What happens inside an enzyme's active site to allow slow and difficult chemical reactions to occur so rapidly? This question has occupied biochemists’ attention for a long time. Computer models of increasing sophistication have predicted an important role for electrostatic interactions in enzymatic reactions, yet this hypothesis has proved vexingly difficult to test experimentally. Recent experiments utilizing the vibrational Stark effect make it possible to measure the electric field a substrate molecule experiences when bound inside its enzyme's active site. These experiments have provided compelling evidence supporting a major electrostatic contribution to enzymatic catalysis. Here, we review these results and develop a simple model for electrostatic catalysis that enables us to incorporate disparate concepts introduced by many investigators to describe how enzymes work into a more unified framework stressing the importance of electric fields at the active site.


Article metrics loading...

Loading full text...

Full text loading...


Literature Cited

  1. Stark J. 1.  1913. Observation of the separation of spectral lines by an electric field. Nature 92:2301401 [Google Scholar]
  2. Lo Surdo A. 2.  1914. L'analogo elettrico del fenomeno di Zeeman e la costituzione dell'atomo. L'eletrotecnica 1:624–34 [Google Scholar]
  3. Leone M, Paoletti A, Robotti N. 3.  2004. A simultaneous discovery: the case of Johannes Stark and Antonino Lo Surdo. Phys. Perspect. 6:271–94 [Google Scholar]
  4. Epstein PS. 4.  1926. The Stark effect from the point of view of Schroedinger's quantum theory. Phys. Rev. 28:695–710 [Google Scholar]
  5. Liptay W. 5.  1969. Electrochromism and solvatochromism. Angew. Chem. Int. Ed. 8:3177–88 [Google Scholar]
  6. Hochstrasser RM. 6.  1973. Electric field effects on oriented molecules and molecular crystals. Acc. Chem. Res. 6:263–69 [Google Scholar]
  7. Mathies R, Albrecht AC. 7.  1974. Experimental and theoretical studies on the excited state polarizabilities of benzene, naphthalene and anthracene. J. Chem. Phys. 60:2500–8 [Google Scholar]
  8. Mathies R, Stryer L. 8.  1976. Retinal has a highly dipolar vertically excited singlet state: implications for vision. PNAS 73:72169–73 [Google Scholar]
  9. Lockhart DJ, Boxer SG. 9.  1987. Magnitude and direction of the change in dipole moment associated with excitation of the primary electron donor in Rhodopseudomonas sphaeroides reaction centers. Biochemistry 26:664–68 [Google Scholar]
  10. Gottfried DS, Steffen MA, Boxer SG. 10.  1991. Large protein-induced dipoles for a symmetric carotenoid in a photosynthetic antenna complex. Science 251:4994662–65 [Google Scholar]
  11. Haldane JBS. 11.  1930. Enzymes London: Longmans Green
  12. Edwards DR, Lohman DC, Wolfenden R. 12.  2012. Catalytic proficiency: the extreme case of S-O cleaving sulfatases. J. Am. Chem. Soc. 134:525–31 [Google Scholar]
  13. Lad C, Williams N, Wolfenden R. 13.  2003. The rate of hydrolysis of phosphomonoester dianions and the exceptional catalytic proficiencies of protein and inositol phosphatases. PNAS 100:5607–10 [Google Scholar]
  14. Radzicka A, Wolfenden R. 14.  1995. A proficient enzyme. Science 267:519490–93 [Google Scholar]
  15. Kries H, Blomberg R, Hilvert D. 15.  2013. De novo enzymes by computational design. Curr. Opin. Chem. Biol. 17:221–28 [Google Scholar]
  16. Garcia-Viloca M, Gao J, Karplus M, Truhlar DG. 16.  2004. How enzymes work: analysis by modern rate theory and computer simulations. Science 303:5655186–95 [Google Scholar]
  17. Blow D. 17.  2000. So do we understand how enzymes work?. Structure 8:4R77–81 [Google Scholar]
  18. Kraut J. 18.  1988. How do enzymes work?. Science 242:533–40 [Google Scholar]
