Quantum Mechanical Design of Enzyme Active Sites

Abstract

The design of active sites has been carried out using quantum mechanical calculations to predict the rate-determining transition state of a desired reaction in presence of the optimal arrangement of catalytic functional groups (theozyme). Eleven versatile reaction targets were chosen, including hydrolysis, dehydration, isomerization, aldol, and Diels-Alder reactions. For each of the targets, the predicted mechanism and the rate-determining transition state (TS) of the uncatalyzed reaction in water is presented. For the rate-determining TS, a catalytic site was designed using naturalistic catalytic units followed by an estimation of the rate acceleration provided by a reoptimization of the catalytic site. Finally, the geometries of the sites were compared to the X-ray structures of related natural enzymes. Recent advances in computational algorithms and power, coupled with successes in computational protein design, have provided a powerful context for undertaking such an endeavor. We propose that theozymes are excellent candidates to serve as the active site models for design processes.

Understanding the Functional Roles of Amino Acid Residues in Enzyme Catalysis

“…Rational enzyme design is still considered to be an enormous challenge and often fails due to a limited understanding of the subtle interplay of the residues in the active site. Thus, rational design becomes a more tractable problem by combining a detailed knowledge of residue function with approaches such as the theoretical enzyme (the theozyme 32,33 ).…”

Controlling complexity and water penetration in functional de novo protein design

“…This type of enzyme generation has proved effective in reproducing the basic activity, although the catalytic efficiencies are significantly lower than those exhibited by natural proteins. Another similar method entails quantum mechanical calculation of the transition state followed by exposure of this hypothetical molecule to a set of protein crystal structures in silico [12–14]. Once suitable structures have been identified, further mutations to facilitate binding and catalysis are designed computationally and then tested in vitro .…”

Binding free energies of inhibitors to iron porphyrin complex as a model for Cytochrome P450

“…50 The theozyme has successfully predicted the activation barriers for 11 versatile reaction targets including hydrolysis, dehydration, isomerization, aldol, and Diels-Alder reactions. 51 We applied this theozyme approach in computing the interaction energies between the inhibitor and the functional groups in the active sites of ketoconazole-and metyrapone-CYP3A4 complexes, whose X-ray structures are deposited as 2V0M 13 Table II. Because the X-ray structure of ketoconazole-CYP3A4 complex has two ketoconazoles in its active site, only the ketoconazole bound directly to the heme moiety was considered for its theozyme.…”