An in silico Approach for Structural and Functional Annotation of Salmonella enterica serovar typhimurium Hypothetical Protein R_27

Abstract

Typhoid fever is a major cause of illness in most developing countries, including Bangladesh. In quest of new potential drug against Typhoid fever, the current study was designed to elucidate structural and functional details of S. typhi hypothetical protein (HP) R_27. HP R_27 has the primary amino acid sequences available only. The structural annotation was determined by ProtParam, SOPMA, and CELLO. The three-dimensional (3D) structure of HP R_27 predicted through homology modeling by using Phyre2. The 3D structure then refined and verified by ModRefiner, PROCHECK, ERRAT, QMEAN. The functional annotation was also performed by InterProScan, SMART, Pfam, NCBI-CDD and found Phospholipase D-like and DNA repair activity. Multiple sequence alignment also supported the existence of PLD-like domain and DNA repair protein domain in the selected hypothetical protein sequences. Finally, the cavity of drug binding was also identified to assist further molecular docking study and potent inhibitor identification. This in silico approach can be further utilized in molecular drug design for other clinically significant pathogens.

Keywords

• Typhoid fever
• Hypothetical protein
• Homology modeling
• PLD-like activity