Antibody CDR H3 modeling rules: extension for the case of absence of Arg H94 and Asp H101.
The third complementary determining region of the immunoglobulin heavy chain (CDR H3) is one of the more difficult structures to model due to genetic reasons. However, the conformation of proximal to beta-framework ("torso") part of the CDR H3 is very predictable. Current "CDR's canonical classes" theory is based on identifying the key positions, H94 and H101. We can determine the CDR H3 "torso" structure if arginine or lysine is present in the H94 position and/or aspartic acid in the H101 position. We target the case characterized by the absence of key residues in both the H94 and H101 positions. There has not been discussion on this case in the literature. 51 CDR H3 structures of this nature are analyzed and we established new sequence-structure rules. These rules contribute to more accurate modeling of the antibody's structure.
Koliasnikov
Oleg V
OV
Chemistry Department Moscow State University, LenGory, Moscow, Russia, 119992, Russia. olkol@enz.chem.msu.ru.
Kiral
Miroslav O
MO
Grigorenko
Vitaly G
VG
Egorov
Alexey M
AM
D000595:Amino Acid Sequence; D019943:Amino Acid Substitution; D000906:Antibodies / Q000737:chemistry* / Q000276:immunology; D001120:Arginine / Q000737:chemistry / Q000276:immunology; D001224:Aspartic Acid / Q000737:chemistry / Q000276:immunology; D001665:Binding Sites; D003198:Computer Simulation; D016503:Drug Delivery Systems / Q000379:methods; D007143:Immunoglobulin Heavy Chains / Q000737:chemistry* / Q000276:immunology; D008956:Models, Chemical; D018448:Models, Immunological; D008958:Models, Molecular; D008969:Molecular Sequence Data; D016297:Mutagenesis, Site-Directed; D011485:Protein Binding; D016415:Sequence Alignment / Q000379:methods; D020539:Sequence Analysis, Protein / Q000379:methods*
D000906:Antibodies; D007143:Immunoglobulin Heavy Chains; D001224:Aspartic Acid; D001120:Arginine