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Chapter 9 Citations

  1. Pauling, L. "Nature of Forces between Large Molecules of Biological Interest," Nature 1948, 161, 707-709, DOI: 10.1038/161707a0.
  2. Amyes, T. L.; Richard, J. P. "Specificity in Transition State Binding: The Pauling Model Revisited," Biochemistry 2013, 52, 2021-2035, DOI: 10.1021/bi301491r.
  3. Warshel, A.; Sharma, P. K.; Kato, M.; Xiang, Y.; Liu, H.; Olsson, M. H. M. "Electrostatic Basis for Enzyme Catalysis," Chem. Rev. 2006, 106, 3210-3235, DOI: 10.1021/cr0503106.
  4. Mobashery, S.; Kotra, L. P. In Encylopedia of Life Sciences; John Wiley & Sons Ltd: Chichester, 2002.
  5. Zhang, X.; Houk, K. N. "Why Enzymes Are Proficient Catalysts:  Beyond the Pauling Paradigm," Acc. Chem. Res. 2005, 38, 379-385, DOI: 10.1021/ar040257s.
  6. Borman, S. "Much Ado About Enzyme Mechanisms," Chem. Eng. News 2004, 82, 35-39, DOI: 10.1021/cen-v082n008.p035.
  7. Simón, L.; Goodman, J. M. "Enzyme Catalysis by Hydrogen Bonds: The Balance between Transition State Binding and Substrate Binding in Oxyanion Holes," J. Org. Chem. 2009, 75, 1831-1840, DOI: 10.1021/jo901503d.
  8. Kamerlin, S. C. L.; Chu, Z. T.; Warshel, A. "On Catalytic Preorganization in Oxyanion Holes: Highlighting the Problems with the Gas-Phase Modeling of Oxyanion Holes and Illustrating the Need for Complete Enzyme Models," J. Org. Chem. 2010, 75, 6391-6401, DOI: 10.1021/jo100651s.
  9. Simon, L.; Goodman, J. M. "Hydrogen-bond stabilization in oxyanion holes: grand jete to three dimensions," Org. Biomol. Chem. 2012, 10, 1905-1913, DOI: 10.1039/C2OB06717J.
  10. Warshel, A. "Electrostatic Origin of the Catalytic Power of Enzymes and the Role of Preorganized Active Sites," J. Biol. Chem. 1998, 273, 27035-27038, DOI: 10.1074/jbc.273.42.27035.
  11. Kohen, A.; Klinman, J. P. "Enzyme Catalysis:  Beyond Classical Paradigms," Acc. Chem. Res. 1998, 31, 397-404, DOI: 10.1021/ar9701225.
  12. Benkovic, S. J.; Hammes-Schiffer, S. "A Perspective on Enzyme Catalysis," Science 2003, 301, 1196-1202, DOI: 10.1126/science.1085515.
  13. Klinman, J. P. "Linking protein structure and dynamics to catalysis: the role of hydrogen tunnelling," Philos. Trans. R. Soc. London, Ser. B 2006, 361, 1323-1331, DOI: 10.1098/rstb.2006.1870.
  14. Hammes-Schiffer, S.; Watney, J. B. "Hydride transfer catalysed by Escherichia coli and Bacillus subtilis dihydrofolate reductase: coupled motions and distal mutations," Philos. Trans. R. Soc. London, Ser. B 2006, 361, 1365-1373, DOI: 10.1098/rstb.2006.1869.
  15. Hammes-Schiffer, S. "Hydrogen Tunneling and Protein Motion in Enzyme Reactions," Acc. Chem. Res. 2005, 39, 93-100, DOI: 10.1021/ar040199a.
  16. Glowacki, D. R.; Harvey, J. N.; Mulholland, A. J. "Taking Ockham's razor to enzyme dynamics and catalysis," Nat Chem 2012, 4, 169-176, DOI: 10.1038/nchem.1244.
  17. Cleland, W. W.; Frey, P. A.; Gerlt, J. A. "The Low Barrier Hydrogen Bond in Enzymatic Catalysis," J. Biol. Chem. 1998, 273, 25529-25532, DOI: 10.1074/jbc.273.40.25529.
