Characterization and Structural Prediction of Proteins in SARS-CoV-2 Bangladeshi Variant Through Bioinformatics

Abstract

The renowned respiratory disease induced by the severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) has become a global epidemic in just less than a year by the first half of 2020. The subsequent efficient human-to-human transmission of this virus eventually affected millions of people worldwide. The most devastating thing is that the infection rate is continuously uprising and resulting in significant mortality especially among the older age population and those with health co-morbidities. This enveloped, positive-sense RNA virus is chiefly responsible for the infection of the upper respiratory system. The virulence of the SARS-CoV-2 is mostly regulated by its proteins such as entry to the host cell through fusion mechanism, fusion of infected cells with neighboring uninfected cells to spread virus, inhibition of host gene expression, cellular differentiation, apoptosis, mitochondrial biogenesis, etc. But very little is known about the protein structures and functionalities. Therefore, the main purpose of this study is to learn more about these proteins through bioinformatics approaches. In this study, ORF10, ORF7b, ORF7a, ORF6, membrane glycoprotein, and envelope protein have been selected from a Bangladeshi Corona-virus strain G039392 and a number of bioinformatics tools (MEGA-X-V10.1.7, PONDR, ProtScale, ProtParam, SCRIBER, NetSurfP v2.0, IntFOLD, UCSF Chimera, and PyMol) and strategies were implemented for multiple sequence alignment and phylogeny analysis with 9 different variants, predicting hydropathicity, amino acid compositions, protein-binding propensity, protein disorders, and 2D and 3D protein modeling. Selected proteins were characterized as highly flexible, structurally and electrostatically extremely stable, ordered, biologically active, hydrophobic, and closely related to proteins of different variants. This detailed information regarding the characterization and structure of proteins of SARS-CoV-2 Bangladeshi variant was performed for the first time ever to unveil the deep mechanism behind the virulence features. And this robust appraisal also paves the future way for molecular docking, vaccine development targeting these characterized proteins.

A Tiny Viral Protein, SARS-CoV-2-ORF7b: Structural Features.

“…[24][25][26]. Unfortunately, these important electrostatic characteristics were rarely highlighted in the structural papers on ORF7b-2, as well as in those on ORF7b-1, because only the central part of the protein is discussed as a trans-membrane helix [7,10,12,14]. In doing so, any structure-function consideration of these proteins could be distorted.…”

“…2 within the trans-membrane segment [7]. On this basis, a report has hypothesized that ORF7b-2 too is a trans-membrane protein localized in the Golgi apparatus [10].…”

Bioinformatics techniques for efficient structure prediction of SARS-CoV-2 protein ORF7a via structure prediction approaches

“…Since then, the technique has been upgraded to use a cutting-edge multiple-template modeling strategy influenced by both global and local quality estimations. The most recent version includes more sequence-structure alignment techniques, which increases model accuracy even more (Debnath et al, 2022).…”