics, GPS 6.0 may identify PK-specific p-sites hierarchically. GPS 6.0 could be a valuable service for further phosphorylation study. 

Keywords: DEAH-Box; Epitope peptides; Ramachandran plot; Structure Modelling; Secondary structure; Phosphorylation; PK-specific and GPS 6.0 


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References


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DOI: http://dx.doi.org/10.62940/als.v11i1.2546

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