In:
Journal of Bioinformatics and Computational Biology, World Scientific Pub Co Pte Ltd, Vol. 08, No. 03 ( 2010-06), p. 471-483
Abstract:
Antibodies are responsible for antigen recognition in vertebrate organisms. Practically any molecule can be bound by antibodies. In this work structures of 73 complexes of antibodies with small antigens were taken from PDB database and compared. The main epitope of studied ligands was an aromatic ring. Antibodies bound it with a deep cavity, lying between complementary determining regions (CDR) H3 and L3 and formed by aromatic residues. In most cases the aromatic ring of ligand was placed parallel to one or two aromatic sidechains of binding site at 3.5-4 Angstrom distance. This disposition of aromatic rings is a sign of the presence of π-stacking. It was found that small ligands with aromatics area percentage 〉 36% predominantly form π-stacking interaction with antibodies. Most often this interaction was observed for residues in positions H33, H95, L32 and L93.
Type of Medium:
Online Resource
ISSN:
0219-7200
,
1757-6334
DOI:
10.1142/S0219720010004835
Language:
English
Publisher:
World Scientific Pub Co Pte Ltd
Publication Date:
2010
SSG:
12
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