title: The diversity of H3 loops determines the antigen-binding tendencies of antibody CDR loops.
abstract: Of the complementarity-determining regions (CDRs) of antibodies, H3 loops, with varying amino acid sequences and loop lengths, adopt particularly diverse loop conformations. The diversity of H3 conformations produces an array of antigen recognition patterns involving all the CDRs, in which the residue positions actually in contact with the antigen vary considerably. Therefore, for a deeper understanding of antigen recognition, it is necessary to relate the sequence and structural properties of each residue position in each CDR loop to its ability to bind antigens. In this study, we proposed a new method for characterizing the structural features of the CDR loops and obtained the antigen-binding ability of each residue position in each CDR loop. This analysis led to a simple set of rules for identifying probable antigen-binding residues. We also found that the diversity of H3 loop lengths and conformations affects the antigen-binding tendencies of all the CDR loops.
authors.affiliation: National Institutes of Biomedical Innovation, Health and Nutrition, 7-6-8 Saito-Asagi, Ibaraki, Osaka, 567-0085, Japan.
authors.forename: Yuko
authors.initials: Y
authors.lastname: Tsuchiya
authors.affiliation: National Institutes of Biomedical Innovation, Health and Nutrition, 7-6-8 Saito-Asagi, Ibaraki, Osaka, 567-0085, Japan.
authors.forename: Kenji
authors.initials: K
authors.lastname: Mizuguchi
mesh_terms: D000465:Algorithms; D000595:Amino Acid Sequence; D000906:Antibodies / Q000737:chemistry* / Q000378:metabolism*; D000941:Antigens / Q000378:metabolism; D022801:Complementarity Determining Regions / Q000737:chemistry* / Q000378:metabolism*; D018360:Crystallography, X-Ray; D008958:Models, Molecular; D011487:Protein Conformation
chemical_list: D000906:Antibodies; D000941:Antigens; D022801:Complementarity Determining Regions
keywords: antigen recognition by antibodies; antigen-binding tendency; diverse conformations of long H3 loops; diversity of CDR-H3; hydrogen bond networks