Welcome to International Network for Natural Sciences | INNSpub

Paper Details

Research Paper | December 1, 2022

| Download 82

In silico identification of Shigella sonnei hypothetical protein RUK71877.1 as interleukin receptor mimic Protein A and a potential drug target

Foeaz Ahmed, Nadim Ahmed, Anindita Ash Prome, Tanjin Barketullah Robin, Nurul Amin Rani

Key Words:

Int. J. Biosci.21(6), 7-17, December 2022

DOI: http://dx.doi.org/10.12692/ijb/21.6.7-17


IJB 2022 [Generate Certificate]


Shigella spp. is strict human pathogens that cause shigellosis (bloody diarrhea) and are linked to a significant amount of morbidity and mortality worldwide. Shigella sonnei causes 90% of shigellosis cases and most of them became resistant to traditional antibiotics. The bacterial genome has been discovered, but there are some proteins whose function is not known. This in silico study was conducted to characterize the hypothetical protein RUK71877.1 of S. sonnei. Different bioinformatics web tools were utilized such as BLASTp, ProtParam, CELLO, Jalview etc. to determine the likely function of the hypothetical sequences by searching Sequence Databases for orthologous enzymatic conserved domains. Molecular modeling, energy minimization and docking analysis was evaluated to further validate our findings. In the study our target hypothetical protein RUK71877.1 showed highly similarity with IrmA Family protein. The protein is found to be outer-membrane and has an important role in Shigella sonnei pathogenicity. In NCBI-CD search the target protein was found to have functioned as interleukin receptor mimic protein A which also showed higher affinity with IL-4R in docking analysis. In silico drug development for the treatment of Shigellosis may use these newly predicted hypothetical proteins as potential drug targets in the future. It can also be utilized as target protein in vaccine construction. Our thorough investigation will contribute to identifying a vast range of therapeutic targets and a better knowledge of how to build unique possible treatment strategies to combat the Shigella infection.


Copyright © 2022
By Authors and International Network for
Natural Sciences (INNSPUB)
This article is published under the terms of the Creative
Commons Attribution Liscense 4.0

In silico identification of Shigella sonnei hypothetical protein RUK71877.1 as interleukin receptor mimic Protein A and a potential drug target

Colovos C, Yeates TO. 1993. Verification of protein structures: Patterns of non-bonded atomic interactions. Protein Science 2(9), 1511-1519.

Combet C, Blanchet C, Geourjon C, Deleage G. 2000. NPS@: Network protein sequence analysis. Trends in biochemical sciences 25(3), 147-150.

Galperin MY, Koonin EV. 2004. ‘Conserved hypothetical proteins: Prioritization of targets for experimental study. Nucleic Acids Research   32(18), 5452-5463.

Gasteiger E, Hoogland C, Gattiker A, Wilkins MR, Appel RD, Bairoch A. 2005. Protein identification and analysis tools on the ExPASy server. The Proteomics Protocols Handbook 571-607.

Hebditch M, Carballo-Amador MA, Charonis S, Curtis R, Warwicker J. 2017. Protein- Sol: A web tool for predicting protein solubility from sequence. Bioinformatics 33(19), 3098-3100.

Hirokawa T, Boon-Chieng S, Mitaku S. 1998. SOSUI: classification and secondary structure prediction system for membrane proteins. Bioinformatics (Oxford, England) 14(4), 378-379.

Huang SY, Zou X. 2014. A knowledge-based scoring function for protein-RNA interactions derived from a statistical mechanics-based iterative method. Nucleic Acids Research 42(7), e55-e55.

Islam MS, Shahik SM, Sohel M, Patwary NI, Hasan M A. 2015. In silico structural and functional annotation of hypothetical proteins of Vibrio cholerae O139. Genomics & informatics 13(2), 53.

Jones DT. 1999. Protein secondary structure prediction based on position-specific scoring matrices. Journal of Molecular Biology 292(2), 195-202.

Ko J, Park H, Heo L, Seok C. 2012. GalaxyWEB server for protein structure prediction and refinement. Nucleic Acids Research 40(W1), W294-W297.

