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.

Keywords: Bangladeshi covid-19 variant; ORF proteins; SARS-CoV-2; bioinformatics; membrane and envelope protein; structural prediction.

Figure 1.

Multiple sequence alignment and phylogenetic analysis of 6 different protein sequences depicting evolutionary relationships with SARS-CoV-2 varieties of 10 different countries (A–F). Sequence alignment of ORF10, ORF7b, ORF7a, and ORF6, membrane glycoprotein, and envelope protein respectively. (G–L) Neighbor joining phylogenetic tree of ORF10, ORF7b, ORF7a, and ORF6, membrane glycoprotein, and envelope protein respectively. All proteins appear closely related to the proteins of different variants of different countries.

Figure 2.

Hydrophobicity plot and GRAVY Scores of selected 6 proteins. (A-F) Hydrophobicity plot of ORF10, ORF7b, ORF7a, and ORF6, membrane glycoprotein, and envelope protein respectively. The hydrophobicity plots were generated according to the Kyte-Doolittle hydropathy plots. (G) GRAVY scores of ORF10, ORF7b, ORF7a, ORF6, membrane glycoprotein, and envelope protein. The numerical values for each score displayed above are their corresponding box. The proteins are recognized as mostly hydrophobic.

Figure 3.

Per-residue disorder plot for ORF10, ORF7b, ORF7a, ORF6, membrane glycoprotein, and envelope protein of SARS-CoV2. All proteins found as highly flexible and ordered. Scores ⩾0.5 indicate disorder residues, while scores within 0.25 to 0.5 and 0.1 to 0.25 suggest highly flexible and moderate flexible residues. Scores ⩽0.1 indicate rigidity.

Figure 4.

(A, B) Aliphatic indexes and transmembrane helix prediction scores of ORF10, ORF7b, ORF7a, ORF6, membrane glycoprotein, and envelope protein respectively. All proteins showed aliphatic index values of more than 100 indicated that they are highly thermo-stable and transmembrane helices of less than 1.

Figure 5.

Secondary structure prediction of 6 selected proteins. (A-F) Secondary structure of ORF10, ORF7b, ORF7a, ORF6, membrane glycoprotein, and envelope protein respectively.

Figure 6.

Protein modeling and hydrophobicity surface 3D map of the selected 6 proteins. (A-F) Ribbon diagram of ORF10, ORF7b, ORF7a, ORF6, membrane glycoprotein, and envelope protein respectively. (G-L) Hydrophobicity surface map of ORF10, ORF7b, ORF7a, ORF6, membrane glycoprotein, and envelope protein respectively. All 6 protein models are found as highly flexible and stable. The blue color represents hydrophilic regions and the orange color expresses hydrophobic regions. Where, the whitish-blue color indicates semi-hydrophobic/hydrophilic character. (M-R) Representation of Ramachandran plot of ORF10, ORF7b, ORF7a, ORF6, membrane glycoprotein, and envelope protein, respectively.