  18. Roy, A.; Zhang, Y. In eLS; John Wiley & Sons, Ltd: 2001.
  19. Zhang, Y. "Progress and challenges in protein structure prediction," Curr. Opin. Struct. Biol. 2008, 18, 342-348, DOI: 10.1016/j.sbi.2008.02.004.
  20. Anfinsen, C. B. "Principles that Govern the Folding of Protein Chains," Science 1973, 181, 223-230, DOI: 10.1126/science.181.4096.223.
  21. Moult, J.; Fidelis, K.; Kryshtafovych, A.; Tramontano, A. "Critical assessment of methods of protein structure prediction (CASP): round IX," Proteins 2011, 79, 1-5, DOI: 10.1002/prot.23200.
  22. Lonsdale, R.; Harvey, J. N.; Mulholland, A. J. "A practical guide to modelling enzyme-catalysed reactions," Chem. Soc. Rev. 2012, 41, 3025-3038, DOI: 10.1039/C2CS15297E.
  23. Salomon-Ferrer, R.; Case, D. A.; Walker, R. C. "An overview of the Amber biomolecular simulation package," WIREs: Comput. Mol. Sci. 2013, 3, 198-210, DOI: 10.1002/wcms.1121.
  24. MacKerell, A. D.; Bashford, D.; Bellott; Dunbrack, R. L.; Evanseck, J. D.; Field, M. J.; Fischer, S.; Gao, J.; Guo, H.; Ha, S.; Joseph-McCarthy, D.; Kuchnir, L.; Kuczera, K.; Lau, F. T. K.; Mattos, C.; Michnick, S.; Ngo, T.; Nguyen, D. T.; Prodhom, B.; Reiher, W. E.; Roux, B.; Schlenkrich, M.; Smith, J. C.; Stote, R.; Straub, J.; Watanabe, M.; Wiórkiewicz-Kuczera, J.; Yin, D.; Karplus, M. "All-Atom Empirical Potential for Molecular Modeling and Dynamics Studies of Proteins," J. Phys. Chem. B 1998, 102, 3586-3616, DOI: 10.1021/jp973084f.
  25. Brooks, B. R.; Brooks, C. L., III; Mackerell, A. D., Jr.; Nilsson, L.; Petrella, R. J.; Roux, B.; Won, Y.; Archontis, G.; Bartels, C.; Boresch, S.; Caflisch, A.; Caves, L.; Cui, Q.; Dinner, A. R.; Feig, M.; Fischer, S.; Gao, J.; Hodoscek, M.; Im, W.; Kuczera, K.; Lazaridis, T.; Ma, J.; Ovchinnikov, V.; Paci, E.; Pastor, R. W.; Post, C. B.; Pu, J. Z.; Schaefer, M.; Tidor, B.; Venable, R. M.; Woodcock, H. L.; Wu, X.; Yang, W.; York, D. M.; Karplus, M. "CHARMM: The biomolecular simulation program," J. Comput. Chem. 2009, 30, 1545-1614, DOI: 10.1002/jcc.21287.
  26. Cramer, C. J. Essentials of Computational Chemistry: Theories and Models; John Wiley & Sons: New York, 2002.
  27. Jensen, F. Introduction to Computational Chemistry; John Wiley & Sons: Chichester, England, 1999.
  28. Ponder, J. W.; Case, D. A. In Advances in Protein Chemistry; Valerie, D., Ed.; Academic Press: 2003; Vol. 66, p 27-85.
  29. MacKerell, A. D., Jr. "Empirical force fields for biological macromolecules: Overview and issues," J. Comput. Chem. 2004, 25, 1584-1604, DOI: 10.1002/jcc.20082.
  30. Halgren, T. A.; Damm, W. "Polarizable force fields," Curr. Opin. Struct. Biol. 2001, 11, 236-242, DOI: 10.1016/s0959-440x(00)00196-2.
