CFP last date
20 June 2024
Call for Paper
July Edition
IJCA solicits high quality original research papers for the upcoming July edition of the journal. The last date of research paper submission is 20 June 2024

Submit your paper
Know more
Reseach Article

In silico Structural Analysis and Binding of Organophosphorus hydrolase of Kocuria sp with Chloropyrifos

by Nagavardhanam Neti, Vishnuvardhan Zakkula
International Journal of Computer Applications
Foundation of Computer Science (FCS), NY, USA
Volume 66 - Number 5
Year of Publication: 2013
Authors: Nagavardhanam Neti, Vishnuvardhan Zakkula
10.5120/11078-6015

Nagavardhanam Neti, Vishnuvardhan Zakkula . In silico Structural Analysis and Binding of Organophosphorus hydrolase of Kocuria sp with Chloropyrifos. International Journal of Computer Applications. 66, 5 ( March 2013), 7-12. DOI=10.5120/11078-6015

@article{ 10.5120/11078-6015,
author = { Nagavardhanam Neti, Vishnuvardhan Zakkula },
title = { In silico Structural Analysis and Binding of Organophosphorus hydrolase of Kocuria sp with Chloropyrifos },
journal = { International Journal of Computer Applications },
issue_date = { March 2013 },
volume = { 66 },
number = { 5 },
month = { March },
year = { 2013 },
issn = { 0975-8887 },
pages = { 7-12 },
numpages = {9},
url = { https://ijcaonline.org/archives/volume66/number5/11078-6015/ },
doi = { 10.5120/11078-6015 },
publisher = {Foundation of Computer Science (FCS), NY, USA},
address = {New York, USA}
}
%0 Journal Article
%1 2024-02-06T21:21:31.840137+05:30
%A Nagavardhanam Neti
%A Vishnuvardhan Zakkula
%T In silico Structural Analysis and Binding of Organophosphorus hydrolase of Kocuria sp with Chloropyrifos
%J International Journal of Computer Applications
%@ 0975-8887
%V 66
%N 5
%P 7-12
%D 2013
%I Foundation of Computer Science (FCS), NY, USA
Abstract

The most popular type of pesticide is the organophosphate (OP) family, which effectively eliminates pests owing to its acute neurotoxicity. Organophosphorus hydrolase is a bacterial enzyme that is capable of degrading a wide range of neurotoxic organophosphate nerve agents. Organophosphorus hydrolase of Kocuria sp was isolated but its protein is not having any predicted 3-Dimentional structure available in PDB (Protein databank) as elucidated by X-ray crystallography or NMR. Its structure was determined in silico by sequence homology. The gene sequence of the Organophosphorus hydrolase of Kocuria sp was known and its protein sequence was subjected to PSI-BLAST at NCBI. There was neither identical sequence available nor the nearest neighbour in the blast analysis. Then an alternative method for finding the homologous protein i. e. , fold prediction method was used. The generated model was subjected to several repeated cycles of energy minimization using SPDBV software and the final model was subjected to stereo chemical evaluation. The homology modeled structure of the Organophosphorus hydrolase of Kocuria sp was docked by different OP by Molgro virtual docker and the data were presented.

References
  1. Kurzel RB and Certrulo CL. (1981). The effect of environmental pollutants on human reproduction, including birth defects. Environ. Sci. Technol. 15: 626-631.
  2. Akhtar S nd Ahmed A. (2002). Pesticides human health and ecosystem. J. Baqai. Med. Univ. 5(2): 16-19.
  3. Sogorb MA and Vilanova E. (2002). Enzymes involved in the detoxification of organophosphorus, carbamate and pyrethroid insecticides through hydrolysis. Toxicology Letters. 128: 215-228.
  4. Qiao CL, Yan YC, Shang HY, Zhou XT, Zhang Y (2003). Biodegradation of pesticides by immobilized recombinant Escherichia coli. Bull. Environ. Contam. Toxicol. 71: 370-374.
  5. Murray RT, Vonstein C, Kennedy IR, Sanchez-Bayo F. (2001). Stability of chlorpyrifos for termiticidal control in six Australian soils. J. Agric. Food Chem. 49: 2844-2847.
  6. Swathi and Singh DK. (2002). Utilization of chlorpyrifos by Aspergillus niger and A. flavus as carbon and phosphorus source. 17th World Congress of soil science. Bangkok, Thailand. 14-21.
  7. Thomas K and Nicholson BC. (1989). Pesticide losses in runoff from a horticultural catchment in South Australia and their relevance to stream and reservoir water quality. Environ. Technol. Lett. 10: 117-129.
  8. Richards RP and Baker DB (1993). Pesticide concentration patterns in agricultural drainage networks in the lake Erie basin. Environ. Toxicol. Chem. 12:13-26.
  9. Giesy JP, Solomon KR, Coats JR, Dixon KR, Giddings JM, Kenaga EE (1999). Chlorpyrifos: Ecological risk assessment in North American aquatic environments. Rev. Environ. Contam. Toxicol. 160: 1-129.
  10. Ragnarsdottir KV. (2000). Environmental fate and toxicology of organophosphate pesticides. J. Geological Soc. 157: 859-876.
  11. Wood B and Stark JD. (2002). Acute toxicity of drainage ditch water from a Washington state cranberry-growing region to Daphnia pulex in laboratory bioassays. Ecotoxicol. Environ. Safety. 53: 273-280.
  12. Galloway T and Handy R. (2003). Immunotoxicity of organophosphorous pesticides. Ecotoxicology. 12: 345-363.
  13. Shelton DR and Doherty MA. (1997). A model describing pesticide bio availability and biodegradation in soil. Soc. Soil Sci. Am. J. 61: 1078-1084.
  14. www. expasy. org/prosite
  15. Guex N and Peitsch MC. (1997). SWISS-MODEL and the Swiss-PdbViewer: an environment for comparative protein modeling. Electrophoresis, 18(15):2714-23.
  16. Thomsen R, Christensen MH. (2006) MolDock: a new technique for highaccuracy molecular docking. J Med Chem 49: 3315-3321.
  17. Gasteiger E, Hoogland C, Gattiker A, Duvaud S, Wilkins MR, Appel RD, Bairoch A. (2005). Protein Identification and Analysis Tools on the ExPASy Server; (In) John M. Walker (ed): The Proteomics Protocols Handbook, Humana Press. 571-607
  18. Geourjon C and Deleage G. (1995). SOPMA: significant improvements in protein secondary structure prediction by consensus prediction from multiple alignments. Comput Appl Biosci, 11(6):681-4.
  19. Sigrist CJA, Cerutti L, Hulo N, Gattiker A, Falquet L, Pagni M, Bairoch A, Bucher P. (2002). PROSITE: a documented database using patterns and profiles as motif descriptors. Brief Bioinform. 3:265-274.
  20. Sali A, Blundell TL. (1993). Comparative protein modelling by satisfaction of spatial restraints. J Mol Biol. 234(3):779-815.
Index Terms

Computer Science
Information Sciences

Keywords

Chloropyrifos Organophosphorus hydrolase SPDBV Molegro Virtual Docker