The goals of this research are to develop computational tools to design enzyme catalysts for reactions not found in nature. Catalytic binding sites for several types of reactions will be designed, based upon both covalent and noncovalent catalytic mechanisms. Combinatorial exploration of potential side-chain catalytic groups, followed by quantum mechanical testing of optimum catalytic arrangements will lead to a hierarchy of potential catalytic sites. Our collaborators, David Baker and his group, will use the coordinates of the designed catalytic sites to predict sequences that will fold into a catalytic site with this geometry. QM and QM/MM methods will be tested and developed in our lab to predict which of the designed proteins are likely to be the best catalysts. The proteins will be synthesized by the Baker group with standard molecular biological techniques, and in collaboration we will test the catalytic activity and mechanisms of these new proteins. Emphasis is on the development of efficient methods for the prediction of effective protein catalysts, and these methods will be tested against known data on enzymes and mutants that have different catalytic proficiencies.
During this grant period, we will develop and use the tools of computational chemistry to design novel enzymes. Our emphasis will be to demonstrate that we can do what has never been done before: design a functioning enzyme from scratch, starting with ideas about a catalytic site and ending with a fully functioning enzyme for a non-natural reaction. The initial target reactions will be of use in the synthesis of pharmaceutical targets and for the decomposition of a broad class of compounds utilized as pesticides and herbicides.
|Yang, Zhongyu; Jiménez-Osés, Gonzalo; López, Carlos J et al. (2014) Long-range distance measurements in proteins at physiological temperatures using saturation recovery EPR spectroscopy. J Am Chem Soc 136:15356-65|
|Medina, Jose M; McMahon, Travis C; Jiménez-Osés, Gonzalo et al. (2014) Cycloadditions of cyclohexynes and cyclopentyne. J Am Chem Soc 136:14706-9|
|Jiménez-Osés, Gonzalo; Osuna, Sílvia; Gao, Xue et al. (2014) The role of distant mutations and allosteric regulation on LovD active site dynamics. Nat Chem Biol 10:431-6|
|Kiss, Gert; Pande, Vijay S; Houk, K N (2013) Molecular dynamics simulations for the ranking, evaluation, and refinement of computationally designed proteins. Methods Enzymol 523:145-70|
|Bjelic, Sinisa; Nivon, Lucas G; Celebi-Olcum, Nihan et al. (2013) Computational design of enone-binding proteins with catalytic activity for the Morita-Baylis-Hillman reaction. ACS Chem Biol 8:749-57|
|Gao, Xue; Jiang, Wei; Jimenez-Oses, Gonzalo et al. (2013) An iterative, bimodular nonribosomal peptide synthetase that converts anthranilate and tryptophan into tetracyclic asperlicins. Chem Biol 20:870-8|
|Hotta, Kinya; Chen, Xi; Paton, Robert S et al. (2012) Enzymatic catalysis of anti-Baldwin ring closure in polyether biosynthesis. Nature 483:355-8|
|Nosrati, Geoffrey R; Houk, K N (2012) SABER: a computational method for identifying active sites for new reactions. Protein Sci 21:697-706|
|Warshaviak, Dora Toledo; Serbulea, Laura; Houk, K N et al. (2011) Conformational analysis of a nitroxide side chain in an ýý-helix with density functional theory. J Phys Chem B 115:397-405|
|Hayden, Amy E; Paton, Robert S; Becker, Jochen et al. (2010) Origins of regioselectivity of Diels-Alder reactions for the synthesis of bisanthraquinone antibiotic BE-43472B. J Org Chem 75:922-8|
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