  31. Jorgensen, W. L.; Chandrasekhar, J.; D., M. J.; W., I. R.; Klein, M. L. "Comparison of Simple Potential Functions for Simulating Liquid Water," J. Chem. Phys. 1983, 79, 926-935, DOI: 10.1063/1.445869.
  32. Eurenius, K. P.; Chatfield, D. C.; Brooks, B. R.; Hodoscek, M. "Enzyme mechanisms with hybrid quantum and molecular mechanical potentials. I. Theoretical considerations," Int. J. Quant. Chem. 1996, 60, 1189-1200, DOI: 10.1002/(SICI)1097-461X(1996)60:6<1189::AID-QUA7>3.0.CO;2-W.
  33. Kollman, P. A.; Kuhn, B.; Peräkylä, M. "Computational Studies of Enzyme-Catalyzed Reactions:  Where Are We in Predicting Mechanisms and in Understanding the Nature of Enzyme Catalysis?," J. Phys. Chem. B 2002, 106, 1537-1542, DOI: 10.1021/jp012017p.
  34. Torrie, G. M.; Valleau, J. P. "Nonphysical sampling distributions in Monte Carlo free-energy estimation: Umbrella sampling," J. Comput. Phys. 1977, 23, 187-199, DOI: 10.1016/0021-9991(77)90121-8.
  35. Mata, R. A.; Werner, H.-J.; Thiel, S.; Thiel, W. "Toward accurate barriers for enzymatic reactions: QM/MM case study on p-hydroxybenzoate hydroxylase," J. Chem. Phys 2008, 128, 025104-025108, DOI: 10.1063/1.2823055.
  36. Schutz, M. "Low-order scaling local electron correlation methods. III. Linear scaling local perturbative triples correction (T)," J. Chem. Phys. 2000, 113, 9986-10001, DOI: 10.1063/1.1323265.
  37. Werner, H.-J.; Manby, F. R.; Knowles, P. J. "Fast linear scaling second-order Moller-Plesset perturbation theory (MP2) using local and density fitting approximations," J. Chem. Phys. 2003, 118, 8149-8160, DOI: 10.1063/1.1564816.
  38. Werner, H.-J.; Schuetz, M. "An efficient local coupled cluster method for accurate thermochemistry of large systems," J. Chem. Phys. 2011, 135, 144116/144111-144116/144115, DOI: 10.1063/1.3641642.
  39. Van Berkel, W. J. H.; Müller, F. "The temperature and pH dependence of some properties of p-hydroxybenzoate hydroxylase from Pseudomonas fluorescens," Eur. J. Biochem. 1989, 179, 307-314, DOI: 10.1111/j.1432-1033.1989.tb14556.x.
  40. Senn, H. M.; Thiel, S.; Thiel, W. "Enzymatic Hydroxylation in p-Hydroxybenzoate Hydroxylase:  A Case Study for QM/MM Molecular Dynamics," J. Chem. Theor. Comput. 2005, 1, 494-505, DOI: 10.1021/ct049844p.
  41. van der Kamp, M. W.; Żurek, J.; Manby, F. R.; Harvey, J. N.; Mulholland, A. J. "Testing High-Level QM/MM Methods for Modeling Enzyme Reactions: Acetyl-CoA Deprotonation in Citrate Synthase," J. Chem. Phys. B 2010, 114, 11303-11314, DOI: 10.1021/jp104069t.
  42. Andrews, P. R.; Smith, G. D.; Young, I. G. "Transition-state stabilization and enzymic catalysis. Kinetic and molecular orbital studies of the rearrangement of chorismate to prephenate," Biochemistry 1973, 12, 3492-3498, DOI: 10.1021/bi00742a022.
  43. Kast, P.; Asif-Ullah, M.; Hilvert, D. "Is chorismate mutase a prototypic entropy trap? - Activation parameters for the Bacillus subtilis enzyme," Tetrahedron Lett. 1996, 37, 2691-2694, DOI: 10.1016/0040-4039(96)00338-3.
  44. Wiest, O.; Houk, K. N. "Stabilization of the Transition State of the Chorismate-Prephenate Rearrangement: An ab Initio Study of Enzyme and Antibody Catalysis," J. Am. Chem. Soc. 1995, 117, 11628-11639, DOI: 10.1021/ja00152a002.
