Rahman Md Foyzur, Hasan Rubait, Biswas Mohammad Shahangir, Shathi Jamiatul Husna, Hossain Md Faruk, Yeasmin Aoulia, Abedin Mohammad Zakerin, Hossain Md Tofazzal
Department of Biochemistry and Biotechnology, School of Biomedical Science, Khwaja Yunus Ali University, Sirajganj 6751, Bangladesh.
Department of Botany, Sirajganj Govt. College, Sirajganj 6700, Bangladesh.
Genomics Inform. 2023 Mar;21(1):e3. doi: 10.5808/gi.22021. Epub 2023 Mar 31.
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.
通过计算机方法从上传到数据库中的氨基酸序列对假设蛋白质的二级和三级结构进行表征以及预测，是计算生物学中的关键问题。严重急性呼吸综合征相关冠状病毒（SARS-CoV）可引发类似肺炎的疾病，它拥有多种蛋白质，其中许多仍未被表征。当前的研究旨在揭示SARS-CoV中一种未被表征的蛋白质Q6S8D9_SARS的理化特性和结构。按照表征假设蛋白质的通用流程，使用了多种精密的计算机工具，如ExPASy Protparam、CD Search、SOPMA、PSIPRED、HHpred等，来发现Q6S8D9_SARS的功能和结构。在描绘出该蛋白质的二级和三级结构后，使用了一些质量评估工具，如PROCHECK、ProSA-web等对结构进行评估，随后还通过CASTp v.3.0确定了活性位点。该蛋白质含有的带负电荷残基比带正电荷残基更多，且脂肪族指数值较高，这使得该蛋白质更稳定。通过多种生物信息学工具构建的二维和三维结构表明，该蛋白质含有结构域，这表明它是一种功能性蛋白质，能够干扰宿主抗病毒炎性细胞因子和干扰素的产生途径。此外，在该蛋白质中发现了可结合配体的活性位点。本研究旨在揭示SARS-CoV一种未被表征蛋白质的特征和结构，该蛋白质可能成为开发针对该病毒疫苗的治疗靶点。还需要进一步的研究来完成这项任务。
