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

Interdisciplinary Sciences, Computational Life Sciences
Neelima AroraU S N Murty

Abstract

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.

References

May 1, 1992·Clinical Infectious Diseases : an Official Publication of the Infectious Diseases Society of America·M L BennishC Ronsmans
Oct 5, 1991·Journal of Molecular Biology·E J Milner-WhiteI A Anton
Jan 1, 1990·Critical Reviews in Biochemistry and Molecular Biology·R Bentley
Jan 20, 1988·Journal of Molecular Biology·D DreusickeG E Schulz
May 5, 1982·Journal of Molecular Biology·J Kyte, R F Doolittle
Dec 5, 1993·Journal of Molecular Biology·A Sali, T L Blundell
Jul 20, 1993·Journal of Molecular Biology·B Rost, C Sander
Sep 1, 1993·Protein Science : a Publication of the Protein Society·C Colovos, T O Yeates
May 23, 1996·Nature·R W HooftE E Abola
Jan 1, 1996·Methods in Enzymology·J GarnierB Robson
Feb 1, 1996·Journal of Molecular Graphics·W HumphreyK Schulten
Dec 1, 1995·Computer Applications in the Biosciences : CABIOS·C Geourjon, G Deléage
Nov 1, 1996·Protein Science : a Publication of the Protein Society·R D King, M J Sternberg
Jan 1, 1997·Clinical Infectious Diseases : an Official Publication of the Infectious Diseases Society of America·R B SackE H Khan
Jan 1, 1997·Methods in Enzymology·D EisenbergJ U Bowie
Feb 28, 1998·Biochimie·G DeléageC Geourjon
Jun 20, 1998·Journal of Molecular Biology·T KrellA J Lapthorn
Mar 1, 2000·Trends in Biochemical Sciences·C CombetG Deléage
Jun 26, 2003·Nucleic Acids Research·Rune LindingToby J Gibson
Nov 8, 2003·Structure·Rune LindingRobert B Russell
Mar 12, 2004·Annual Review of Plant Physiology and Plant Molecular Biology·Klaus M. Herrmann, Lisa M. Weaver
Nov 23, 2005·Bioinformatics·Konstantin ArnoldTorsten Schwede
Apr 18, 2006·Journal of Molecular Graphics & Modelling·Hong ZhouKwang S Kim
May 23, 2007·Nucleic Acids Research·Markus Wiederstein, Manfred J Sippl
Jun 15, 2007·Nucleic Acids Research·Takashi Ishida, Kengo Kinoshita
Dec 6, 2008·PLoS Genetics·Geoffrey FucileDinesh Christendat
Apr 30, 1998·The Journal of Physical Chemistry. B·A D MacKerellM Karplus

❮ Previous
Next ❯

Citations

Apr 18, 2012·Proceedings of the National Academy of Sciences of the United States of America·Aditya BarveAndreas Wagner

❮ Previous
Next ❯

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.