Structural origins of efficient proton abstraction from carbon by a catalytic antibody

Abstract

Antibody 34E4 catalyzes the conversion of benzisoxazoles to salicylonitriles with high rates and multiple turnovers. The crystal structure of its complex with the benzimidazolium hapten at 2.5-Å resolution shows that a combination of hydrogen bonding, stacking, and van der Waals interactions is exploited to position both the base, Glu H50 , and the substrate for efficient proton transfer. Suboptimal placement of the catalytic carboxylate, as observed in the 2.8-Å structure of the Glu H50 Asp variant, results in substantially reduced catalytic efficiency. In addition to imposing high positional order on the transition state, the antibody pocket provides a highly structured microenvironment for the reaction in which the carboxylate base is activated through partial desolvation, and the highly polarizable transition state is stabilized by dispersion interactions with the aromatic residue Trp L91 and solvation of the leaving group oxygen by external water. The enzyme-like efficiency of general base catalysis in this system directly reflects the original hapten design, in which a charged guanidinium moiety was strategically used to elicit an accurately positioned functional group in an appropriate reaction environment and suggests that even larger catalytic effects may be achievable by extending this approach to the induction of acidbase pairs capable of bifunctional catalysis.crystal structure ͉ base catalysis ͉ proton transfer ͉ medium effects ͉ orientation effects P roton abstraction from carbon constitutes a fundamental process catalyzed by numerous enzymes, including isomerases, epimerases, racemases, lyases, and some synthases (1). Although heterolytic COH bond cleavage is a kinetically and thermodynamically demanding reaction, deprotonation catalysts rank among the most efficient enzymes known. For example, triosephosphate isomerase, ketosteroid isomerase, and fumarase operate at the diffusion limit (2). The mechanisms by which proteins that contain only weak acids and bases accelerate proton transfers by such enormous factors has long intrigued biochemists (3). Crystal structures and biochemical experiments of such enzymes have highlighted the importance of precisely positioned functional groups with optimized pK a s (3-5), but the precise origins of their high activities remain controversial (6).Valuable insight into the factors that contribute to efficient proton abstraction can be gained from the base-promoted Kemp elimination (1 3 3, Fig. 1), a widely used model system that is sensitive to base strength and solvent environment (7-9). This reaction is also susceptible to catalysis by antibodies (10, 11), albumins (12-14), polyethyleneimine ''synzymes'' (15, 16), organic hosts (17), cationic vesicles (18), and even natural coals (19). Antibody 34E4, which was raised against the cationic 2-aminobenzimidazolium derivative 4, is particularly effective in this regard (11). It promotes the decomposition of benzisoxazole 1 with Ͼ10 3 turnovers per active site and achieves a rate acceleration of 10 6 over backgrou...

Kemp elimination catalysts by computational enzyme design

“…A hydrogen bond donor was used to stabilize the developing negative charge on the phenolic oxygen in the otherwise hydrophobic active site. Catalytic motifs lacking the H-bond donor were also tested, because the developing negative charge is relatively small in the transition state and can be easily solvated by water 9,10 . For each choice of catalytic site composition, density functional theory quantum-mechanical methods [11][12][13] were used to optimize the placement and orientations of the catalytic groups around the transition state for maximal stabilization (see Methods).…”

Bridging the gaps in design methodologies by evolutionary optimization of the stability and proficiency of designed Kemp eliminase KE59

“…computational protein design | enzyme mimic T he endeavor of making enzyme-like catalysts spans several decades (1) with the Kemp elimination being a thoroughly explored model (2)(3)(4)(5)(6)(7). In this activated model system, basecatalyzed proton elimination from carbon is concerted with the cleavage of nitrogen-oxygen bond, thus leading to the cyanophenol product (Fig.…”

Exploring challenges in rational enzyme design by simulating the catalysis in artificial kemp eliminase

“…Thus we tried to explore this challenge and chose as a test system the Kemp elimination reaction (14). The design of enzymes that catalyze this reaction has been the center of recent excitements (15,16), but as will be argued below the design has not obtained effective transition state stabilization. Our study focused on both validation of the power of the EVB and more importantly on exploring the effect of the directed evolution and on the requirement for improving the catalysis of the previously designed enzymes.…”