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The three-dimensional structure of the complex between the Fab fragment of an anti-human rhinovirus neutralizing antibody (8F5) and a cross-reactive synthetic peptide from the viral capsid protein VP2 has been determined at 2.5 A resolution by crystallographic methods. The refinement is presently at an R factor of 0.18 and the antigen-binding site and viral peptide are well defined. The peptide antigen adopts a compact fold by two tight turns and interacts through hydrogen bonds, some with ionic character, and van der Waals contacts with antibody residues from the six hypervariable loops as well as several framework amino acids. The conformation adopted by the peptide is closely related to the corresponding region of the viral protein VP2 on the surface of human rhinovirus 1A whose three-dimensional structure is known. Implications for the cross-reactivity between peptides and the viral capsid are discussed. The peptide-antibody interactions, together with the analysis of mutant viruses that escape neutralization by 8F5 suggest two different mechanisms for viral escape. The comparison between the complexed and uncomplexed antibody structures shows important conformational rearrangements, especially in the hypervariable loops of the heavy chain. Thus, it constitutes a clear example of the 'induced fit' molecular recognition mechanism.

Type

Journal article

Journal

EMBO J

Publication Date

15/05/1994

Volume

13

Pages

2247 - 2256

Keywords

Amino Acid Sequence, Antibodies, Viral, Binding Sites, Antibody, Capsid, Capsid Proteins, Cross Reactions, Crystallography, X-Ray, Humans, Hydrogen Bonding, Immunoglobulin Fab Fragments, Models, Molecular, Molecular Sequence Data, Neutralization Tests, Peptide Fragments, Protein Binding, Protein Conformation, Rhinovirus