Structural and Functional Annotation of Hypothetical Protein AVO28_00330 of Yersinia pestis: An In Silico Approach

06 October 2021, Version 1
This content is a preprint and has not undergone peer review at the time of posting.

Abstract

Yersinia pestis is an infamous gram-negative, coccobacillus enterobacterium responsible for three devastating plague pandemics worldwide. The recent outbreak of this zoonotic disease demands in silico study of the hypothetical proteins for efficient drug and vaccine discovery. As hypothetical proteins constitute a substantial portion of the proteome, it’s essential to annotate them structurally and functionally. The current study characterized physicochemical properties, predicted homology-based 3D structure and annotated functions of the hypothetical protein AVO28_00330 of Y. pestis using a range of bioinformatic tools and softwares. Swiss Model and Phyre2 server were utilized to predict the tertiary model which was minimized energetically using YASARA server. The quality assessment servers found the model as a good one. For future molecular docking analysis, active binding sites were predicted using CASTp. Protein-protein interaction analysis was performed in STRING server. For functional prediction InterPro, Pfam, Motif and other tools were used. The hypothetical protein revealed tricopeptide repeat domain and rubredoxin metal-binding domain which regulates lipopolysaccharide metabolic process in the outer cell membrane which contributes to virulence property of the protein. Therefore, this in silico analysis will improve the current understanding of the protein and aid in the future analysis regarding therapeutic drug and vaccine investigation.

Keywords

Yersinia pestis
homology modeling
rubredoxin
hypothetical protein
functional annotation

Supplementary materials

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Description
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Title
3D model predicted by Phyre2 server
Description
Homology-based modeling approach using Phyre2 server was applied to determine the tertiary structure which was later compared with the Swiss Model to conclude the best one among the two.
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Title
Multiple Sequence Alignment file using MEGA X
Description
Phylogenetic tree was cross-checked with MEGA after building in Phylogeny.fr. Both show similar concepts of origin and similarity.
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