  19. Pauling L. 19.  1946. Molecular architecture and biological reactions. Chem. Eng. News 24:101375–77 [Google Scholar]
  20. Blake CCF, Koenig DF, Mair GA, North ACT, Phillips DC, Sarma VR. 20.  1965. Structure of hen egg-white lysozyme: a three-dimensional Fourier synthesis at 2 Å resolution. Nature 206:757–61 [Google Scholar]
  21. Levitt M. 21.  1974. On the nature of the binding of hexa-N-acetyl glucosamine substrate to lysozyme. Peptides, Polypeptides, and Proteins ER Blout, FA Bovey, M Goodman, N Lotan 99–113 New York: Wiley [Google Scholar]
  22. Jencks WP. 22.  1975. Binding energy, specificity, and enzymic catalysis: the Circe effect. Adv. Enzymol. Relat. Areas Mol. Biol. 43:219–410 [Google Scholar]
  23. Amyes TL, Richard JP. 23.  2013. Specificity in transition state binding: the Pauling model revisited. Biochemistry 52:122021–35 [Google Scholar]
  24. Morrow JR, Amyes TL, Richard JP. 24.  2008. Phosphate binding energy and catalysis by small and large molecules. Acc. Chem. Res. 41:4539–48 [Google Scholar]
  25. Goryanova B, Amyes TL, Gerlt JA, Richard JP. 25.  2011. OMP decarboxylase: phosphodianion binding energy is used to stabilize a vinyl carbanion intermediate. J. Am. Chem. Soc. 133:6545–48 [Google Scholar]
  26. Schwans JP, Kraut DA, Herschlag D. 26.  2009. Determining the catalytic role of remote substrate binding interactions in ketosteroid isomerase. PNAS 106:14271–75 [Google Scholar]
  27. Kurz JL. 27.  1963. Transition state characterization for catalyzed reactions. J. Am. Chem. Soc. 85:987–91 [Google Scholar]
  28. Wolfenden R. 28.  1972. Analog approaches to the structure of the transition state in enzyme reactions. Acc. Chem. Res. 5:10–18 [Google Scholar]
  29. Frey P, Whitt S, Tobin J. 29.  1994. A low-barrier hydrogen bond in the catalytic triad of serine proteases. Science 264:51671927–30 [Google Scholar]
  30. Cleland WW, Frey PA, Gerlt JA. 30.  1998. The low barrier hydrogen bond in enzymatic catalysis. J. Biol. Chem. 273:25529–32 [Google Scholar]
  31. Fersht AR. 31.  1999. Structure and Mechanism in Protein Science. New York: Freeman, 2nd ed..
  32. Robertus JD, Kraut J, Alden RA, Birktoft JJ. 32.  1972. Subtilisin. Stereochemical mechanism involving transition-state stabilization. Biochemistry 11:4293–303 [Google Scholar]
  33. Warshel A, Sharma PK, Kato M, Xiang Y, Liu H, Olsson MHM. 33.  2006. Electrostatic basis for enzyme catalysis. Chem. Rev. 106:3210–35 [Google Scholar]
  34. Williams D. 34.  2010. Enzyme catalysis from improved packing in their transition-state structures. Curr. Opin. Chem. Biol. 14:666–70 [Google Scholar]
  35. Seebeck FP, Hilvert D. 35.  2005. Positional ordering of reacting groups contributes significantly to the efficiency of proton transfer at an antibody active site. J. Am. Chem. Soc. 127:1307–12 [Google Scholar]
  36. Amzel LM. 36.  1998. Loss of translational entropy in binding, folding, and catalysis. Proteins 28:144–49 [Google Scholar]
  37. Page M, Jencks W. 37.  1971. Entropic contributions to rate accelerations in enzymic and intramolecular reactions and the chelate effect. PNAS 68:1678–83 [Google Scholar]
  38. Bruice TC, Pandit UK. 38.  1960. The effect of geminal substitution ring size and rotamer distribution on the intramolecular nucleophilic catalysis of the hydrolysis of monophenyl esters of dibasic acids and the solvolysis of the intermediate anhydrides. J. Am. Chem. Soc. 82:5858–65 [Google Scholar]
  39. Bruice TC, Benkovic SJ. 39.  2000. Chemical basis for enzyme catalysis. Biochemistry 39:6267–74 [Google Scholar]
  40. Hur S, Bruice TC. 40.  2003. Enzymes do what is expected (chalcone isomerase versus chorismate mutase). J. Am. Chem. Soc. 125:1472–73 [Google Scholar]
