title: Induced pocket to accommodate the cell attachment Arg-Gly-Asp motif in a neutralizing antibody against foot-and-mouth-disease virus.
abstract: The three-dimensional structure of the Fab fragment of a neutralizing monoclonal antibody (SD6) elicited against foot-and-mouth disease virus (FMDV) has been determined at 2.5 A resolution and refined to a crystallography agreement R-factor of 0.186. The structure has been compared with that of the same Fab molecule complexes with a 15 amino acid peptide (A15) representing a major antigenic site of FMDV, and determined at 2.8 A resolution. The Fab quaternary structure, defined both by the elbow angle between modules and by the relative disposition of the light and heavy domains inside the modules, remains essentially unchanged. However, the comparison shows important conformational variations in the paratope, especially in the hypervariable loops of the heavy chain. The CDR-H3 loop has a peculiar amino acid sequence (RREDGGDEGF) with a high content of charged residues. Some of these Fab residues were fully reoriented upon complex formation. The reorientation resulted not only in an alteration of shape but also in an important redistribution of charges, providing multiple points of interaction with the A15 antigen and in particular with the cell attachment Arg-Gly-Asp motif in the peptide. Thus the recognition of A15 by SD6 represents an extreme example of the induced fit mechanism in antibody interactions. The electron density maps provide evidence that in the uncomplexed Fab structure some CDR residues show, with lower occupancy, the conformations found in the complex, suggesting that the rearrangements observed can have only minor energetic requirements.
authors.affiliation: Department of d'Enginyeria Química, Universitat Politècnica de Catalunya, Barcelona, Spain.
authors.forename: N
authors.initials: N
authors.lastname: Verdaguer
authors.forename: M G
authors.initials: MG
authors.lastname: Mateu
authors.forename: J
authors.initials: J
authors.lastname: Bravo
authors.forename: E
authors.initials: E
authors.lastname: Domingo
authors.forename: I
authors.initials: I
authors.lastname: Fita
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D000911:Antibodies, Monoclonal / Q000737:chemistry / Q000276:immunology; D000914:Antibodies, Viral / Q000737:chemistry* / Q000276:immunology; D000937:Antigen-Antibody Reactions; D000956:Antigens, Viral / Q000737:chemistry / Q000276:immunology; D005537:Aphthovirus / Q000276:immunology*; D001483:Base Sequence; D001666:Binding Sites, Antibody / Q000276:immunology; D018360:Crystallography, X-Ray; D004247:DNA; D007140:Immunoglobulin Fab Fragments / Q000737:chemistry* / Q000276:immunology; D008969:Molecular Sequence Data; D009500:Neutralization Tests; D009842:Oligopeptides / Q000276:immunology*; D011487:Protein Conformation
chemical_list: D000911:Antibodies, Monoclonal; D000914:Antibodies, Viral; D000956:Antigens, Viral; D007140:Immunoglobulin Fab Fragments; D009842:Oligopeptides; C047981:arginyl-glycyl-aspartic acid; D004247:DNA