Kemp elimination catalysts by computational enzyme design
- D. Röthlisberger, O. Khersonsky, D. Baker
- BiologyNature
- 8 May 2008
The computational design of eight enzymes that use two different catalytic motifs to catalyse the Kemp elimination—a model reaction for proton transfer from carbon—with measured rate enhancements of up to 105 and multiple turnovers are described.
Free radical biology and medicine: it's a gas, man!
- W. Pryor, K. Houk, K. Davies
- Biology, ChemistryAmerican Journal of Physiology. Regulatory…
- 1 September 2006
Gasses that can affect oxidative stress and that themselves may be radicals are reviewed, fearing that many of the gasses discussed in this review will induce transient adaptive responses in gene expression that enable cells and tissues to survive.
De Novo Computational Design of Retro-Aldol Enzymes
- Lin Jiang, Eric A. Althoff, D. Baker
- BiologyScience
- 7 March 2008
Using new algorithms that rely on hashing techniques to construct active sites for multistep reactions, retro-aldolases that use four different catalytic motifs to catalyze the breaking of a carbon-carbon bond in a nonnatural substrate are designed.
Computational Design of an Enzyme Catalyst for a Stereoselective Bimolecular Diels-Alder Reaction
- J. Siegel, A. Zanghellini, D. Baker
- Chemistry, BiologyScience
- 16 July 2010
The design of enzymes that catalyze the bimolecular Diels-Alder reaction, a carbon-carbon bond formation reaction that is central to organic synthesis but unknown in natural metabolism, is described.
Accounts of Chemical Research.
- J. Valentine, K. Houk, P. Barbara
- BusinessAccounts of Chemical Research
- 2008
The traditional abstract has been replaced by the conspectus, literally a synopsis or summary affording the reader a close look at the content and significance of an article, thereby enhancing its discoverability by search engines.
Benchmarking the Conductor-like Polarizable Continuum Model (CPCM) for Aqueous Solvation Free Energies of Neutral and Ionic Organic Molecules.
The conductor-like polarizable continuum model (CPCM) using several cavity models is applied to compute aqueous solvation free energies for a number of organic molecules (30 neutral molecules, 21 anions, and 19 cations) to compare to the available experimental data.
A model for binding of structurally diverse natural product inhibitors of protein phosphatases PP1 and PP2A.
- V. Gupta, A. Ogawa, X. Du, K. Houk, R. W. Armstrong
- Biology, ChemistryJournal of Medicinal Chemistry
- 26 September 1997
The standardization of an assay to be used in acquisition of the structure--activity relationship of inhibition data is reported and the comparison of the IC50 values of these inhibitors against corresponding literature data provided validation for the method.
Iterative approach to computational enzyme design
- H. Privett, G. Kiss, S. L. Mayo
- Chemistry, BiologyProceedings of the National Academy of Sciences
- 22 February 2012
An iterative approach to computational enzyme design, including detailed MD and structural analysis of both active and inactive designs, promises a more complete understanding of the underlying principles of enzymatic catalysis and furthers progress toward reliably producing active enzymes.
Bridging the gaps in design methodologies by evolutionary optimization of the stability and proficiency of designed Kemp eliminase KE59
- O. Khersonsky, G. Kiss, Dan S. Tawfik
- BiologyProceedings of the National Academy of Sciences
- 8 June 2012
Overall, the directed evolution of three different designed Kemp eliminases, KE07, KE70, and KE59, demonstrates that computational designs are highly evolvable and can be optimized to high catalytic efficiencies.
The physiological chemistry and biological activity of nitroxyl (HNO): the neglected, misunderstood, and enigmatic nitrogen oxide.
- J. Fukuto, M. D. Bartberger, Andrew S Dutton, N. Paolocci, D. Wink, K. Houk
- ChemistryChemical Research in Toxicology
- 1 May 2005
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