  41. Wolfenden R, Snider M, Ridgway C, Miller B. 41.  1999. The temperature dependence of enzyme rate enhancements. J. Am. Chem. Soc. 121:7419–20 [Google Scholar]
  42. Sievers A, Beringer M, Rodnina MV, Wolfenden R. 42.  2004. The ribosome as an entropy trap. PNAS 101:7897–901 [Google Scholar]
  43. Warshel A, Weiss RM. 43.  1980. An empirical valence bond approach for comparing reactions in solutions and in enzymes. J. Am. Chem. Soc. 102:6218–26 [Google Scholar]
  44. Warshel A. 44.  1981. Electrostatic basis of structure-function correlation in proteins. Acc. Chem. Res. 14:284–90 [Google Scholar]
  45. Pollack RM. 45.  2004. Enzymatic mechanisms for catalysis of enolization: ketosteroid isomerase. Bioorg. Chem. 32:341–53 [Google Scholar]
  46. Kraut DA, Carroll KS, Herschlag D. 46.  2003. Challenges in enzyme mechanism and energetics. Annu. Rev. Biochem. 72:517–71 [Google Scholar]
  47. Onsager L. 47.  1936. Electric moments of molecules in liquids. J. Am. Chem. Soc. 58:1486–93 [Google Scholar]
  48. Kirkwood JG. 48.  1939. The dielectric polarization of polar liquids. J. Chem. Phys. 7:911–19 [Google Scholar]
  49. Bagchi B, Oxtoby DW, Fleming GR. 49.  1984. Theory of the time development of the Stokes shift in polar media. Chem. Phys. 86:257–67 [Google Scholar]
  50. Kahlow MA, Jarzeba W, Kang TJ, Barbara PF. 50.  1989. Femtosecond resolved solvation dynamics in polar solvents. J. Chem. Phys. 90:151–58 [Google Scholar]
  51. Zwolinski B, Marcus R, Eyring H. 51.  1955. Inorganic oxidation-reduction reactions in solution electron transfers. Chem. Rev. 55:157–80 [Google Scholar]
  52. Marcus R. 52.  1956. On the theory of oxidation‐reduction reactions involving electron transfer. J. Chem. Phys. 24:966 [Google Scholar]
  53. Fried SD, Boxer SG. 53.  2015. Measuring electric fields and noncovalent interactions using the vibrational Stark effect. Acc. Chem. Res. 48:998–1006 [Google Scholar]
  54. Fried SD, Bagchi S, Boxer SG. 54.  2013. Measuring electrostatic fields in both hydrogen-bonding and non-hydrogen-bonding environments using carbonyl vibrational probes. J. Am. Chem. Soc. 135:11181–92 [Google Scholar]
  55. Saggu M, Levinson NM, Boxer SG. 55.  2011. Direct measurements of electric fields in weak OH⋅⋅⋅π hydrogen bonds. J. Am. Chem. Soc. 133:17414–19 [Google Scholar]
  56. Reichardt R. 56.  2003. Solvents and Solvent Effects in Organic Chemistry Weinheim, Ger.: Wiley-VCH, 3rd ed..
  57. Abraham MH. 57.  1972. Substitution at saturated carbon. Part XIV. Solvent effects on the free energies of ions, ion-pairs, non-electrolytes, and transition states in some SN and SE reactions. J. Chem. Soc. Perkin Trans 2 10:1343–57 [Google Scholar]
  58. Warshel A. 58.  1978. Energetics of enzyme catalysis. PNAS 75:5250–54 [Google Scholar]
  59. Warshel A, Levitt M. 59.  1976. Theoretical studies of enzymic reactions: dielectric, electrostatic and steric stabilization of the carbonium ion in the reaction of lysozyme. J. Mol. Biol. 103:227–49 [Google Scholar]
  60. Warshel A. 60.  1981. Calculations of enzymic reactions: calculations of pKa, proton transfer reactions, and general acid catalysis reactions in enzymes. Biochemistry 20:3167–77 [Google Scholar]
  61. Feierberg I, Aqvist J. 61.  2002. The catalytic power of ketosteroid isomerase investigated by computer simulation. Biochemistry 41:15728–35 [Google Scholar]
  62. Szefczyk B, Claeyssens F, Mulholland AJ, Sokalski WA. 62.  2007. Quantum chemical analysis of reaction paths in chorismate mutase: conformational effects and electrostatic stabilization. Int. J. Quantum Chem. 107:2274–85 [Google Scholar]
  63. Gilson M, Honig B. 63.  1987. Calculation of electrostatic potentials in an enzyme active site. Nature 330:84–86 [Google Scholar]
