Catalytic Mechanism and Performance of Computationally Designed Enzymes for Kemp Elimination
- 31 October 2008
- journal article
- research article
- Published by American Chemical Society (ACS) in Journal of the American Chemical Society
- Vol. 130 (47), 15907-15915
- https://doi.org/10.1021/ja804040s
Abstract
A series of enzymes for Kemp elimination of 5-nitrobenzisoxazole has been recently designed and tested. In conjunction with the design process, extensive computational analyses were carried out to evaluate the potential performance of four of the designs, as presented here. The enzyme-catalyzed reactions were modeled using mixed quantum and molecular mechanics (QM/MM) calculations in the context of Monte Carlo (MC) statistical mechanics simulations. Free-energy perturbation (FEP) calculations were used to characterize the free-energy surfaces for the catalyzed reactions as well as for reference processes in water. The simulations yielded detailed information about the catalytic mechanisms, activation barriers, and structural evolution of the active sites over the course of the reactions. The catalytic mechanism for the designed enzymes KE07, KE10(V131N), and KE15 was found to be concerted with proton transfer, generally more advanced in the transition state than breaking of the isoxazolyl N−O bond. On the basis of the free-energy results, all three enzymes were anticipated to be active. Ideas for further improvement of the enzyme designs also emerged. On the technical side, the synergy of parallel QM/MM and experimental efforts in the design of artificial enzymes is well illustrated.Keywords
This publication has 42 references indexed in Scilit:
- Kemp elimination catalysts by computational enzyme designNature, 2008
- De Novo Computational Design of Retro-Aldol EnzymesScience, 2008
- Protein Design: Reengineering Cellular Retinoic Acid Binding Protein II into a Rhodopsin Protein MimicJournal of the American Chemical Society, 2007
- De novo design of catalytic proteinsProceedings of the National Academy of Sciences, 2004
- Computational design of a Zn2+receptor that controls bacterial gene expressionProceedings of the National Academy of Sciences, 2003
- Enzyme-like proteins by computational designProceedings of the National Academy of Sciences, 2001
- Critical Analysis of Antibody CatalysisAnnual Review of Biochemistry, 2000
- Construction of a catalytically active iron superoxide dismutase by rational protein designProceedings of the National Academy of Sciences of the United States of America, 1997
- Protein design automationProtein Science, 1996
- At the Crossroads of Chemistry and Immunology: Catalytic AntibodiesScience, 1991