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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, Online J Bioinformatics, 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.