title: Evidence for the extended helical nature of polysaccharide epitopes. The 2.8 A resolution structure and thermodynamics of ligand binding of an antigen binding fragment specific for alpha-(2-->8)-polysialic acid.
abstract: The antigen binding fragment from an IgG2a kappa murine monoclonal antibody with specificity for alpha-(2-->8)-linked sialic acid polymers has been prepared and crystallized in the absence of hapten. Crystals were grown by vapor diffusion equilibrium with 16-18% polyethylene glycol 4000 solutions. The structure was solved by molecular replacement methods and refined to a conventional R factor of 0.164 for data to 2.8 A. The binding site is observed to display a shape and distribution of charges that is complementary to that of the predicted conformation of the oligosaccharide epitope. A thermodynamic description of ligand binding has been compiled for oligosaccharides ranging in length from 9 to 41 residues, and the data for the largest ligand has been used in a novel way to estimate the size of the antigen binding site. A model of antigen binding is presented that satisfies this thermodynamic data, as well as a previously reported requirement of conformational specificity of the oligosaccharide. X-ray crystallographic and thermodynamic evidence are consistent with a binding site that accommodates at least eight sialic acid residues.
authors.affiliation: Institute for Biological Sciences, National Research Council of Canada, Ottawa.
authors.forename: S V
authors.initials: SV
authors.lastname: Evans
authors.forename: B W
authors.initials: BW
authors.lastname: Sigurskjold
authors.forename: H J
authors.initials: HJ
authors.lastname: Jennings
authors.forename: J R
authors.initials: JR
authors.lastname: Brisson
authors.forename: R
authors.initials: R
authors.lastname: To
authors.forename: W C
authors.initials: WC
authors.lastname: Tse
authors.forename: E
authors.initials: E
authors.lastname: Altman
authors.forename: M
authors.initials: M
authors.lastname: Frosch
authors.forename: C
authors.initials: C
authors.lastname: Weisgerber
authors.forename: H D
authors.initials: HD
authors.lastname: Kratzin
mesh_terms: D000911:Antibodies, Monoclonal / Q000737:chemistry* / Q000378:metabolism; D001666:Binding Sites, Antibody; D003460:Crystallization; D018360:Crystallography, X-Ray; D000939:Epitopes / Q000737:chemistry* / Q000276:immunology; D006241:Haptens / Q000737:chemistry; D007140:Immunoglobulin Fab Fragments / Q000737:chemistry / Q000378:metabolism; D007074:Immunoglobulin G / Q000737:chemistry / Q000378:metabolism; D046911:Macromolecular Substances; D008958:Models, Molecular; D010446:Peptide Fragments / Q000737:chemistry*; D017433:Protein Structure, Secondary; D012794:Sialic Acids / Q000737:chemistry / Q000276:immunology*; D013816:Thermodynamics
chemical_list: D000911:Antibodies, Monoclonal; D000939:Epitopes; D006241:Haptens; D007140:Immunoglobulin Fab Fragments; D007074:Immunoglobulin G; D046911:Macromolecular Substances; D010446:Peptide Fragments; D012794:Sialic Acids; C021319:polysialic acid