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Structural and Physical Basis for Anti-IgE Therapy.

Wright JD, Chu HM, Huang CH, Ma C, Chang TW, Lim C - Sci Rep (2015)

Bottom Line: Mutagenesis studies indicate overlapping FcεRI and omalizumab-binding sites in the Cε3 domain, but crystallographic studies show FcεRI and CD23-binding sites that are far apart, so how can omalizumab block IgE from binding both receptors?These results provide a structural and physical basis as to why omalizumab cannot bind receptor-bound IgE and why omalizumab-bound IgE cannot bind to CD23/FcεRI.They reveal the key IgE residues and their roles in binding omalizumab, CD23, and FcεRI.

View Article: PubMed Central - PubMed

Affiliation: 1] Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan [2] The Genomics Research Center, Academia Sinica 115, Taiwan.

ABSTRACT
Omalizumab, an anti-IgE antibody, used to treat severe allergic asthma and chronic idiopathic urticaria, binds to IgE in blood or membrane-bound on B lymphocytes but not to IgE bound to its high (FcεRI) or low (CD23) affinity receptor. Mutagenesis studies indicate overlapping FcεRI and omalizumab-binding sites in the Cε3 domain, but crystallographic studies show FcεRI and CD23-binding sites that are far apart, so how can omalizumab block IgE from binding both receptors? We report a 2.42-Å omalizumab-Fab structure, a docked IgE-Fc/omalizumab-Fab structure consistent with available experimental data, and the free energy contributions of IgE residues to binding omalizumab, CD23, and FcεRI. These results provide a structural and physical basis as to why omalizumab cannot bind receptor-bound IgE and why omalizumab-bound IgE cannot bind to CD23/FcεRI. They reveal the key IgE residues and their roles in binding omalizumab, CD23, and FcεRI.

No MeSH data available.


Related in: MedlinePlus

Two omalizumab molecules bind to IgE in an extended Cε2 conformation with the Cε3-Cε4 dimer in a closed or open conformation.(a) The Cε2 domains in the free IgE structure clashes with the second omalizumab-Fv domain after superposition of each Cε3 domain (blue) from the 1:2 IgE-Fc/omalizumab-Fv complex onto that from the free IgE structure (PDB 2wqr) and displaying only omalizumab-Fv. (b) Both omalizumab-Fv domains exhibit no clashes with IgE after one of the Cε3 domains from the 1:2 IgE-Fc/omalizumab-Fv complex is superimposed onto the closed Cε3 conformation of chain A in PDB 2wqr, whereas the other Cε3 domain is superimposed onto the open Cε3 conformation of chain B; only omalizumab-Fv and the Cε2 domains in the omalizumab–Fab/IgE-Fc complex are displayed, while the Cε2 domains in the free structure are hidden.
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f6: Two omalizumab molecules bind to IgE in an extended Cε2 conformation with the Cε3-Cε4 dimer in a closed or open conformation.(a) The Cε2 domains in the free IgE structure clashes with the second omalizumab-Fv domain after superposition of each Cε3 domain (blue) from the 1:2 IgE-Fc/omalizumab-Fv complex onto that from the free IgE structure (PDB 2wqr) and displaying only omalizumab-Fv. (b) Both omalizumab-Fv domains exhibit no clashes with IgE after one of the Cε3 domains from the 1:2 IgE-Fc/omalizumab-Fv complex is superimposed onto the closed Cε3 conformation of chain A in PDB 2wqr, whereas the other Cε3 domain is superimposed onto the open Cε3 conformation of chain B; only omalizumab-Fv and the Cε2 domains in the omalizumab–Fab/IgE-Fc complex are displayed, while the Cε2 domains in the free structure are hidden.

Mentions: The IgE/omalizumab-Fab complex structure indicates that (i) the Cε2 domains have to move away from the bent conformation in the free IgE structure to unmask the second omalizumab-binding site and (ii) omalizumab could bind to both open and closed conformations of Cε3-4 domains. Free IgE-Fc in solution is predominantly bent with the Cε2 domains folded back onto the Cε3-4 domain of one chain363738 (Fig. 2, bottom left), but the Cε2 domains can flip to the other Cε3-4 domain, forming another bent conformation via transiently extended conformations20 (Fig. 2, bottom right). Free IgE-Fc with predominantly bent or transiently extended Cε2 conformations can bind a single omalizumab (Fig. 6). However, if the IgE-Fc were to remain bent after binding one omalizumab, then the Cε2 domain, which packs against the Cε3 domain, would obstruct binding of a second omalizumab, in conflict with the experimentally observed 1:2 IgE/omalizumab complex1133. This is evident in Fig. 6a, where the Cε3 domains in the 1:2 IgE-Fc/omalizumab-Fv complex in Fig. 4a are superimposed onto those in the free IgE crystal structure (PDB 2 wqr). This superposition also shows that omalizumab can bind to both closed and open conformations of the Cε3-4 domains, as long as the Cε2 domains are in an upright position: The two omalizumabs exhibit no clashes with IgE after the Cε3 domains from the 1:1 IgE-Fc/omalizumab-Fv complex were separately superimposed onto the closed and open Cε3-4 conformations of the 2 wqr structure (Fig. 6b).


Structural and Physical Basis for Anti-IgE Therapy.

