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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.
References
[1] Frushicheva, M. P.; Cao, J.; Chu, Z. T.; Warshel, A. Proc. Natl. Acad. Sci. U. S.
A. 2010, 107, 16869.
[2] Jindal, G.; Ramachandran, B.; Bora, R. B.; Warshel, A. ACS Catal. 2017, 7,
3301.
[3] Jindal, G.; Slánská, K.; Kolev, V.; Damborsky, J.; Prokop, Z.; Warshel, A.
Proc. Natl. Acad. Sci. U. S. A. 2018 (Under Revision) |