5ICY

Cetuximab Fab in complex with linear meditope

Summary for 5ICY

• Entry DOI: 10.2210/pdb5icy/pdb
• Related: 1YY8 4GW1 4GW5 4HBB 5ESQ 5ETU 5EUK 5F88 5FF6 5HPM 5HYQ 5I2I 5ICX 5ICZ 5ID0 5ID1
• Descriptor: Cetuximab Fab light chain, Cetuximab Fab heavy chain, Meditope, ... (5 entities in total)
• Functional Keywords: antibody, anti-egfr, immune system
• Biological source: MUS MUSCULUS, HOMO SAPIENS; More
• Total number of polymer chains: 6
• Total formula weight: 97538.41

Authors

Bzymek, K.P.,Williams, J.C. (deposition date: 2016-02-23, release date: 2016-06-15, Last modification date: 2023-09-27)

Primary citation

Bzymek, K.P.,Ma, Y.,Avery, K.A.,Horne, D.A.,Williams, J.C.
Cyclization strategies of meditopes: affinity and diffraction studies of meditope-Fab complexes.
Acta Crystallogr F Struct Biol Commun, 72:434-442, 2016

PubMed Abstract: Recently, a unique binding site for a cyclic 12-residue peptide was discovered within a cavity formed by the light and heavy chains of the cetuximab Fab domain. In order to better understand the interactions that drive this unique complex, a number of variants including the residues within the meditope peptide and the antibody, as well as the cyclization region of the meditope peptide, were created. Here, multiple crystal structures of meditope peptides incorporating different cyclization strategies bound to the central cavity of the cetuximab Fab domain are presented. The affinity of each cyclic derivative for the Fab was determined by surface plasmon resonance and correlated to structural differences. Overall, it was observed that the disulfide bond used to cyclize the peptide favorably packs against a hydrophobic `pocket' and that amidation and acetylation of the original disulfide meditope increased the overall affinity ∼2.3-fold. Conversely, replacing the terminal cysteines with serines and thus creating a linear peptide reduced the affinity over 50-fold, with much of this difference being reflected in a decrease in the on-rate. Other cyclization methods, including the formation of a lactam, reduced the affinity but not to the extent of the linear peptide. Collectively, the structural and kinetic data presented here indicate that small perturbations introduced by different cyclization strategies can significantly affect the affinity of the meditope-Fab complex.

PubMed: 27303895
DOI: 10.1107/S2053230X16007202

Experimental method

X-RAY DIFFRACTION (2.5 Å)