  64. Sun D, Liao D, Remington S. 64.  1989. Electrostatic fields in the active sites of lysozymes. PNAS 86:5361–65 [Google Scholar]
  65. García-Moreno B, Dwyer JJ, Gittis AG, Lattman EA, Spencer DS, Stites WE. 65.  1997. Experimental measurement of the effective dielectric in the hydrophobic core of a protein. Biophys. Chem. 64:211–24 [Google Scholar]
  66. Harris TK, Turner GJ. 66.  2002. Structural basis of perturbed pKa values of catalytic groups in enzyme active sites. IUBMB Life 53:85–98 [Google Scholar]
  67. Isom DG, Castañeda CA, Cannon BR, García-Moreno B. 67.  2011. Large shifts in pKa values of lysine residues buried inside a protein. PNAS 108:5260–65 [Google Scholar]
  68. Varadarajan R, Lambright DG, Boxer SG. 68.  1989. Electrostatic interactions in wild-type and mutant recombinant human myoglobins. Biochemistry 28:3771–81 [Google Scholar]
  69. Mao J, Hauser K, Gunner MR. 69.  2003. How cytochromes with different folds control heme redox potentials. Biochemistry 42:9829–40 [Google Scholar]
  70. Varadarajan R, Zewert TE, Gray HB, Boxer SG. 70.  1989. Effects of buried ionizable amino acids on the reduction potential of recombinant myoglobin. Science 243:69–72 [Google Scholar]
  71. Kraut DA, Sigala PA, Pybus B, Liu CW, Ringe D. 71.  et al. 2006. Testing electrostatic complementarity in enzyme catalysis: hydrogen bonding in the ketosteroid isomerase oxyanion hole. PLOS Biol 4:4e99 [Google Scholar]
  72. Cohen BE, McAnaney TB, Park ES, Jan YN, Boxer SG, Jan LY. 72.  2002. Probing protein electrostatics with a synthetic fluorescent amino acid. Science 296:1700–3 [Google Scholar]
  73. Vivian JT, Callis PR. 73.  2001. Mechanisms of tryptophan fluorescence shifts in proteins. Biophys. J. 80:2093–109 [Google Scholar]
  74. Pearson J, Oldfield E, Lee F, Warshel A. 74.  1993. Chemical shifts in proteins: a shielding trajectory analysis of the fluorine nuclear magnetic resonance spectrum of the Escherichia coli galactose binding protein. J. Am. Chem. Soc. 115:6851–62 [Google Scholar]
  75. Augspurger J, Dykstra C. 75.  1993. Correlation of fluorine-19 chemical shielding and chemical shift nonequivalence. J. Am. Chem. Soc. 115:12016–19 [Google Scholar]
  76. Augspurger J, Dykstra C, Oldfield E. 76.  1991. Correlation of carbon-13 and oxygen-17 chemical shifts and the vibrational frequency of electrically perturbed carbon monoxide. J. Am. Chem. Soc. 113:2447–51 [Google Scholar]
  77. Buckingham AD. 77.  1960. Chemical shifts in the NMR spectra of molecules containing polar groups. Can. J. Chem. 38:300–7 [Google Scholar]
  78. Han B, Liu Y, Ginzinger SW, Wishart DS. 78.  2011. SHIFTX2: significantly improved protein chemical shift prediction. J. Biomol. NMR 50:43–57 [Google Scholar]
  79. Waegele MM, Culik RM, Gai F. 79.  2011. Site-specific spectroscopic reporters of the local electric field, hydration, structure, and dynamics of biomolecules. J. Phys. Chem. Lett. 2:2598–609 [Google Scholar]
  80. Kim H, Cho M. 80.  2013. Infrared probes for studying the structure and dynamics of biomolecules. Chem. Rev. 113:5817–47 [Google Scholar]
  81. Fafarman AT, Sigala PA, Schwans JP, Fenn TD, Herschlag D, Boxer SG. 81.  2012. Quantitative, directional measurement of electric field heterogeneity in the active site of ketosteroid isomerase. PNAS 109:6E299–308 [Google Scholar]
  82. Andrews SS, Boxer SG. 82.  2000. Vibrational Stark effects of nitriles I. Methods and experimental results. J. Phys. Chem. A 104:11853–63 [Google Scholar]
  83. Chattopadhyay A, Boxer SG. 83.  1995. Vibrational Stark effect spectroscopy. J. Am. Chem. Soc. 117:1449–50 [Google Scholar]
  84. Bublitz GU, Boxer SG. 84.  1997. Stark spectroscopy: applications in chemistry, biology, and materials science. Annu. Rev. Phys. Chem. 48:213–42 [Google Scholar]
