title: Positional ordering of reacting groups contributes significantly to the efficiency of proton transfer at an antibody active site.
abstract: Catalytic antibody 34E4 accelerates the conversion of benzisoxazoles to salicylonitriles with surprising efficiency, exploiting a carboxylate base with an elevated pKa for proton abstraction. Mutagenesis of this antibody, produced as a chimeric Fab, confirms the prediction of a homology model that GluH50 is the essential catalytic residue. Replacement of this residue by glutamine, alanine, or glycine reduces catalytic activity by more than 2.6 x 10(4)-fold. By comparing the chemical proficiencies of the parent antibody with the chemical proficiencies of acetate and the mutants, the effective concentration of the catalytic side chain was estimated to be >51 000 M. The 2.1 kcal/mol destabilization of the transition state observed when GluH50 is replaced by aspartate suggests that positional ordering imposed by the antibody active site contributes significantly to the efficiency of proton transfer. The observation that the GluH50Ala and GluH50Gly variants could not be chemically rescued by exogenous addition of high concentrations of formate or acetate further underscores the advantage the antibody derives from covalently fixing its base at the active site. Although medium effects also play an important role in 34E4, for example in enhancing the reactivity of the carboxylate side chain through desolvation, comparison of 34E4 with less proficient antibodies shows that positioning a carboxylate in a hydrophobic binding pocket alone is insufficient for efficient general base catalysis. Our results demonstrate that structural complementarity between the antibody and its substrate in the transition state is an important and necessary component of 34E4's high activity. By harnessing an additional catalytic group that could serve as a general acid to stabilize developing negative charge in the leaving group, overall efficiencies rivaling those of highly evolved enzymes should be accessible.
authors.affiliation: Laboratorium für Organische Chemie, Swiss Federal Institute of Technology, ETH Hönggerberg, CH-8093, Zürich, Switzerland.
authors.forename: Florian P
authors.initials: FP
authors.lastname: Seebeck
authors.forename: Donald
authors.initials: D
authors.lastname: Hilvert
mesh_terms: D000818:Animals; D017151:Antibodies, Catalytic / Q000096:biosynthesis / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D001665:Binding Sites; D004926:Escherichia coli / Q000235:genetics / Q000276:immunology; D006801:Humans; D006863:Hydrogen-Ion Concentration; D007128:Immunoglobulin Fragments / Q000096:biosynthesis / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D007555:Isoxazoles / Q000737:chemistry / Q000378:metabolism; D007700:Kinetics; D051379:Mice; D016297:Mutagenesis, Site-Directed; D009570:Nitriles / Q000737:chemistry / Q000378:metabolism; D015202:Protein Engineering; D011522:Protons; D011993:Recombinant Fusion Proteins / Q000096:biosynthesis / Q000235:genetics; D013816:Thermodynamics
chemical_list: D017151:Antibodies, Catalytic; D007128:Immunoglobulin Fragments; D007555:Isoxazoles; D009570:Nitriles; D011522:Protons; D011993:Recombinant Fusion Proteins