Structural and Functional Characterization of a Hypothetical Protein from Streptococcus mitis Using In silico Approaches
Published: 2023-12-28
Page: 236-248
Issue: 2023 - Volume 6 [Issue 2]
Md. Easin Mia
Department of Biotechnology and Genetic Engineering, Noakhali Science and Technology University, Noakhali-3814, Bangladesh.
Tanvir Hossain Emon
Department of Biotechnology and Genetic Engineering, Noakhali Science and Technology University, Noakhali-3814, Bangladesh.
Md. Shipul Islam
Department of Biotechnology and Genetic Engineering, Noakhali Science and Technology University, Noakhali-3814, Bangladesh.
Md. Anwar Hossain *
Department of Biotechnology and Genetic Engineering, Noakhali Science and Technology University, Noakhali-3814, Bangladesh.
*Author to whom correspondence should be addressed.
Abstract
Streptococcus mitis, a member of the Viridans Group Streptococci (VGS), is commonly found in the normal flora of the human oropharynx, and can cause various infections in humans, including orbital cellulitis, infective endocarditis, and bacteremia in neutropenic individuals. Identifying specific proteins, particularly hypothetical proteins (HPs), is crucial for developing effective treatments. This research aimed to determine the structure as well as the function of a nonannotated hypothetical protein (HP) from Streptococcus mitis. Several aspects of the HP (accession no. BCJ11593.1), including physiochemical properties, 3D structures, and functional annotation, were predicted using a variety of computational tools, followed by further validation and quality assessment. The HP was identified as a cytoplasmic and stable protein. NCBI-CD search, and InterProScan, two functional annotation tools, predicted that the target HP was the ribosome-associated protein YbcJ, specifically the S4-like RNA-binding protein. Secondary structural investigations found that the alpha helix was prevalent. The study determined its three-dimensional (3D) structure through homology modeling by the SWISS-MODEL server and verified it using quality evaluation tools such as PROCHECK, QMEAN, ERRAT, and ProSA. The findings lay the groundwork for potential antibacterial treatments, highlighting the importance of understanding the structure and function of specific proteins in Streptococcus mitis.
Keywords: Functional annotation, hypothetical protein, in silico characterization, Streptococcus mitis, three-dimensional structure
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