Expression of binding energy on an antibody reaction coordinate

Article abstract of DOI:10.1021/ja9928879

In this paper, we report the investigation of how the catalytic antibody 17E8 uses remote binding energy along the catalyzed hydrolytic reaction coordinate. With the use of alternative substrate analogues, we find that 17E8 can use free energy from binding interactions between the substrate side chain and antibody recognition pocket to equally stabilize the transition state and the Michaelis complex. In these cases, the interactions are not used to increase k(cat). We have also identified substrates for which the interactions are used to preferentially stabilize the transition state over the Michaelis complex. In these cases, the interactions are used to increase k(cat). Mechanistic studies support the idea that the differences in the substrates' kinetic activities results from differences in the expression of side-chain-pocket binding energy along the reaction coordinates. These results suggest that generating catalytic antibodies to transition-state analogues may be limited because the selective use of remote binding interactions cannot be programmed into transition-state analogues.