  85. Boxer SG. 85.  2009. Stark realities. J. Phys. Chem. B. 113:2972–83 [Google Scholar]
  86. Lakowicz JR. 86.  2003. Solvent and environmental effects. Principles of Fluorescence Spectroscopy205–35 New York: Springer, 3rd ed.. [Google Scholar]
  87. Park ES, Boxer SG. 87.  2002. Origins of the sensitivity of molecular vibrations to electric fields: carbonyl and nitrosyl stretches in model compounds and proteins. J. Phys. Chem. B 106:5800–6 [Google Scholar]
  88. Park ES, Andrews SS, Hu RB, Boxer SG. 88.  1999. Vibrational Stark spectroscopy in proteins: a probe and calibration for electrostatic fields. J. Phys. Chem. B. 103:9813–17 [Google Scholar]
  89. Suydam IT, Snow CD, Pande VS, Boxer SG. 89.  2006. Electric fields at the active site of an enzyme: direct comparison of experiment with theory. Science 313:200–4 [Google Scholar]
  90. Bagchi S, Fried SD, Boxer SG. 90.  2012. A solvatochromic model calibrates nitriles’ vibrational frequencies to electrostatic fields. J. Am. Chem. Soc. 134:10373–76 [Google Scholar]
  91. Schneider SH, Kratocvhil HT, Zanni MT, Boxer SG. 91.  2017. Solvent-independent anharmonicity for carbonyl oscillators. J. Phys. Chem. B 121:102331 [Google Scholar]
  92. Fafarman AT, Boxer SG. 92.  2010. Nitrile bonds as infrared probes of electrostatics in ribonuclease S. J. Phys. Chem. B 114:13536–44 [Google Scholar]
  93. Chung JK, Thielges MC, Fayer MD. 93.  2011. Dynamics of the folded and unfolded villin headpiece (HP35) measured with ultrafast 2D IR vibrational echo spectroscopy. PNAS 108:3578–83 [Google Scholar]
  94. Liu CT, Layfield JP, Stewart RJ III, French JB, Hanoian P. 94.  et al. 2014. Probing the electrostatics of active site microenvironments along the catalytic cycle for Escherichia coli dihydrofolate reductase. J. Am. Chem. Soc. 136:10349–60 [Google Scholar]
  95. Lindquist BA, Furse KE, Corcelli SA. 95.  2009. Nitrile groups as vibrational probes of biomolecular structure and dynamics: an overview. Phys. Chem. Chem. Phys. 11:8119–32 [Google Scholar]
  96. Schultz KC, Supekova L, Ryu Y, Xie J, Perera R, Schultz PG. 96.  2006. A genetically encoded infrared probe. J. Am. Chem. Soc. 128:13984–85 [Google Scholar]
  97. Levinson NM, Boxer SG. 97.  2013. A conserved water-mediated hydrogen bond network defines bosutinib's kinase selectivity. Nat. Chem. Biol. 10:127–32 [Google Scholar]
  98. Hu W, Webb LJ. 98.  2011. Direct measurement of the membrane dipole field in bicelles using vibrational Stark effect spectroscopy. J. Phys. Chem. Lett. 2:1925–30 [Google Scholar]
  99. Aschaffenburg D, Moog R. 99.  2009. Probing hydrogen bonding environments: solvatochromic effects on the CN vibration of benzonitrile. J. Phys. Chem. B 113:12736–43 [Google Scholar]
  100. Fafarman A, Sigala P, Herschlag D, Boxer S. 100.  2010. Decomposition of vibrational shifts of nitriles into electrostatic and hydrogen-bonding effects. J. Am. Chem. Soc. 132:12811–13 [Google Scholar]
  101. Deb P, Haldar T, Kashid SM, Banerjee S, Chakrabarty S, Bagchi S. 101.  2016. Correlating nitrile IR frequencies to local electrostatics quantifies noncovalent interactions of peptides and proteins. J. Phys. Chem. B 120:4034–46 [Google Scholar]
  102. Choi J-H, Cho M. 102.  2011. Vibrational solvatochromism and electrochromism of infrared probe molecules containing C≡O, C≡N, C=O, or C−F vibrational chromophore. J. Chem. Phys. 134:154513 [Google Scholar]
  103. Belasco JG, Knowles JR. 103.  1980. Direct observation of substrate distortion by triosephosphate isomerase using Fourier transform infrared spectroscopy. Biochemistry 19:3472–77 [Google Scholar]
  104. Anderson VE. 104.  2005. Quantifying energetic contributions to ground state destabilization. Arch. Biochem. Biophys. 433:27–33 [Google Scholar]
