Structure and kinetics of a transient antibody binding intermediate reveal a kinetic discrimination mechanism in antigen recognition.
Induced fit is a predominant phenomenon in protein-ligand interactions, yet it is invariably attributed without establishing the existence, let alone the structure, of the initial, low-affinity encounter complex. We determined the crystal structure of the encounter complex on the pathway of ligand binding by IgE antibody SPE7. We show that this complex is formed by a wide range of ligands that initially bind with identical affinity. Nonspecific ligands rapidly dissociate, whereupon the antibody isomerizes to a nonbinding isomer. Specific ligand complexes, however, slowly isomerize to give a high-affinity complex. This isomerization involves backbone and side-chain rearrangements of up to 14 A and the formation of specific hydrogen bonds. The postbinding conformational switch, combined with the prebinding isomerization to an energetically favorable nonbinding isomer, results in a "kinetic discrimination" mechanism that mediates selective binding, by a factor of >10(3), between highly related ligands that initially bind with the same affinity. This model may apply to proteins that bind multiple ligands in a specific manner or other proteins that, although capable of binding many ligands, are activated by only a few.
James
Leo C
LC
Laboratory of Molecular Biology, Medical Research Council, Cambridge CB2 2HQ, United Kingdom. lcj@mrc-lmb.cam.ac.uk
Tawfik
Dan S
DS
D000873:Anthracenes / Q000737:chemistry; D000918:Antibody Specificity; D000941:Antigens / Q000737:chemistry* / Q000276:immunology*; D001665:Binding Sites; D018360:Crystallography, X-Ray; D006860:Hydrogen Bonding; D007073:Immunoglobulin E / Q000737:chemistry* / Q000276:immunology*; D007536:Isomerism; D007700:Kinetics; D008024:Ligands; D008958:Models, Molecular; D011485:Protein Binding; D020836:Protein Structure, Quaternary; D000095322:Anthrones
D000873:Anthracenes; D000941:Antigens; D007073:Immunoglobulin E; D008024:Ligands; C004522:anthrone; D000095322:Anthrones