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OJBTM

 Online Journal of Bioinformatics 

 Volume 12(2):289-303, 2011.


Toxicity of  butachlor assessed by molecular docking to NusB and GroES protein.

 

Kumari N1 MSc, Singh VK2 MSc, Narayan OP1 MSc, Rai LC1 PhD.

 

1Molecular Biology Section, 2Centre for Bioinformatics, Centre of Advanced Study in Botany, Banaras Hindu University, Varanasi, India

 

ABSTRACT

 

Kumari N, Singh VK, Narayan OP, Rai LC., Toxicity of  butachlor assesssed by molecular docking with NusB and GroES protein, Onl J Bioinform., 12(2):289-303, 2011. Proteomic analysis of butachlor treated Aulosira fertilissima vividly demonstrated that up regulation of NusB and down regulation of GroES proteins was primarily responsible for cell death. A mechanism for butachlor toxicity on NusB and GroES was assessed using molecular docking, CDD and STRING database. Homology modeling revealed the 3-D structure of NusB and GroES receptor molecules. After energy minimization and validation of 3-D model, Molegro Virtual Docker program was used for docking butachlor (as ligand) with NusB and GroES separately. The Q-site finder revealed that butachlor docking takes place on fifteen and eleven amino acid residues in NusB and GroES respectively. The docking model predicted binding of butachlor molecules on to 72Arg, 73Ala, 74Ser and 81Asn which flank putative RNA binding site 76Leu and 80Arg of NusB. While these residues encircle the NusB RNA binding site, the hydrophobic interactions at conserved residues 178Glu, 180Val, 181Glu, 184Lys and 185Arg may cause toxicity. Likewise the GroES polypeptide binding site at 83Val is occupied by butachlor, other conserved residues at 21Lys, 42Lys and 43Pro of this protein also interacted with butachlor simultaneously thereby hindering the normal functions of GroES. In view of the STRING database predicted interactions of NusB and GroES with elongation factor P, riboflavin synthase, chaperonin GroEL, dnaK2, ATP synthase and other proteins and butachlor docking, the cellular proteins networking may be disturbed leading to the failure of cell survival.

 

Key words: Butachlor; NusB protein; molecular docking; Conserved Domain Database.


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