Computational design and characterisation of artificial enzymes for Kemp elimination

Abstract

De novo design of enzymes for the catalysis of reactions that interest humankind has been long desired. In this field, one of the most successful recent efforts, and the subject of this paper, is the design of artificial enzymes catalysing the Kemp elimination – a model reaction for proton transfer from carbon. A number of new enzymes have been designed computationally. Subsequently, their activity was confirmed and refined experimentally. This success is a manifestation of our understanding and ability to rationally manipulate protein structure. At the same time, through this research, the complexity of the problem of designing functional enzymes became apparent. Everything from the precise positioning of residues at the enzyme active site to solvent accessibility, backbone dynamics and stability of the protein fold plays a pivotal role in the catalytic performance. The large number of negative designs also illustrates the limited precision with which modern computational methods can handle the problem. Major results, observations and future prospects are discussed.

Keywords:

• artificial enzymes
• enzyme design
• Kemp elimination

Acknowledgements

The support from the University of California is gratefully acknowledged.