Kotloff KL, Riddle MS, Platts-Mills JA, Pavlinac P, Zaidi AK. 2018. Shigellosis. The Lancet 391(10122), 801-812.

Land H, Humble MS. 2018. YASARA: a tool to obtain structural guidance in biocatalytic investigations. In Protein Engineering p. 43-67.

Laskowski RA, Rullmann JAC, MacArthur MW, Kaptein R, Thornton JM. 1996. AQUA and PROCHECK-NMR: programs for checking the quality of protein structures solved by NMR. Journal of Biomolecular NMR 8(4), 477-486.

Lu S, Wang J, Chitsaz F, Derbyshire MK, Geer RC, Gonzales NR, Gwadz M, Hurwitz DI, Marchler GH, Song JS. 2020. CDD/SPARCLE: The conserved domain database in 2020. Nucleic Acids Research 48(D1), D265-D268.

Lubec G, Afjehi-Sadat L, Yang J-W, John JPP. 2005. Searching for hypothetical proteins: Theory and practice based upon original data and literature. Progress in Neurobiology 77(1-2), 90-127.

Moriel DG, Heras B, Paxman JJ, Lo AW, Tan L, Sullivan MJ, Dando SJ, Beatson SA, Ulett GC, Schembri MA. 2016. Molecular and Structural Characterization of a Novel Escherichia coli Interleukin Receptor Mimic Protein. mBio 7(2), e02046.

Muthuirulandi Sethuvel D, Devanga Ragupathi N, Anandan S, Veeraraghavan B. 2017. Update on: Shigella new serogroups/serotypes and their antimicrobial resistance. Letters in Applied Microbiology 64(1), 8-18.

Niwa T, Ying B-W, Saito K, Jin W, Takada S, Ueda T, Taguchi H. 2009. Bimodal protein solubility distribution revealed by an aggregation analysis of the entire ensemble of Escherichia coli proteins. Proceedings of the National Academy of Sciences 106(11), 4201-4206.

Pearson WR, Lipman DJ. 1988. Improved tools for biological sequence comparison. Proceedings of the National Academy of Sciences 85(8), 2444-2448.

Rabbi MF, Akter SA, Hasan MJ, Amin A. 2021. In silico characterization of a hypothetical protein from Shigella dysenteriae ATCC 12039 Reveals a Pathogenesis-Related Protein of the Type-VI Secretion System. Bioinformatics and Biology Insights 15, 11779322211011140.

Singh V, Dhankhar P, Dalal V, Tomar S, Kumar P. 2022. In-silico functional and structural annotation of hypothetical protein from Klebsiella pneumonia: A potential drug target. Journal of Molecular Graphics and Modelling 116, 108262.

Thompson CN, Duy PT, Baker S. 2015. The rising dominance of Shigella sonnei: an intercontinental shift in the etiology of bacillary dysentery. PLoS neglected tropical diseases 9(6), e0003708.

Varma PBS, Adimulam YB, Kodukula S. 2015. In silico functional annotation of a hypothetical protein from Staphylococcus aureus. Journal of Infection and Public Health 8(6), 526-532.

Waterhouse A, Procter J, Martin D. 2009. a, Clamp M, Barton GJ. 2009. Jalview Version 680 2–a multiple sequence alignment editor and analysis workbench. Bioinformatics 25, 1189-1681.

Wiederstein M, Sippl MJ. 2007. ProSA-web: interactive web service for the recognition of errors in three-dimensional structures of proteins. Nucleic acids research 35(suppl_2), W407-W410.

Yan Y, Tao H, He J, Huang S-Y. 2020. The HDOCK server for integrated protein–protein docking. Nature protocols 15(5), 1829-1852.

Yu CS, Lin CJ, Hwang JK. 2004. Predicting subcellular localization of proteins for Gram‐negative bacteria by support vector machines based on n‐peptide compositions. Protein Science 13(5), 1402-1406.

Zheng W, Zhang C, Li Y, Pearce R, Bell EW, Zhang Y. 2021. Folding non-homologous proteins by coupling deep-learning contact maps with I-TASSER assembly simulations. Cell reports methods 1(3), 100014.


Style Switcher

Select Layout
Chose Color
Chose Pattren
Chose Background