  45. Bruice, T. C.; Lightstone, F. C. "Ground State and Transition State Contributions to the Rates of Intramolecular and Enzymatic Reactions," Acc. Chem. Res. 1998, 32, 127-136, DOI: 10.1021/ar960131y.
  46. Hur, S.; Bruice, T. C. "The near attack conformation approach to the study of the chorismate to prephenate reaction," Proc. Nat. Acad. Sci. USA 2003, 100, 12015-12020, DOI: 10.1073/pnas.1534873100.
  47. Hur, S.; Bruice, T. C. "Enzymes Do What Is Expected (Chalcone Isomerase versus Chorismate Mutase)," J. Am. Chem. Soc. 2003, 125, 1472-1473, DOI: 10.1021/ja0293047.
  48. Hur, S.; Bruice, T. C. "Just a Near Attack Conformer for Catalysis (Chorismate to Prephenate Rearrangements in Water, Antibody, Enzymes, and Their Mutants)," J. Am. Chem. Soc. 2003, 125, 10540-10542, DOI: 10.1021/ja0357846.
  49. Kuczera, K. "One- and multidimensional conformational free energy simulations," J. Comput. Chem. 1996, 17, 1726-1749, DOI: 10.1002/(SICI)1096-987X(19961130)17:15<1726::AID-JCC4>3.0.CO;2-R.
  50. Guimarães, C. R. W.; Repasky, M. P.; Chandrasekhar, J.; Tirado-Rives, J.; Jorgensen, W. L. "Contributions of Conformational Compression and Preferential Transition State Stabilization to the Rate Enhancement by Chorismate Mutase," J. Am. Chem. Soc. 2003, 125, 6892-6899, DOI: 10.1021/ja021424r.
  51. Jorgensen, W. L.; Maxwell, D. S.; Tirado-Rives, J. "Development and Testing of the OPLS All-Atom Force Field on Conformational Energetics and Properties of Organic Liquids," J. Am. Chem. Soc. 1996, 118, 11225-11236, DOI: 10.1021/ja9621760.
  52. Ranaghan, K. E.; Mulholland, A. J. "Conformational effects in enzyme catalysis: QM/MM free energy calculation of the 'NAC' contribution in chorismate mutase," Chem. Commun. 2004, 0, 1238-1239, DOI: 10.1039/B402388A.
  53. Claeyssens, F.; Ranaghan, K. E.; Manby, F. R.; Harvey, J. N.; Mulholland, A. J. "Multiple high-level QM/MM reaction paths demonstrate transition-state stabilization in chorismate mutase: correlation of barrier height with transition-state stabilization," Chem. Commun. 2005, 0, 5068-5070, DOI: 10.1039/B508181E.
  54. Claeyssens, F.; Ranaghan, K. E.; Lawan, N.; Macrae, S. J.; Manby, F. R.; Harvey, J. N.; Mulholland, A. J. "Analysis of chorismate mutase catalysis by QM/MM modelling of enzyme-catalysed and uncatalysed reactions," Org. Biomol. Chem. 2011, 9, 1578-1590, DOI: 10.1039/C0OB00691B.
  55. Ishida, T. "Effects of Point Mutation on Enzymatic Activity: Correlation between Protein Electronic Structure and Motion in Chorismate Mutase Reaction," J. Am. Chem. Soc. 2010, 132, 7104-7118, DOI: 10.1021/ja100744h.
  56. Kienhöfer, A.; Kast, P.; Hilvert, D. "Selective Stabilization of the Chorismate Mutase Transition State by a Positively Charged Hydrogen Bond Donor," J. Am. Chem. Soc. 2003, 125, 3206-3207, DOI: 10.1021/ja0341992.
  57. Cload, S. T.; Liu, D. R.; Pastor, R. M.; Schultz, P. G. "Mutagenesis Study of Active Site Residues in Chorismate Mutase from Bacillus subtilis," J. Am. Chem. Soc. 1996, 118, 1787-1788, DOI: 10.1021/ja953152g.