  105. Carey PR. 105.  2006. Spectroscopic characterization of distortion in enzyme complexes. Chem. Rev. 106:3043–54 [Google Scholar]
  106. Tonge PJ, Carey PR. 106.  1992. Forces, bond lengths, and reactivity: fundamental insight into the mechanism of enzyme catalysis. Biochemistry 31:9122–25 [Google Scholar]
  107. Reddish MJ, Peng H-L, Deng H, Panwar KS, Callener R, Dyer RB. 107.  2014. Direct evidence of catalytic heterogeneity in lactate dehydrogenase by temperature jump infrared spectroscopy. J. Phys. Chem. B 118:10854–62 [Google Scholar]
  108. Schneider SH, Boxer SG. 108.  2016. Vibrational Stark effects of carbonyl probes applied to re-interpret IR and Raman data for enzyme inhibitors in terms of electric fields at the active site. J. Phys. Chem. B 120:9672–84 [Google Scholar]
  109. Pan X, Schwartz SD. 109.  2016. Conformational heterogeneity in the Michaelis complex of lactate dehydrogenase: an analysis of vibrational spectroscopy using Markov and hidden Markov models. J. Phys. Chem. B 120:6612–20 [Google Scholar]
  110. Talalay P, Wang VS. 110.  1955. Enzymic isomerization of Δ5-3-ketosteroids. Biochim. Biophys. Acta 18:300–1 [Google Scholar]
  111. Talalay P, Dobson MM, Tapley DF. 111.  1952. Oxidative degradation of testosterone by adaptive enzymes. Nature 170:620–21 [Google Scholar]
  112. Wang S, Kawahara F, Talalay P. 112.  1963. The mechanism of the Δ5-3-ketosteroid isomerase reaction: absorption and fluorescence spectra of enzyme-steroid complexes. J. Biol. Chem. 238:576–85 [Google Scholar]
  113. Zeng B, Bounds P, Steiner R, Pollack R. 113.  1992. Nature of the intermediate in the 3-oxo-Δ5-steroid isomerase reaction. Biochemistry 31:1521–28 [Google Scholar]
  114. Kuliopulos A, Mildvan A, Shortle D, Talalay P. 114.  1989. Kinetic and ultraviolet spectroscopic studies of active-site mutants of Δ5-3-ketosteroid isomerase. Biochemistry 28:149–59 [Google Scholar]
  115. Zeng B, Pollack RM. 115.  1991. Microscopic rate constants for the acetate ion catalyzed isomerization of 5-androstene-3,17-dione to 4-androstene-3,17-dione: a model for steroid isomerase. J. Am. Chem. Soc. 113:3838–42 [Google Scholar]
  116. Lamba V, Yabukarski F, Pinney M, Herschlag D. 116.  2016. Evaluation of the catalytic contribution of a positioned general base in ketosteroid isomerase. J. Am. Chem. Soc. 138:9902–9 [Google Scholar]
  117. Schwans JP, Hanoian P, Lengerich BJ, Sunden F, Gonzalez A. 117.  et al. 2014. Experimental and computational mutagenesis to investigate the positioning of a general base within an enzyme active site. Biochemistry 53:152541–55 [Google Scholar]
  118. Fried SD, Bagchi S, Boxer SG. 118.  2014. Extreme electric fields power catalysis in the active site of ketosteroid isomerase. Science 346:1510–14 [Google Scholar]
  119. Wu Y, Boxer SG. 119.  2016. A critical test of the electrostatic contribution to catalysis with non-canonical amino acids in ketosteroid isomerase. J. Am. Chem. Soc. 138:11890–95 [Google Scholar]
  120. Natarajan A, Schwans JP, Herschlag D. 120.  2014. Using unnatural amino acids to probe the energetics of oxyanion hole hydrogen bonds in the ketosteroid isomerase active site. J. Am. Chem. Soc. 136:7643–54 [Google Scholar]
  121. Hedstrom L. 121.  2002. Serine protease mechanism and specificity. Chem. Rev. 102:4501–24 [Google Scholar]
  122. Harrison RK, Stein RL. 122.  1990. Mechanistic studies of peptide prolyl cis-trans isomerase: evidence for catalysis by distortion. Biochemistry 29:1684–89 [Google Scholar]
  123. Fischer S, Michnick S, Karplus M. 123.  1993. A mechanism for rotamase catalysis by the FK506 binding protein. Biochemistry 32:13830–37 [Google Scholar]
