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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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