  58. Männistö, P. T.; Kaakkola, S. "Catechol-O-methyltransferase (COMT): Biochemistry, Molecular Biology, Pharmacology, and Clinical Efficacy of the New Selective COMT Inhibitors," Pharmacol. Rev. 1999, 51, 593-628, DOI: http://pharmrev.aspetjournals.org/content/51/4/593.short.
  59. Schluckebier, G.; O'Gara, M.; Saenger, W.; Cheng, X. "Universal Catalytic Domain Structure of AdoMet-dependent Methyltransferases," J. Mol. Biol. 1995, 247, 16-20, DOI: 10.1006/jmbi.1994.0117.
  60. Zheng, Y.-J.; Bruice, T. C. "A Theoretical Examination of the Factors Controlling the Catalytic Efficiency of a Transmethylation Enzyme:  Catechol O-Methyltransferase," J. Am. Chem. Soc. 1997, 119, 8137-8145, DOI: 10.1021/ja971019d.
  61. Hegazi, M. F.; Borchardt, R. T.; Schowen, R. L. "α-Deuterium and carbon-13 isotope effects for methyl transfer catalyzed by catechol O-methyltransferase. SN2-like transition state," J. Am. Chem. Soc. 1979, 101, 4359-4365, DOI: 10.1021/ja00509a052.
  62. Woodard, R. W.; Tsai, M. D.; Floss, H. G.; Crooks, P. A.; Coward, J. K. "Stereochemical course of the transmethylation catalyzed by catechol O-methyltransferase," J. Biol. Chem. 1980, 255, 9124-9127, DOI: http://www.jbc.org/content/255/19/9124.abstract.
  63. Vidgren, J.; Svensson, L. A.; Liljas, A. "Crystal structure of catechol O-methyltransferase," Nature 1994, 368, 354-358, DOI: 10.1038/368354a0.
  64. Mihel, I.; Knipe, J. O.; Coward, J. K.; Schowen, R. L. "α-Deuterium isotope effects and transition-state structure in an intramolecular model system for methyl-transfer enzymes," J. Am. Chem. Soc. 1979, 101, 4349-4351, DOI: 10.1021/ja00509a050.
  65. Lau, E. Y.; Bruice, T. C. "Importance of Correlated Motions in Forming Highly Reactive Near Attack Conformations in Catechol O-Methyltransferase," J. Am. Chem. Soc. 1998, 120, 12387-12394, DOI: 10.1021/ja9827447.
  66. Kuhn, B.; Kollman, P. A. "QM−FE and Molecular Dynamics Calculations on Catechol O-Methyltransferase:  Free Energy of Activation in the Enzyme and in Aqueous Solution and Regioselectivity of the Enzyme-Catalyzed Reaction," J. Am. Chem. Soc. 2000, 122, 2586-2596, DOI: 10.1021/ja992218v.
  67. Schultz, E.; Nissinen, E. "Inhibition of rat liver and duodenum soluble catechol-O-methyltransferase by a tight-binding inhibitor OR-462," Biochem. Pharmacol. 1989, 38, 3953-3956, DOI: 10.1016/0006-2952(89)90673-4.
  68. Kollman, P. A.; Kuhn, B.; Donini, O.; Perakyla, M.; Stanton, R.; Bakowies, D. "Elucidating the Nature of Enzyme Catalysis Utilizing a New Twist on an Old Methodology:  Quantum Mechanical−Free Energy Calculations on Chemical Reactions in Enzymes and in Aqueous Solution," Acc. Chem. Res. 2000, 34, 72-79, DOI: 10.1021/ar000032r.
  69. Strajbl, M.; Sham, Y. Y.; Villa, J.; Chu, Z. T.; Warshel, A. "Calculations of Activation Entropies of Chemical Reactions in Solution," J. Phys. Chem. B 2000, 104, 4578-4584, DOI: 10.1021/jp0003095.
