Structural Basis for Antibody Catalysis of a Cationic Cyclization Reaction

Zhu, Xueyong; Heine, A.; Monnat, Frédéric; Houk, K. N.; Janda, Kim D.; Wilson, Ian A.

doi:10.1016/s0022-2836(03)00406-6

Cited by 22 publications

(28 citation statements)

References 56 publications

Supporting

Mentioning

Contrasting

Unclassified

Order By: Relevance

“…Purified 4C6 Fab (200 l, 26 mg͞ml in 0.1 M sodium-acetate buffer, pH 5.5) was irradiated on a transilluminator with UV light (312 nm, 0.8 mW⅐cm Ϫ2 ) for 30 min. Crystals of the UV-irradiated 4C6 Fab were grown as described (8). A data set (2.51-Å resolution) was collected from a single crystal of the UV-irradiated 4C6 Fab by using 25% glycerol as a cryoprotectant.…”

Section: Methodsmentioning

confidence: 99%

See 1 more Smart Citation

Evidence for the production of trioxygen species during antibody-catalyzed chemical modification of antigens

Wentworth

Zhu

et al. 2003

Proc. Natl. Acad. Sci. U.S.A.

Self Cite

115

View full text Add to dashboard Cite

Recent work in our laboratory showed that products formed by the antibody-catalyzed water-oxidation pathway can kill bacteria. Dihydrogen peroxide, the end product of this pathway, was found to be necessary, but not sufficient, for the observed efficiency of bacterial killing. The search for further bactericidal agents that might be formed along the pathway led to the recognition of an oxidant that, in its interaction with chemical probes, showed the chemical signature of ozone. Here we report that the antibodycatalyzed water-oxidation process is capable of regioselectively converting antibody-bound benzoic acid into para-hydroxy benzoic acid as well as regioselectively hydroxylating the 4-position of the phenyl ring of a single tryptophan residue located in the antibody molecule. We view the occurrence of these highly selective chemical reactions as evidence for the formation of a shortlived hydroxylating radical species within the antibody molecule. In line with our previously presented hypothesis according to which the singlet-oxygen ( 1 O* 2) induced antibody-catalyzed wateroxidation pathways proceeds via the formation of dihydrogen trioxide (H 2O3), we now consider the possibility that the hydroxylating species might be the hydrotrioxy radical HO 3• , and we point to the remarkable potential of this either H 2O3-or O3-derivable species to act as a masked hydroxyl radical (HO • ) in a biological environment.

show abstract

Section: Methodsmentioning

confidence: 99%

“…The data were integrated and scaled by using HKL2000 (9). The structure of the UV-irradiated 4C6 Fab was determined by standard refinement with the program CNS (10), starting from the refined native 4C6 Fab crystal structure (8). Trp L163 was refined as an alanine residue to avoid potential bias in the electron-density maps.…”

Section: Methodsmentioning

confidence: 99%

Evidence for the production of trioxygen species during antibody-catalyzed chemical modification of antigens

Wentworth

Zhu

et al. 2003

Proc. Natl. Acad. Sci. U.S.A.

Self Cite

115

View full text Add to dashboard Cite

show abstract

“…Data were indexed, integrated, and scaled with the HKL2000 package (34). The original PFA2 triclinic apo structure was solved by molecular replacement, using the constant (CLϩCH1) and variable portions of FAB4C6 (PDB ID code 1NCW) separately (35). Protein rebuilding, including water-picking, was performed in Coot (36); refinement was conducted with Refmac5 (37).…”

Section: Chap 9)mentioning

confidence: 99%

Molecular basis for passive immunotherapy of Alzheimer's disease

Gardberg

Dice

et al. 2007

Proc. Natl. Acad. Sci. U.S.A.

136

View full text Add to dashboard Cite

Amyloid aggregates of the amyloid-␤ (A␤) peptide are implicated in the pathology of Alzheimer's disease. Anti-A␤ monoclonal antibodies (mAbs) have been shown to reduce amyloid plaques in vitro and in animal studies. Consequently, passive immunization is being considered for treating Alzheimer's, and anti-A␤ mAbs are now in phase II trials. We report the isolation of two mAbs (PFA1 and PFA2) that recognize A␤ monomers, protofibrils, and fibrils and the structures of their antigen binding fragments (Fabs) in complex with the A␤(1-8) peptide DAEFRHDS. The immunodominant EFRHD sequence forms salt bridges, hydrogen bonds, and hydrophobic contacts, including interactions with a striking WWDDD motif of the antigen binding fragments. We also show that a similar sequence (AKFRHD) derived from the human protein GRIP1 is able to cross-react with both PFA1 and PFA2 and, when cocrystallized with PFA1, binds in an identical conformation to A␤(1-8). Because such cross-reactivity has implications for potential side effects of immunotherapy, our structures provide a template for designing derivative mAbs that target A␤ with improved specificity and higher affinity.amyloid ͉ crystal structure ͉ EFRH ͉ monoclonal antibody ͉ EFRHD

show abstract

“…In three catalysts, an aromatic side chain flips into the binding pocket as in 34E4, occupying or partly overlapping with the substrate-binding site. In antibody 4C6, which catalyzes a cationic cyclization reaction, the Trp L89 indole regulates ligand binding in this way (41). In antibodies CNJ206 (42,43) and 5C8 (44), which promote an esterolytic reaction and a disfavored cyclization of trans-epoxy alcohols, respectively, the mobile residue is a tyrosine.…”

Section: Discussionmentioning

confidence: 99%

Conformational Isomerism Can Limit Antibody Catalysis

Debler

Müller

Hilvert

et al. 2008

Journal of Biological Chemistry

Self Cite

View full text Add to dashboard Cite

Ligand binding to enzymes and antibodies is often accompanied by protein conformational changes. Although such structural adjustments may be conducive to enzyme catalysis, much less is known about their effect on reactions promoted by engineered catalytic antibodies. Crystallographic and pre-steady state kinetic analyses of antibody 34E4, which efficiently promotes the conversion of benzisoxazoles to salicylonitriles, show that the resting catalyst adopts two interconverting active-site conformations, only one of which is competent to bind substrate. In the predominant isomer, the indole side chain of Trp L91 occupies the binding site and blocks ligand access. Slow conformational isomerization of this residue, on the same time scale as catalytic turnover, creates a deep and narrow binding site that can accommodate substrate and promote proton transfer using Glu H50 as a carboxylate base. Although 34E4 is among the best catalysts for the deprotonation of benzisoxazoles, its efficiency appears to be significantly limited by this conformational plasticity of its active site. Future efforts to improve this antibody might profitably focus on stabilizing the active conformation of the catalyst. Analogous strategies may also be relevant to other engineered proteins that are limited by an unfavorable conformational pre-equilibrium.

show abstract

Structural Basis for Antibody Catalysis of a Cationic Cyclization Reaction

Cited by 22 publications

References 56 publications

Evidence for the production of trioxygen species during antibody-catalyzed chemical modification of antigens

Evidence for the production of trioxygen species during antibody-catalyzed chemical modification of antigens

Molecular basis for passive immunotherapy of Alzheimer's disease

Conformational Isomerism Can Limit Antibody Catalysis

Contact Info

Product

Resources

About