title: Incorporation of long CDR3s into V domains: implications for the structural evolution of the antibody-combining site.
abstract: Available data suggest that 'primitive' antibody-combining sites often include longer than average HCDR3s. Long HCDR3 sequences have been reported in diverse vertebrates, including humans, cattle, camels and sharks. These long HCDR3 segments contain unusual sequence features such as stretches of Gly or Pro residues and multiple Cys residues. We examined how longer than average HCDR3s were accommodated in the V domains of human, murine and camel antibodies with known three-dimensional structures. The main conclusions were that (1) HCDR3s longer than 12 residues should protrude outward from the V domains; (2) descending HCDR3 polypeptides may utilize VL (including LCDR3) constituents as a platform, supporting the protruding segments; (3) intra- and inter-HCDR disulfides are frequently formed to rigidify the structure of HCDR3 or the combining site, and (4) V and C domains were possibly more similar in primordial antibodies than they are in their present day counterparts.
authors.affiliation: Crystallography Program, Oklahoma Medical Research Foundation, Oklahoma City, OK 73104, USA.
authors.forename: P A
authors.initials: PA
authors.lastname: Ramsland
authors.forename: A
authors.initials: A
authors.lastname: Kaushik
authors.forename: J J
authors.initials: JJ
authors.lastname: Marchalonis
authors.forename: A B
authors.initials: AB
authors.lastname: Edmundson
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D001666:Binding Sites, Antibody / Q000235:genetics*; D002162:Camelus; D022801:Complementarity Determining Regions / Q000737:chemistry* / Q000235:genetics*; D018360:Crystallography, X-Ray; D004220:Disulfides / Q000737:chemistry; D019143:Evolution, Molecular; D006801:Humans; D007127:Immunoglobulin Constant Regions / Q000737:chemistry / Q000235:genetics; D007128:Immunoglobulin Fragments / Q000737:chemistry / Q000235:genetics; D007075:Immunoglobulin M / Q000737:chemistry / Q000235:genetics; D007135:Immunoglobulin Variable Region / Q000737:chemistry* / Q000235:genetics*; D051379:Mice; D008958:Models, Molecular; D018716:Molecular Mimicry; D008969:Molecular Sequence Data; D011487:Protein Conformation; D017434:Protein Structure, Tertiary; D012754:Sharks
chemical_list: D022801:Complementarity Determining Regions; D004220:Disulfides; D007127:Immunoglobulin Constant Regions; D007128:Immunoglobulin Fragments; D007075:Immunoglobulin M; D007135:Immunoglobulin Variable Region