Wright JD, Chu HM, Huang CH, Ma C, Chang TW, Lim C - Sci Rep (2015)

Two omalizumab molecules bind to IgE in an extended Cε2 conformation with the Cε3-Cε4 dimer in a closed or open conformation.(a) The Cε2 domains in the free IgE structure clashes with the second omalizumab-Fv domain after superposition of each Cε3 domain (blue) from the 1:2 IgE-Fc/omalizumab-Fv complex onto that from the free IgE structure (PDB 2wqr) and displaying only omalizumab-Fv. (b) Both omalizumab-Fv domains exhibit no clashes with IgE after one of the Cε3 domains from the 1:2 IgE-Fc/omalizumab-Fv complex is superimposed onto the closed Cε3 conformation of chain A in PDB 2wqr, whereas the other Cε3 domain is superimposed onto the open Cε3 conformation of chain B; only omalizumab-Fv and the Cε2 domains in the omalizumab–Fab/IgE-Fc complex are displayed, while the Cε2 domains in the free structure are hidden.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4481376&req=5

f6: Two omalizumab molecules bind to IgE in an extended Cε2 conformation with the Cε3-Cε4 dimer in a closed or open conformation.(a) The Cε2 domains in the free IgE structure clashes with the second omalizumab-Fv domain after superposition of each Cε3 domain (blue) from the 1:2 IgE-Fc/omalizumab-Fv complex onto that from the free IgE structure (PDB 2wqr) and displaying only omalizumab-Fv. (b) Both omalizumab-Fv domains exhibit no clashes with IgE after one of the Cε3 domains from the 1:2 IgE-Fc/omalizumab-Fv complex is superimposed onto the closed Cε3 conformation of chain A in PDB 2wqr, whereas the other Cε3 domain is superimposed onto the open Cε3 conformation of chain B; only omalizumab-Fv and the Cε2 domains in the omalizumab–Fab/IgE-Fc complex are displayed, while the Cε2 domains in the free structure are hidden.
Mentions: The IgE/omalizumab-Fab complex structure indicates that (i) the Cε2 domains have to move away from the bent conformation in the free IgE structure to unmask the second omalizumab-binding site and (ii) omalizumab could bind to both open and closed conformations of Cε3-4 domains. Free IgE-Fc in solution is predominantly bent with the Cε2 domains folded back onto the Cε3-4 domain of one chain363738 (Fig. 2, bottom left), but the Cε2 domains can flip to the other Cε3-4 domain, forming another bent conformation via transiently extended conformations20 (Fig. 2, bottom right). Free IgE-Fc with predominantly bent or transiently extended Cε2 conformations can bind a single omalizumab (Fig. 6). However, if the IgE-Fc were to remain bent after binding one omalizumab, then the Cε2 domain, which packs against the Cε3 domain, would obstruct binding of a second omalizumab, in conflict with the experimentally observed 1:2 IgE/omalizumab complex1133. This is evident in Fig. 6a, where the Cε3 domains in the 1:2 IgE-Fc/omalizumab-Fv complex in Fig. 4a are superimposed onto those in the free IgE crystal structure (PDB 2 wqr). This superposition also shows that omalizumab can bind to both closed and open conformations of the Cε3-4 domains, as long as the Cε2 domains are in an upright position: The two omalizumabs exhibit no clashes with IgE after the Cε3 domains from the 1:1 IgE-Fc/omalizumab-Fv complex were separately superimposed onto the closed and open Cε3-4 conformations of the 2 wqr structure (Fig. 6b).

Bottom Line: Mutagenesis studies indicate overlapping FcεRI and omalizumab-binding sites in the Cε3 domain, but crystallographic studies show FcεRI and CD23-binding sites that are far apart, so how can omalizumab block IgE from binding both receptors?These results provide a structural and physical basis as to why omalizumab cannot bind receptor-bound IgE and why omalizumab-bound IgE cannot bind to CD23/FcεRI.They reveal the key IgE residues and their roles in binding omalizumab, CD23, and FcεRI.

View Article: PubMed Central - PubMed

Affiliation: 1] Institute of Biomedical Sciences, Academia Sinica, Taipei 115, Taiwan [2] The Genomics Research Center, Academia Sinica 115, Taiwan.

ABSTRACT
Omalizumab, an anti-IgE antibody, used to treat severe allergic asthma and chronic idiopathic urticaria, binds to IgE in blood or membrane-bound on B lymphocytes but not to IgE bound to its high (FcεRI) or low (CD23) affinity receptor. Mutagenesis studies indicate overlapping FcεRI and omalizumab-binding sites in the Cε3 domain, but crystallographic studies show FcεRI and CD23-binding sites that are far apart, so how can omalizumab block IgE from binding both receptors? We report a 2.42-Å omalizumab-Fab structure, a docked IgE-Fc/omalizumab-Fab structure consistent with available experimental data, and the free energy contributions of IgE residues to binding omalizumab, CD23, and FcεRI. These results provide a structural and physical basis as to why omalizumab cannot bind receptor-bound IgE and why omalizumab-bound IgE cannot bind to CD23/FcεRI. They reveal the key IgE residues and their roles in binding omalizumab, CD23, and FcεRI.

No MeSH data available.


Related in: MedlinePlus