A bioinformatics approach to characterize a hypothetical protein Q6S8D9_SARS of SARS-CoV

Abstract

Characterization as well as prediction of the secondary and tertiary structure of hypothetical proteins from their amino acid sequences uploaded in databases by in silico approach are the critical issues in computational biology. Severe acute respiratory syndrome-associated coronavirus (SARS-CoV), which is responsible for pneumonia alike diseases, possesses a wide range of proteins of which many are still uncharacterized. The current study was conducted to reveal the physicochemical characteristics and structures of an uncharacterized protein Q6S8D9_SARS of SARS-CoV. Following the common flowchart of characterizing a hypothetical protein, several sophisticated computerized tools e.g., ExPASy Protparam, CD Search, SOPMA, PSIPRED, HHpred, etc. were employed to discover the functions and structures of Q6S8D9_SARS. After delineating the secondary and tertiary structures of the protein, some quality evaluating tools e.g., PROCHECK, ProSA-web etc. were performed to assess the structures and later the active site was identified also by CASTp v.3.0. The protein contains more negatively charged residues than positively charged residues and a high aliphatic index value which make the protein more stable. The 2D and 3D structures modeled by several bioinformatics tools ensured that the proteins had domain in it which indicated it was functional protein having the ability to trouble host antiviral inflammatory cytokine and interferon production pathways. Moreover, active site was found in the protein where ligand could bind. The study was aimed to unveil the features and structures of an uncharacterized protein of SARS-CoV which can be a therapeutic target for development of vaccines against the virus. Further research are needed to accomplish the task.

Keywords: SARS-CoV; bioinformatics; functional annotation; hypothetical protein.

Fig. 1.

Flow chart of the proposed study. GO, gene ontology; SARS-CoV, severe acute respiratory syndrome–associated coronavirus.

Fig. 2.

Amino acid composition of the hypothetical protein Q6S8D9_SARS. SARS, severe acute respiratory syndrome.

Fig. 3.

Secondary structure of the hypothetical protein developed by PSIPRED.

Fig. 4.

Tertiary structure of Q6S8D9_SARS protein predicted by HHpred with Modeller tool. SARS, severe acute respiratory syndrome.

Fig. 5.

Ramachandran plot of the hypothetical protein.

Fig. 6.

Active site of the Q6S8D9 protein. (A) Red sphere denoting the active sites. (B) Four amino acid residues (ILE, GLN, LEU, and ALA) in the active site (shaded).