Designing enzymes ab initio

Authors: 
K.N. Houk, G. Kiss, F. Schoenebeck, S.A. Johnson, S. Kim, G. Nosrati
Department of Chemistry and Biochemistry University of California Los Angeles Los Angeles, CA 90095-1569 USA

The computational design of enzymes for new reactions, and the expression of these designed proteins and measurement of catalytic activity have been carried out in collaboration with David Baker at the University of Washington and Stephen Mayo at Caltech. This protocol holds promise for the production of new therapeutic enzymes. Catalytic sites are designed through quantum mechanical calculations, and these theoretical catalytic sites ("theozymes") are incorporated into stable protein scaffolds with the Rosetta programs of Baker et al. Redesigning enzyme active sites to maximize protein stability and catalytic geometries and properties, followed by computational evaluation using molecular dynamics simulations, provides final designs that are tested experimentally. Plans to design enzymes to reverse formation of AGEs, such as CMLs, will be described.

Keywords: 
catalysis
protein
quantum mechanics
molecular dynamics
Category: 
Invited