ArticleProtein science : a publication of the Protein Society2007
How similar are enzyme active site geometries derived from quantum mechanical theozymes to crystal structures of enzyme-inhibitor complexes? Implications for enzyme design.
Article in Protein science : a publication of the Protein Society, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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14 citing papers in PubMed, 41 citations in OpenAlex.
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- Predicting protein-ligand binding affinity and correcting crystal structures with quantum mechanical calculations: lactate dehydrogenase A.Chemical science · 2019Article
- Investigations on recyclisation and hydrolysis in avibactam mediated serine β-lactamase inhibition.Organic & biomolecular chemistry · 2016Article
- Modulation of inherent dynamical tendencies of the bisabolyl cationChemical science · 2015Article
- Synthetic biology for the directed evolution of protein biocatalysts: navigating sequence space intelligently.Chemical Society reviews · 2015Review
- Structural and electronic snapshots during the transition from a Cu(II) to Cu(I) metal center of a lytic polysaccharide monooxygenase by X-ray photoreduction.The Journal of biological chemistry · 2014Article
- Acceleration of an aromatic Claisen rearrangement via a designed spiroligozyme catalyst that mimics the ketosteroid isomerase catalytic dyad.Journal of the American Chemical Society · 2014Article
- Quantum mechanical calculations suggest that lytic polysaccharide monooxygenases use a copper-oxyl, oxygen-rebound mechanism.Proceedings of the National Academy of Sciences of the United States of America · 2014Article
- Molecular modeling of the reaction pathway and hydride transfer reactions of HMG-CoA reductase.Biochemistry · 2012Article
- Engineering synthetic recursive pathways to generate non-natural small molecules.Nature chemical biology · 2012Review
- SABER: a computational method for identifying active sites for new reactions.Protein science : a publication of the Protein Society · 2012Article
- Computational enzyme design approaches with significant biological outcomes: progress and challenges.Computational and structural biotechnology journal · 2012Review
- Structural reorganization and preorganization in enzyme active sites: comparisons of experimental and theoretically ideal active site geometries in the multistep serine esterase reaction cycle.Journal of the American Chemical Society · 2008Article
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7 authors at 1 institution in 1 country.
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Abstract
Quantum mechanical optimizations of theoretical enzymes (theozymes), which are predicted catalytic arrays of biological functionalities stabilizing a transition state, have been carried out for a set of nine diverse enzyme active sites. For each enzyme, the theozyme for the rate-determining transition state plus the catalytic groups modeled by side-chain mimics was optimized using B3LYP/6-31G(d) or, in one case, HF/3-21G(d) quantum mechanical calculations. To determine if the theozyme can reproduce the natural evolutionary catalytic geometry, the positions of optimized catalytic atoms, i.e., covalent, partial covalent, or stabilizing interactions with transition state atoms, are compared to the positions of the atoms in the X-ray crystal structure with a bound inhibitor. These structure comparisons are contrasted to computed substrate-active site structures surrounded by the same theozyme residues. The theozyme/transition structure is shown to predict geometries of active sites with an average RMSD of 0.64 A from the crystal structure, while the RMSD for the bound intermediate complexes are significantly higher at 1.42 A. The implications for computational enzyme design are discussed.
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