Homology modeling of anti-parathion antibody and its interaction with organophosphorous pesticides and analogues.
The mechanism of specific recognition in pesticide immunochemistry was investigated by computer-based strategy, and a rapid method for the identification of antibody specificity was developed. Based on the previously produced anti-parathion monoclonal antibody (mAb), the DNA sequence was analyzed by polymerase chain reaction (PCR). From the translated amino acid sequences, a three-dimensional structure of the antibody was constructed by homology modeling method, and then it was coordinated by 1 ns molecular dynamics under the explicit solvent condition. The stereochemical property and folding quality were further assessed by Procheck and Profile-3D. The self-compatibility score for the antibody model was 98.7, which was greater than the low score 46.2 and close to the top score 102.6. In addition, parathion and several structural analogues were docked to the constructed antibody structure. The docking results showed that the interaction energy (-40.54 kcal/mol) of antibody-parathion complex was the lowest among all the tested pesticides, which accounted for the high specificity of the antibody to parathion and perfectly matched with the experimental data. Moreover, three residues, Phe165, Asp107 and Thr100 were recognized as the most important residues for antibody reacting with parathion. The interaction energy negatively correlated with the antibody specificity.
Liu
Yi H
YH
Institute of Pesticide and Environmental Toxicology, Zhejiang University, Hangzhou, China.
Guo
Yi R
YR
Wang
Chun M
CM
Gui
Wen J
WJ
Zhu
Guo N
GN
D000595:Amino Acid Sequence; D000906:Antibodies / Q000737:chemistry* / Q000235:genetics / Q000276:immunology; D000918:Antibody Specificity; D001665:Binding Sites; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009943:Organophosphorus Compounds / Q000737:chemistry*; D010278:Parathion / Q000737:chemistry* / Q000276:immunology; D010575:Pesticides / Q000737:chemistry* / Q000276:immunology; D011485:Protein Binding; D013329:Structure-Activity Relationship
D000906:Antibodies; D009943:Organophosphorus Compounds; D010575:Pesticides; D010278:Parathion