  70. Gilson, M. K.; Given, J. A.; Bush, B. L.; McCammon, J. A. "The statistical-thermodynamic basis for computation of binding affinities: a critical review," Biophysical J. 1997, 72, 1047-1069, DOI: 10.1016/S0006-3495(97)78756-3.
  71. Roca, M.; Martí, S.; Andrés, J.; Moliner, V.; Tuñön, I. ; Bertrán, J.; Williams, I. H. "Theoretical Modeling of Enzyme Catalytic Power:  Analysis of "Cratic" and Electrostatic Factors in Catechol O-Methyltransferase," J. Am. Chem. Soc. 2003, 125, 7726-7737, DOI: 10.1021/ja0299497.
  72. Roca, M.; Andrés, J.; Moliner, V.; Tuñön, I.; Bertrá, J. "On the Nature of the Transition State in Catechol O-Methyltransferase. A Complementary Study Based on Molecular Dynamics and Potential Energy Surface Explorations," J. Am. Chem. Soc. 2005, 127, 10648-10655, DOI: 10.1021/ja051503d.
  73. Kanaan, N.; Ruiz Pernia, J. J.; Williams, I. H. "QM/MM simulations for methyl transfer in solution and catalysed by COMT: ensemble-averaging of kinetic isotope effects," Chem. Commun. 2008, 6114-6116, DOI: 10.1039/B814212B.
  74. Gray, C. H.; Coward, J. K.; Schowen, K. B.; Schowen, R. L. "α-Deuterium and carbon-13 isotope effects for a simple, intermolecular sulfur-to-oxygen methyl-transfer reaction. Transition-state structures and isotope effects in transmethylation and transalkylation," J. Am. Chem. Soc. 1979, 101, 4351-4358, DOI: 10.1021/ja00509a051.
  75. Kiss, G.; Çelebi-Ölçüm, N.; Moretti, R.; Baker, D.; Houk, K. N. "Computational Enzyme Design," Angew. Che, Int. Ed. 2013, 52, 5700-5725, DOI: 10.1002/anie.201204077.
  76. Siegel, J. B.; Zanghellini, A.; Lovick, H. M.; Kiss, G.; Lambert, A. R.; St.Clair, J. L.; Gallaher, J. L.; Hilvert, D.; Gelb, M. H.; Stoddard, B. L.; Houk, K. N.; Michael, F. E.; Baker, D. "Computational Design of an Enzyme Catalyst for a Stereoselective Bimolecular Diels-Alder Reaction," Science 2010, 329, 309-313, DOI: 10.1126/science.1190239.
  77. Tantillo, D. J.; Jiangang, C.; Houk, K. N. "Theozymes and compuzymes: theoretical models for biological catalysis," Curr. Opin. Chem. Biol. 1998, 2, 743-750, DOI: 10.1016/S1367-5931(98)80112-9.
  78. Hu, C.-H.; Brinck, T.; Hult, K. "Ab initio and density functional theory studies of the catalytic mechanism for ester hydrolysis in serine hydrolases," Int. J. Quant. Chem. 1998, 69, 89-103, DOI: 10.1002/(SICI)1097-461X(1998)69:1<89::AID-QUA11>3.0.CO;2-0.
  79. Zanghellini, A.; Jiang, L.; Wollacott, A. M.; Cheng, G.; Meiler, J.; Althoff, E. A.; Röthlisberger, D.; Baker, D. "New algorithms and an in silico benchmark for computational enzyme design," Protein Sci. 2006, 15, 2785-2794, DOI: 10.1110/ps.062353106.
  80. Richter, F.; Leaver-Fay, A.; Khare, S. D.; Bjelic, S.; Baker, D. "De Novo Enzyme Design Using Rosetta3," PLoS ONE 2011, 6, e19230, DOI: 10.1371/journal.pone.0019230.
  81. Kuhlman, B.; Baker, D. "Native protein sequences are close to optimal for their structures," Proc. Nat. Acad. Sci. USA 2000, 97, 10383-10388, DOI: pnas.97.19.10383.
