In collaboration with David Baker of the University of Washington and with Stephen Mayo of Caltech, our group has designed enzymes for catalysis of three reactions, the so-called Kemp elimination, a retro-aldol reaction, and a Diels-Alder reaction. In each case, our group used quantum mechanical computational methods to predict the 3D arrangement of catalytic groups that can accelerate the reaction. Programs from the Baker or Mayo groups then locate a stable protein in which the designed active site can be inserted. After redesign of the catalytic site to accommodate the new substrate and transition states, molecular dynamicas are used in our group to evaluated the stability of the design and the environment of the active site. Designs that are stable are then expressed in E coli. and purified and tested for catalysis. Successful designs are described in:
1. Lin Jiang, Eric A. Althoff, Kendall N. Houk et al: "De Novo Computational Design of Retro-Aldol Enzymes," Science, 319, 1387-1391 (2008).
2. Daniela Rothlisberger, Olga Khersonsky, Kendall N. Houk et al: "Kemp Elimination Catalysts by Computation Enzyme Design," Nature, 453, 190-195 (2008).
3. Justin B. Siegel, Alexandre Zanghellini, Kendall N. Houk et al: "Computational Design of an Enzyme Catalyst for a Stereoselective Bimolecular Diels-Alder Reaction," Science, 329, 309-313 (2010).
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