The role of reorganization energy in rational enzyme design.
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[1] F. Arnold,et al. Directed evolution of enzyme catalysts. , 1997, Trends in biotechnology.
[2] W. Jencks,et al. Entropic contributions to rate accelerations in enzymic and intramolecular reactions and the chelate effect. , 1971, Proceedings of the National Academy of Sciences of the United States of America.
[3] David Baker,et al. Structural analyses of covalent enzyme-substrate analog complexes reveal strengths and limitations of de novo enzyme design. , 2011, Journal of molecular biology.
[4] Eric A. Althoff,et al. De Novo Computational Design of Retro-Aldol Enzymes , 2008, Science.
[5] David Baker,et al. Optimization of the in-silico-designed kemp eliminase KE70 by computational design and directed evolution. , 2011, Journal of molecular biology.
[6] Dan S. Tawfik,et al. Off-the-shelf proteins that rival tailor-made antibodies as catalysts , 1996, Nature.
[7] T. C. Bruice,et al. The near attack conformation approach to the study of the chorismate to prephenate reaction , 2003, Proceedings of the National Academy of Sciences of the United States of America.
[8] Rudolph A. Marcus,et al. On the Theory of Oxidation‐Reduction Reactions Involving Electron Transfer. I , 1956 .
[9] A. North,et al. Crystallographic studies of the activity of hen egg-white lysozyme , 1967, Proceedings of the Royal Society of London. Series B. Biological Sciences.
[10] Jory Z. Ruscio,et al. The influence of protein dynamics on the success of computational enzyme design. , 2009, Journal of the American Chemical Society.
[11] Summer B. Thyme,et al. Improved modeling of side-chain--base interactions and plasticity in protein--DNA interface design. , 2012, Journal of molecular biology.
[12] Y. Mo,et al. Ab initio QM/MM simulations with a molecular orbital‐valence bond (MOVB) method: application to an SN2 reaction in water , 2000 .
[13] David Baker,et al. An exciting but challenging road ahead for computational enzyme design , 2010, Protein science : a publication of the Protein Society.
[14] R. Lerner,et al. Direct observation of an enamine intermediate in amine catalysis. , 2009, Journal of the American Chemical Society.
[15] L. Pauling. Chemical achievement and hope for the future. , 1948, American scientist.
[16] Arieh Warshel,et al. Exploring the origin of the ion selectivity of the KcsA potassium channel , 2003, Proteins.
[17] David Baker,et al. Evolutionary optimization of computationally designed enzymes: Kemp eliminases of the KE07 series. , 2010, Journal of molecular biology.
[18] A. Warshel,et al. Electrostatic basis for enzyme catalysis. , 2006, Chemical reviews.
[19] A. Warshel,et al. Origin of the catalytic power of acetylcholinesterase: Computer simulation studies , 1998 .
[20] W. DeGrado,et al. De novo design of catalytic proteins. , 2004, Proceedings of the National Academy of Sciences of the United States of America.
[21] R. Wolfenden,et al. The depth of chemical time and the power of enzymes as catalysts. , 2001, Accounts of chemical research.
[22] Arieh Warshel,et al. Exploring challenges in rational enzyme design by simulating the catalysis in artificial kemp eliminase , 2010, Proceedings of the National Academy of Sciences.
[23] David Baker,et al. Evaluation and ranking of enzyme designs , 2010, Protein science : a publication of the Protein Society.
[24] Donald Hilvert,et al. De novo enzymes by computational design. , 2013, Current opinion in chemical biology.
[25] T. Van Voorhis,et al. Extracting electron transfer coupling elements from constrained density functional theory. , 2006, The Journal of chemical physics.
[26] F. Arnold. Combinatorial and computational challenges for biocatalyst design , 2001, Nature.
[27] S. L. Mayo,et al. Enzyme-like proteins by computational design , 2001, Proceedings of the National Academy of Sciences of the United States of America.
[28] A. Warshel,et al. Remarkable rate enhancement of orotidine 5'-monophosphate decarboxylase is due to transition-state stabilization rather than to ground-state destabilization. , 2000, Biochemistry.
[29] Jasmine L. Gallaher,et al. Alteration of enzyme specificity by computational loop remodeling and design , 2009, Proceedings of the National Academy of Sciences.
[30] David Baker,et al. Origins of catalysis by computationally designed retroaldolase enzymes , 2010, Proceedings of the National Academy of Sciences.
[31] Jasmine L. Gallaher,et al. Computational Design of an Enzyme Catalyst for a Stereoselective Bimolecular Diels-Alder Reaction , 2010, Science.
[32] A. Warshel,et al. Calculations of antibody-antigen interactions: microscopic and semi-microscopic evaluation of the free energies of binding of phosphorylcholine analogs to McPC603. , 1992, Protein engineering.
[33] Arieh Warshel,et al. An empirical valence bond approach for comparing reactions in solutions and in enzymes , 1980 .
[34] Daniel W. Kulp,et al. Design of a switchable eliminase , 2011, Proceedings of the National Academy of Sciences.
[35] Daniel Herschlag,et al. Robust design and optimization of retroaldol enzymes , 2012, Protein science : a publication of the Protein Society.
[36] Brian K Shoichet,et al. Engineering a model protein cavity to catalyze the Kemp elimination , 2012, Proceedings of the National Academy of Sciences.
[37] C. Cameron,et al. Evidence for a functional role of the dynamics of glycine-121 of Escherichia coli dihydrofolate reductase obtained from kinetic analysis of a site-directed mutant. , 1997, Biochemistry.
[38] Donald Hilvert,et al. Precision is essential for efficient catalysis in an evolved Kemp eliminase , 2013, Nature.
[39] M. Fuxreiter,et al. Optimization of reorganization energy drives evolution of the designed Kemp eliminase KE07. , 2013, Biochimica et biophysica acta.
[40] Eric A. Althoff,et al. Kemp elimination catalysts by computational enzyme design , 2008, Nature.
[41] Arieh Warshel,et al. Challenges and advances in validating enzyme design proposals: the case of kemp eliminase catalysis. , 2011, Biochemistry.
[42] K N Houk,et al. Theozymes and compuzymes: theoretical models for biological catalysis. , 1998, Current opinion in chemical biology.
[43] David Baker,et al. Bridging the gaps in design methodologies by evolutionary optimization of the stability and proficiency of designed Kemp eliminase KE59 , 2012, Proceedings of the National Academy of Sciences.
[44] A. Warshel,et al. Evaluation of catalytic free energies in genetically modified proteins. , 1988, Journal of molecular biology.
[45] A. Warshel,et al. Energetics of enzyme catalysis. , 1978, Proceedings of the National Academy of Sciences of the United States of America.
[46] A. Warshel,et al. A fast estimate of electrostatic group contributions to the free energy of protein-inhibitor binding. , 1997, Protein engineering.
[47] Roberto A. Chica,et al. Iterative approach to computational enzyme design , 2012, Proceedings of the National Academy of Sciences.
[48] D. Hilvert,et al. Protein design by directed evolution. , 2008, Annual review of biophysics.
[49] M. Karplus,et al. How Enzymes Work: Analysis by Modern Rate Theory and Computer Simulations , 2004, Science.
[50] K. Houk,et al. A proficient enzyme revisited: the predicted mechanism for orotidine monophosphate decarboxylase. , 1997, Science.
[51] Donald Hilvert,et al. Design of protein catalysts. , 2013, Annual review of biochemistry.