Exploring the Challenges in Computational Enzyme Design
Enzymes are nature’s most efficient catalysts and are also harnessed in synthetic chemistry for the sustainable production of several non-natural products. However, the design of new enzymes presents a major practical and fundamental challenge. Despite an interesting progress, the main advances are achieved through directed evolution and not by computational design.1 Moreover, several designed systems adopt the less efficient route of ground state destabilization instead of transition state stabilization. In the talk, I will discuss the design of two enzymes; Kemp eliminases and haloalkane dehalogenase. Kemp eliminases are computationally designed enzymes that catalyze the conversion of 5-nitrobenzisoxazole to cyanophenol product. Haloalkane dehalogenase; DhlA is an important enzyme that helps in breaking down the toxic haloalkanes (1,2-dichloroethane) to alcohol via a series of steps. EVB (Empirical valence bond) approach is used to calculate the activation energies for the wild type and mutants. For Kemp eliminases, the origin of catalysis in different systems is rationalized on the basis of solvation free energies.2 The different trends observed in the directed evolution of different systems is investigated to understand the effect of multiple mutations. For halolalkane dehalogenase, after successfully reproducing the activation barriers of known mutants, new mutations are proposed on the basis of structural data.3 We mutated residues that are known to contribute to catalysis and then attempted to restore the activity by mutating residues in the first and second solvation shells. Various factors responsible for certain anomalies and the challenges encountered during computational enzyme design will be discussed.
 Frushicheva, M. P.; Cao, J.; Chu, Z. T.; Warshel, A. Proc. Natl. Acad. Sci. U. S. A. 2010, 107, 16869.
 (a) Jindal, G.; Ramachandran, B.; Bora, R. B.; Warshel, A. ACS Catal. 2017, 7, 3301. (b) Jindal, G.; Mondal, D.; Warshel, A. J. Phys. Chem. B 2017, 121, 6831.
 Jindal, G.; Slánská, K.; Kolev, V.; Damborsky, J.; Prokop, Z.; Warshel, A. Proc. Natl. Acad. Sci. U. S. A. 2018 (Under Revision).