  124. Camilloni C, Sahakyan AB, Holliday MJ, Isern NG, Zhang F. 124.  et al. 2014. Cyclophilin A catalyzes proline isomerization by an electrostatic handle mechanism. PNAS 111:10203–8 [Google Scholar]
  125. Crooks GP, Xu L, Barkley RM, Copley SD. 125.  1995. Exploration of possible mechanisms for 4-chlorobenzoyl CoA dehalogenase: evidence for an aryl-enzyme intermediate. J. Am. Chem. Soc. 117:10791 [Google Scholar]
  126. Zheng Y-J, Bruice TC. 126.  1997. On the dehalogenation mechanism of 4-chlorobenzyl CoA by 4-chlorobenzyl CoA dehalogenase. J. Am. Chem. Soc. 119:3868–77 [Google Scholar]
  127. Wu J, Xu D, Lu X, Wang C, Guo H, Dunaway-Mariano D. 127.  2006. Contributions of long-range electrostatic interactions to 4-chlorobenzoyl-CoA dehalogenase catalysis: a combined theoretical and experimental study. Biochemistry 45:102–12 [Google Scholar]
  128. Corey DR, Craik CS. 128.  1992. An investigation into the minimum requirements for peptide hydrolysis by mutation of the catalytic triad of trypsin. J. Am. Chem. Soc. 114:1784–90 [Google Scholar]
  129. Blow DM, Birktoft JJ, Hartley BS. 129.  1969. Role of a buried acid group in the mechanism of action of chymotrypsin. Nature 221:337–40 [Google Scholar]
  130. Henderson R. 130.  1970. Structure of crystalline α-chymotrypsin: IV. The structure of indoleacryloyl-α-chymotrypsin and its relevance to the hydrolytic mechanism of the enzyme. J. Mol. Biol. 54:341–54 [Google Scholar]
  131. Warshel A, Narray-Szabo G, Sussman F, Hwang J-K. 131.  1989. How do serine proteases really work?. Biochemistry 28:3629–37 [Google Scholar]
  132. Wu N, Mo Y, Gao J, Pai EF. 132.  2000. Electrostatic stress in catalysis: structure and mechanism of the enzyme orotidine monophosphate decarboxylase. PNAS 97:2017–22 [Google Scholar]
  133. Stec B, Holtz KM, Kantrowitz ER. 133.  2000. A revised mechanism for the alkaline phosphatase reaction involving three metal ions. J. Mol. Biol. 299:1303–11 [Google Scholar]
  134. Andrews LD, Zalatan JG, Herschlag D. 134.  2014. Probing the origins of catalytic discrimination between phosphate and sulfate monoester hydrolysis: comparative analysis of alkaline phosphatase and protein tyrosine phosphatases. Biochemistry 53:6811–19 [Google Scholar]
  135. Laschat S. 135.  1996. Pericyclic reactions in biological systems—Does nature know about the Diels–Alder reaction?. Angew. Chem. Int. Ed. 35:289–91 [Google Scholar]
  136. Patel A, Chen Z, Yang Z, Gutiérrez O, Liu H-w. 136.  et al. 2016. Dynamically complex [6+4] and [4+2] cycloadditions in the biosynthesis of spinosyn A. J. Am. Chem. Soc. 138:3631–34 [Google Scholar]
  137. Klas K, Tsukamoto S, Sherman DH, Williams RM. 137.  2015. Natural Diels–Alderases: elusive and irresistable. J. Org. Chem. 80:11672–85 [Google Scholar]
  138. Siegel JB, Zanghellini A, Lovick HM, Kiss G, Lambert AR. 138.  et al. 2010. Computational design of an enzyme catalyst for a stereoselective bimolecular Diels-Alder reaction. Science 329:309–13 [Google Scholar]
  139. Holliday GL, Mitchell JBO, Thornton JM. 139.  2009. Understanding the functional roles of amino acid residues in enzyme catalysis. J. Mol. Biol. 390:560–77 [Google Scholar]
  140. Holliday GL, Fischer JD, Mitchell JBO, Thornton JM. 140.  2011. Characterizing the complexity of enzymes on the basis of their mechanisms and structures with a bio-computational analysis. FEBS J 278:3835–45 [Google Scholar]
  141. Andreini C, Bertini I, Cavallaro G, Holliday GL, Thornton JM. 141.  2009. Metal-MACiE: a database of metals involved in biological catalysis. Bioinformatics 25:2088–89 [Google Scholar]
  142. Pandya C, Farelli JD, Dunaway-Mariano D, Allen KN. 142.  2014. Enzyme promiscuity: engine of evolutionary innovation. J. Biol. Chem. 289:30229–36 [Google Scholar]
