Modeling the antigen combining site of an anti‐dinitrophenyl antibody, ANO2

Abstract

A model structure has been constructed for a monoclonal anti-dinitrophenyl antibody. The antibody, AN02, has been sequenced and cloned (Anglister, J., Frey ) was used to model the six hypervariable loops that contain the antigen-combining site. All the possible conformations of the loop backbones were constructed and the best loop structures were selected using a combination of the CHARMM potential energy function and evaluation of the solvent-accessible surface area of the conformers. The order in which the loops were searched was carried out based on the relative locations of the loops with reference to the framework of the 6-barrel, namely, L2-Hl-L3-H2-H3-L1. The model structures thus obtained were compared to the high resolution X-ray structure (Briinger, A.T., Leahy, D.J., Hynes, T.R., & Fox, R.O., 1991, J. Mol. Bioi. 221, 239-256).Keywords: antibody modeling; canonical structures; conformational search; homology modeling; hypervariable loops Antibodies of the IgG class consist of heavy and light polypeptide chains linked by disulfide bonds and folded into independent @-sheet domains. The light chain is approximately 220 residues and contains a variable N-terminal domain (VL) and a constant C-terminal region. The heavy chain is made up of an N-terminal variable domain (VH) and three or four constant domains. The heavy chain can contain from 450 to 575 residues. The fragment containing the noncovalent dimer of VL and the VH domains is called the Fv. The VL and VH are each antiparallel @-barrels, and the contact between them forms an eightstranded @-barrel with four strands from each domain (Richardson, 1981;Novotny et al., 1983). In each variable region, three hypervariable loops are attached to a constant &sheet framework region (FR). The specificity ~ . .~

Modeling the Binding Sites of Anti-Hen Egg White Lysozyme Antibodies HyHEL-8 and HyHEL-26: An Insight into the Molecular Basis of Antibody Cross-Reactivity and Specificity

“…L3 has one homologous substitution (S93 VH N). CDRs with identical lengths and same critical residues assume canonical structures (Chothia and Lesk, 1987;Anchin et al, 1991;Bassolino-Klimas et al, 1992;Mas et al, 1992;Tanner et al, 1992;Orlandini et al, 1994;Tenette-Souaille and Smith, 1998;Tenette et al, 1996). Therefore the backbone conformations of CDRs L1, L2, L3, and H1 are assumed to be the same as that of the template.…”

“…The sequences of thousands of antibodies of the IgG class have been determined (Kabat et al, 1991). However, the three-dimensional structures of only a small subset of sequenced antibodies have been determined by x-ray crystallography, but several have been homology-modeled (Anchin et al, 1991;Bassolino-Klimas et al, 1992;Mas et al, 1992;Tanner et al, 1992;Barry et al, 1994;Orlandini et al, 1994;Tenette-Souaille and Smith, 1998;Tenette et al, 1996).…”

Drugs as Haptens, Antigens, and Immunogens

“…Further work confirmed that in addition to the effects of the parent compounds, nitrophenylated cells and proteins were also potent immunogens [23,24] , although this was cell type and protein dependent. Antibodies generated in response to DNP-and TNPmodified proteins and peptides have been well studied and appear to be heterogenous in specificity and affinity for DNP [25][26][27] , although most react both to the modified amino acids and modified peptides.…”