In silico characterization of Shikimate Kinase of Shigella flexneri: A potential drug target

• Published in: Interdisciplinary sciences : computational life sciences Vol. 2; no. 3; pp. 280 - 290
• Main Authors: Arora, Neelima, Banerjee, Amit Kumar, Murty, U. S. N.
• Format: Journal Article
• Language: English
• Published: Springer International Association of Scientists in the Interdisciplinary Areas 01-09-2010; Springer Nature B.V
• Subjects: Biomedical and Life Sciences; Computational Biology/Bioinformatics; Computational Science and Engineering; Computer Appl. in Life Sciences; Cysteine - analysis; Disulfides - analysis; Dysentery, Bacillary - microbiology; E coli; Escherichia coli - enzymology; Health Sciences; Life Sciences; Mathematical and Computational Physics; Medicine; Models, Molecular; Phosphotransferases (Alcohol Group Acceptor) - chemistry; Protein Conformation; Shigella flexneri; Shigella flexneri - enzymology; Statistics for Life Sciences; Theoretical; Theoretical and Computational Chemistry; homology modeling; molecular modeling; Shikimate Kinase; Shigellosis; bioinformatics
• ISSN: 1913-2751; 1867-1462
• DOI: 10.1007/s12539-010-0012-2

Shigella flexneri is
a major pathogen responsible for Shigellosis causing massive morbidity among young population and imposes huge socio-economic burden. In this study, Shikimate Kinase (SK) from
S. flexneri
was characterized
in silico
and disordered regions were predicted. Motifs and domains were calculated using computational tools. A three dimensional model of Shikimate Kinase of
S.flexneri
was constructed using Shikimate Kinase of
E.coli
(PDBID: 1KAG_A) as template by comparative modeling approach. Molecular dynamics calculations were carried out to check the stable conformation embedded in water sphere with least RMSD possible. Perusal of backbone conformation of the modeled structure by PROCHECK revealed that more than 98% of the residues fell in the allowed regions and ERRAT results confirmed good quality of modeled structure. Active site and its important residues were predicted for the derived model. Disulphide bridges were estimated by computational method and most probable pattern of cysteine residues was found in the pairs 8–22. Results of this study will shed light on the structural aspects of Shikimate Kinase of
S. flexneri
and will aid in rational drug designing.