  143. Khersonsky O, Tawfik DS. 143.  2010. Enzyme promiscuity: a mechanistic and evolutionary perspective. Annu. Rev. Biochem. 79:471–505 [Google Scholar]
  144. Lassila JK, Herschlag D. 144.  2008. Promiscuous sulfatase activity and thio-effects in a phosphodiesterase of the alkaline phosphatase superfamily. Biochemistry 47:12853–59 [Google Scholar]
  145. Shoichet BK, Baase WA, Kuroki R, Matthews BW. 145.  1995. A relationship between protein stability and protein function. PNAS 92:452–56 [Google Scholar]
  146. Dellus-Gur E, Toth-Petroczy A, Elias M, Tawfik DS. 146.  2013. What makes a protein fold amenable to functional innovation? Fold polarity and stability trade-offs. J. Mol. Biol. 425:2609–21 [Google Scholar]
  147. Arcus VL, Prentice EJ, Hobbs JK, Mulholland AJ, van der Kamp MW. 147.  et al. 2016. On the temperature dependence of enzyme-catalyzed rates. Biochemistry 55:1681–88 [Google Scholar]
  148. Somarowthu S, Brodkin HR, D'Aquino JA, Ringe D, Ondrechen MJ, Beuning PJ. 148.  2011. A tale of two isomerases: compact versus extended active sites in ketosteroid isomerase and phosphoglucose isomerase. Biochemistry 50:4923–35 [Google Scholar]
  149. Kim SW, Cha SS, Cho HS, Kim JS, Ha NC. 149.  et al. 1997. High-resolution crystal structures of Δ5-3-ketosteroid isomerase with and without a reaction intermediate analogue. Biochemistry 36:14030–36 [Google Scholar]
  150. Fried SD, Boxer SG. 150.  2015. Response to comments on “Extreme electric fields power catalysis in the active site of ketosteroid isomerase.”. Science 349:936 [Google Scholar]
  151. Schwans JP, Sunden F, Gonzalez A, Tsai Y, Herschlag D. 151.  2011. Evaluating the catalytic contribution from the oxyanion hole in ketosteroid isomerase. J. Am. Chem. Soc. 133:20052–55 [Google Scholar]
  152. Fersht AR. 152.  1974. Catalysis, binding and enzyme-substrate complementarity. Proc. R. Soc. B 187:397–407 [Google Scholar]
  153. Sigala PA, Kraut DA, Caaveiro JMM, Pybus B, Ruben EA. 153.  et al. 2008. Testing geometrical discrimination within an enzyme active site: constrained hydrogen bonding in the ketosteroid isomerase oxyanion hole. J. Am. Chem. Soc. 130:13696–708 [Google Scholar]
  154. Hammes GG, Benkovic SJ, Hammes-Schiffer S. 154.  2011. Flexibility, diversity, and cooperativity: pillars of enzyme catalysis. Biochemistry 50:10422–30 [Google Scholar]
  155. Kohen A. 155.  2015. Role of dynamics in enzyme catalysis: substantial versus semantic controversies. Acc. Chem. Res. 48:466–73 [Google Scholar]
  156. Kamerlin SCL, Warshel A. 156.  2010. At the dawn of the 21st century: Is dynamics the missing link for understanding enzyme catalysis?. Proteins 78:1339–75 [Google Scholar]
  157. Warshel A, Bora RP. 157.  2016. Defining and quantifying the role of dynamics in enzyme catalysis. J. Chem. Phys. 144:180901 [Google Scholar]
  158. Jha SK, Ji M, Gaffney KJ, Boxer SG. 158.  2011. Direct measurement of the protein response to an electrostatic perturbation that mimics the catalytic cycle in ketosteroid isomerase. PNAS 108:16612–17 [Google Scholar]
  159. Schnell JR, Dyson HJ, Wright PE. 159.  2004. Structure, dynamics, and catalytic function of dihydrofolate reductase. Annu. Rev. Biophys. Biomol. Struct. 33:119–40 [Google Scholar]
  160. Loveridge EJ, Behiry EM, Guo J, Allemann RK. 160.  2012. Evidence that a ‘dynamic knockout’ in Escherichia coli dihydrofolate reductase does not affect the chemical step of catalysis. Nat. Chem. 4:292–97 [Google Scholar]
  161. Schwans JP, Sunden F, Gonzalez A, Tsai Y, Herschlag D. 161.  2016. Correction to “Evaluating the catalytic contribution from the oxyanion hole in ketosteroid isomerase.”. J. Am. Chem. Soc. 138:7801–2 [Google Scholar]

Data & Media loading...

  • Article Type: Review Article
This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error