  82. Jiang, L.; Althoff, E. A.; Clemente, F. R.; Doyle, L.; Röthlisberger, D.; Zanghellini, A.; Gallaher, J. L.; Betker, J. L.; Tanaka, F.; Barbas, C. F.; Hilvert, D.; Houk, K. N.; Stoddard, B. L.; Baker, D. "De Novo Computational Design of Retro-Aldol Enzymes," Science 2008, 319, 1387-1391, DOI: 10.1126/science.1152692.
  83. Althoff, E. A.; Wang, L.; Jiang, L.; Giger, L.; Lassila, J. K.; Wang, Z.; Smith, M.; Hari, S.; Kast, P.; Herschlag, D.; Hilvert, D.; Baker, D. "Robust design and optimization of retroaldol enzymes," Protein Sci. 2012, 21, 717-726, DOI: 10.1002/pro.2059.
  84. Richter, F.; Blomberg, R.; Khare, S. D.; Kiss, G.; Kuzin, A. P.; Smith, A. J. T.; Gallaher, J.; Pianowski, Z.; Helgeson, R. C.; Grjasnow, A.; Xiao, R.; Seetharaman, J.; Su, M.; Vorobiev, S.; Lew, S.; Forouhar, F.; Kornhaber, G. J.; Hunt, J. F.; Montelione, G. T.; Tong, L.; Houk, K. N.; Hilvert, D.; Baker, D. "Computational Design of Catalytic Dyads and Oxyanion Holes for Ester Hydrolysis," J. Am. Chem. Soc. 2012, 134, 16197-16206, DOI: 10.1021/ja3037367.
  85. Na, J.; Houk, K. N.; Hilvert, D. "Transition State of the Base-Promoted Ring-Opening of Isoxazoles. Theoretical Prediction of Catalytic Functionalities and Design of Haptens for Antibody Production," J. Am. Chem. Soc. 1996, 118, 6462-6471, DOI: 10.1021/ja953550j.
  86. Alexandrova, A. N.; Röthlisberger, D.; Baker, D.; Jorgensen, W. L. "Catalytic Mechanism and Performance of Computationally Designed Enzymes for Kemp Elimination," J. Am. Chem. Soc. 2008, 130, 15907-15915, DOI: 10.1021/ja804040s.
  87. Frushicheva, M. P.; Cao, J.; Chu, Z. T.; Warshel, A. "Exploring challenges in rational enzyme design by simulating the catalysis in artificial kemp eliminase," Proc. Nat. Acad. Sci. USA 2010, 107, 16869-16874, DOI: 10.1073/pnas.1010381107.
  88. Warshel, A.; Weiss, R. M. "An empirical valence bond approach for comparing reactions in solutions and in enzymes," J. Am. Chem. Soc. 1980, 102, 6218-6226, DOI: 10.1021/ja00540a008.
  89. Roca, M.; Vardi-Kilshtain, A.; Warshel, A. "Toward Accurate Screening in Computer-Aided Enzyme Design," Biochemistry 2009, 48, 3046-3056, DOI: 10.1021/bi802191b.
  90. Ruscio, J. Z.; Kohn, J. E.; Ball, K. A.; Head-Gordon, T. "The Influence of Protein Dynamics on the Success of Computational Enzyme Design," J. Am. Chem. Soc. 2009, 131, 14111-14115, DOI: 10.1021/ja905396s.
  91. Linder, M.; Johansson, A. J.; Olsson, T. S. G.; Liebeschuetz, J.; Brinck, T. "Designing a New Diels-Alderase: A Combinatorial, Semirational Approach Including Dynamic Optimization," J. Chem. Inf. Mod. 2011, 51, 1906-1917, DOI: 10.1021/ci200177d.
  92. Linder, M.; Johansson, A. J.; Olsson, T. S. G.; Liebeschuetz, J.; Brinck, T. "Computational design of a Diels-Alderase from a thermophilic esterase: the importance of dynamics," J. Comput.-Aid. Mol. Design 2012, 26, 1079-1095, DOI: 10.1007/s10822-012-9601-y.
  93. Baker, D. "An exciting but challenging road ahead for computational enzyme design," Protein Sci. 2010, 19, 1817-1819, DOI: 10.1002/pro.481.